Annual Report 2005 - ASCI

Transcription

Annual Report 2005
Advanced School for Computing and Imaging
ASCI Annual Report 2005
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Chapter 1. ASCI and its Research
© 2006 Advanced School for Computing and Imaging
p/a DUT / EWI
P.O. Box 5031
2600 GA DELFT
The Netherlands
+ 31 15 27 88032
Fax: +31 15 27 86632
[email protected]
http://www.asci.tudelft.nl
ASCI is a Dutch graduate school established in 1993 and accredited by the Royal Netherlands Academy of Arts and Sciences. Research
groups of Delft University of Technology, Vrije Universiteit, University of Amsterdam, Leiden University, University Utrecht, University of
Twente, University of Groningen, Eindhoven University of Technology and the Erasmus University Rotterdam participate in ASCI.
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Contents
Preface.................................................................................................................................................................................. 5
Chapter 1 ASCI and its Research........................................................................................................................................ 7
1.1
About ASCI ........................................................................................................................................................... 7
1.2
Participating Groups.............................................................................................................................................. 7
1.3
ASCI Research Themes ..................................................................................................................................... 10
Chapter 2 Scientific Output along Research Themes...................................................................................................... 14
2.1
A: High Performance Computing and Computational Science ............................................................................. 14
2.1.1
Contribution of TUD-TNW-tn-qi....................................................................................................................14
2.1.2
Contribution of UL-LIACS ............................................................................................................................15
2.1.3
Contribution of TUD-EWI-me-ce ..................................................................................................................17
2.1.4
Contribution of UvA FdNWI-scs ...................................................................................................................18
2.2
B: Large scale distributed Information Systems and Embedded Systems............................................................ 26
2.2.1
Contribution of UvA-FdNWI-caps.................................................................................................................26
2.2.2
2.2.3
Contribution of TUE-EE-dmes .....................................................................................................................31
2.2.4
Contribution of UT- EEMCS-dacs ................................................................................................................35
2.2.5
Contribution of VU – WI...............................................................................................................................39
2.2.6
Contribution of TUD-EWI-ST-pds.................................................................................................................43
2.2.7
Contribution of TUD-me-ce..........................................................................................................................46
2.2.8
Contribution of UvA-FdNWI-csa...................................................................................................................49
2.3
C: Image and Multimedia Sensing, Processing, Interpretation and Visualisation ................................................. 50
2.3.1
Contribution of UG-CS-svcg ........................................................................................................................50
2.3.2
Contribution of TU/e-vis...............................................................................................................................52
2.3.3
Contribution of TUE-EE-dmes .....................................................................................................................55
2.3.4
Contribution of TUD-mm-ict .........................................................................................................................57
2.3.5
Contribution of TUE-BT-bmia.......................................................................................................................62
2.3.6
Contribution of TUD-TNW-tn-qi....................................................................................................................68
2.3.7
2.3.8
Contribution of UvA-FdNWI-ias....................................................................................................................72
2.3.9
Contribution of EUR-RMI-bigr ......................................................................................................................77
2.3.10
Contribution of UU-WI-ics ............................................................................................................................80
2.3.11
Contribution of TUD-LR-frs ..........................................................................................................................84
2.3.12
Contribution of TUD-EWI-mm-cgcc..............................................................................................................85
2.3.13
Contribution of UvA- FdNWI-isis ..................................................................................................................89
2.3.14
Contribution of UL-LUMC-lkeb.....................................................................................................................95
2.3.15
Contribution of UG-CS-IS ..........................................................................................................................100
2.4
D: Multimedia Information Systems................................................................................................................... 103
2.4.1
Contribution of TUD-mm-ict .......................................................................................................................103
2.4.2
Contribution of UVA-FdNWI-isis ................................................................................................................107
Chapter 3 ASCI-wide Events ........................................................................................................................................... 108
3.1
Cooperation within ASCI ................................................................................................................................... 110
3.2
ASCI 2005 Conference ..................................................................................................................................... 114
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Preface
With so many things done and so many different organisations involved it took some time to assemble, but here they are.
This is the annual report of the results of ASCI research for 2005. And a busy year it was.
As a continuation of a long tradition, in June the eleventh ASCI conference was held at ‘Het Heijderbos’, Heijen. With more
than 100 participants to the three day conference including the majority of ASCI's Ph.D student population, the conference
was a great success.
The focus of the conference was on the use of computer vision and on distributed computing for smart surroundings. Hence,
three distinguished keynote speakers were invited to present their insights enhancing the themes: James Crowley from
INRIA Grenoble, Richard Kleihorst from Philips Research Eindhoven, and Andrew Herbert from Microsoft Research
Cambridge.
ASCI takes pride in forming the home base for PhD-students in the area of imaging and computation and variations. One of
the measures of success is participation in the yearly ASCI conference, another is in the participation in ASCI's educational
program. ASCI organized successfully GNARP2005, the Graduate Network of Applied Research in Parallel systems. The
workshop was held in Garderen.
Another event was the Medical Imaging Symposium for PhD students held at Erasmus Medical Center Rotterdam. Organised
for the first time, the workshop aims at PhD students in the field of Medical Image Computing, Processing and Analysis and
related fields. The primary goal of these workshops and symposiums is to bring PhD students together to learn and to
exchange experiences in research in an informal and friendly setting with ample opportunities for discussion and feedback.
On the formal side of things, ASCI renewed in 2005 its accreditation as a research school with the Royal Netherlands
Academy of Arts and Sciences for another 6 year period into 2011. At the same time, the number of associated universities,
the number of groups from these universities and the number of Ph.D students of ASCI grew again. The number of PhD
students in ASCI passed the 140 mark in 2005.
I hope you find the report an interesting read if only by the following key-numbers: 10 PhD degrees were granted, some 550
scientific papers were published in international journals, books and conferences, 39 advanced software packages are
described, and some 110 participations in externally funded research programs.
This is the first report in the post-Andy era. Andy Tanenbaum who has lead ASCI from the onset for the past 10 years has
stepped down to concentrate on his KNAW-professorship. Andy, well done and happy trails in science!
For additional information about ASCI, please visit our web page at http://www.asci.tudelft.nl
Prof.dr.ir. Arnold W.M. Smeulders
- Scientific Director -
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Chapter 1 ASCI and its Research
1.1
About ASCI
ASCI is a national research school on advanced computer and imaging systems. The school was founded in December
1993, and it was approved by the KNAW (Dutch Royal Academy of Sciences) in May 1995. In 2000 the school got its new
accreditation for the coming five years.
Participants in ASCI are groups from Delft University of Technology, the University of Amsterdam, the Vrije Universiteit,
Leiden University and the University of Utrecht; the University of Twente, the University of Groningen, and Eindhoven
Technical University have joined ASCI by association agreements.
Research within the school can be characterized as applied, experimental and technical computer science, focussed
primarily on parallel and distributed systems and processing, as well as the processing of sensor data, image data and other
media. With the emphasis on system development, integration of software and hardware, and the processing of sensory
information, it directly addresses the needs in high-performance computing and computing intensive applications, with a
special emphasis on computational science, and media-oriented applications such as multimedia, medical imaging, computer
vision, industrial automation and CAD/CAM. Other important topics are embedded systems and wide-area systems.
The school organizes a graduate program and a research program covering all major subjects concerning parallel,
distributed, embedded, and real-time systems, performance analysis, image processing, image analysis, image synthesis,
sensor interpretation, pattern recognition and computer vision. Every year ASCI organises the Annual ASCI Conference, the
scientific meeting place for all participants in ASCI. Another annual activity is the GNARP workshop (GNARP Graduate
Network of Applied Research in Parallel systems) which is organized by PhD students and which is a platform for presenting
work in progress. There is also a workshop on imaging topics. This workshop is organized every two or three years.
1.2
Participating Groups
The following reseach groups participate in ASCI. They are represented together with their abbreviations. For each group the
members are listed (situation January 2007).
VU-WI-I
Vrije Universiteit, Faculty of Sciences, Division of Mathematics and Computer Science, Dept. of
Computer Science
http://www.cs.vu.nl/
Prof.dr. A.S. Tanenbaum, Prof.dr. H.E. Bal, Dr. W. de Jonge, Prof.dr. M.R. van Steen,, Dr. C.D.
Gamage, Dr.ing. T. Kielmann, Dr. G.E.O. Pierre, Dr. B.J. Overeinder, Dr. R. van Nieuwpoort,
Dr. J. Maassen, Dr.ir. H.J. Bos, Dr.B. Crispo, Dr.ir. C. van Reeuwijk, B.C. Popescu M.Sc., Drs
M.D. den Burger, Drs. A.M. Dobber, Drs. N. Drost, Drs. T. van der Schaaf, S. Sivasubramanian
M.Sc, drs. M. Szymaniak, drs. S. Voulgaris, drs. J.M.S. Wams, drs. M. Wrzesinska; D. Gavidia
Simonetti, MSc, M.R. Rieback MS, drs. W.J. de Bruijn, S. Krishnan Nair, Drs. MH.J. Nijhuis,
Drs. G. Portokalidis, Drs. J.N. Herder, J.Slowinska
UvA-FdNWI-caps
University of Amsterdam, Department of Computer Science,System and Network Engineering
http://www.science.uva.nl/research/sne/
Prof.dr. L.O. Hertzberger, Dr. A. Belloum, Prof.drs. M. Boasson, dr. C.T.A.M. de Laat, C.Erbas
MSc, drs. J.J. van der Ham
UvA-FdNWI-ias
University of Amsterdam, Faculty of Science, Informatics Institute, Intelligent Autonomous
Systems. http://www.science.uva.nl/research/isla/
Prof.dr. F.C.A. Groen, Prof.dr. D.M. Gavrila, Dr. B.J.A. Kröse, Dr. L. Dorst, Dr. N. Vlassis, Dr.
Z. Zivkovic, drs. W. van der Mark, drs. J.J. Verbeek, drs. J.R. Kok, drs. M.T.J. Spaan, drs. W.P.
Zajdel, drs. S. van Gosliga, O. Booij MSc, ir.J.A. van Kleef, M. Hofmann, Th. Noulas MSc., Drs.
J.R.J. Nunnink.
UvA- FdNWI-isis
University of Amsterdam, Faculty of Sciences, Informatics Institute, Intelligent Sensory
Information Systems Group. http://www.science.uva.nl/research/isis
Prof. dr. A.W.M. Smeulders, Dr. R. van den Boomgaard, Dr. M. Worring, Dr.Ing. J.M.
Geusebroek, Dr. T. Gevers, Dr. C.J. Veenman, R.F. Aldershoff, Dr. V.T. Pham, Dr. F.J.
Seinstra, A. Diplaros M.Sc., Drs. C.G.M. Snoek, ir. G.J. Burghouts, Mw. G.P. Nguyen, S. Mehra
M.A., Drs. J.C. van Gemert, T.K. Dang MSc.
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UvA-FdNWI-scs
University of Amsterdam, Faculty of Science, (Informatics Institute/CSP Laboratory), Section
Computational Science.
http://www.science.uva.nl/research/scs
Prof.dr. P.M.A. Sloot, Dr. G.D. van Albada, Dr. A.G. Hoekstra, Dr. J.A. Kaandorp, Dr. R.G.
Belleman, K. Iskra M.Sc, Drs. M. Scarpa
UvA-FdNWI-csa
University of Amsterdam, Faculty of Sicence, Informatics Institute, Computer Systems
Architecture Group http://www.science.uva.nl/research/csa/
Prof.dr. C. Jesshope, Dr. P.M.W. Knijnenburg, Dr. A. Pimentel, Drs. T.B. Bernard
K. Bousias, Guang Liang MSc, Drs. M. Thompson, Drs Li Zhang
TUD-EWI-isa-pds
Delft University of Technology, Faculty of Electrical Engineering, Mathematics & Computer
Science, Parallel and Distributed Systems Group.
http://www.pds.ewi.tudelft.nl
Prof.dr. H.J. Sips, dr. D.H.J. Epema, Prof.dr.ir. A.J.C. van Gemund, Prof.dr. C. Witteveen,
dr. K. Langendoen, dr. A.G. Baggio, P.J. Garbacki MSc, ir. G.P. Halkes, Haratcherev M.Sc., ir.
J. Pietersma, ir. A. Iosup, A.L. Varbanescu MSc, ir. J.D. Mol, O.O. Sonmez
TUD-EWI-me-ce
Science, Computer Engineering Group
http://ce.et.tudelft.nl
Prof. dr. S. Vassiliadis, Dr. B.H.H. Juurlink, ir. P.J. de Langen
TUD-EWI-mm-cgcc
Science, Computer Graphics and CAD/CAM Group. http://graphics.tudelft.nl
Prof.dr. F.W. Jansen, Dr. W.F. Bronsvoort, ir. F.H. Post, Dr. W. Pasman, M. Koutek, , C.P.
Botha M.Sc., ir.B.Vrolijk, ir. H.A. van der Meiden, L.Zhao, MSc., E.J. Griffith, MSc, ir. G. de
Haan
TUD-EWI-mm-ict
Science, Department of Mediamatics, Information and Communication Theory Group.
http://www.ict.ewi.tudelft.nl
Prof.dr.ir. J. Biemond, Prof.dr.ir. R.L Lagendijk, dr.ir.R.P.W. Duin,Dr. E.A Hendriks,
Dr.ir. J.C.A. van der Lubbe,Prof.dr.ir. M.J.T Reinders, Dr. A Hanjalic, dr. L.F.A. Wessels,. dr.ir.
D. de Ridder, dr.ir.E.P. van Someren, Dr. E.M. Pekalska, ir. R.J.M. den Hollander, MTD A.I.
Deac, ir. P.J.O. Doets, P.Juszczak M.Sc., C. Lai MSc., ir.J.F. Lichtenauer, ir. M. van
Staalduinen, ir. J.R. Taal, A. Harol MSc, ir. Th.A. Knijnenburg, S.A. Verzakov MSc, J.Wang, ir.
R.J.P. van Berlo, H. Celik MSc, Drs. G.A. ten Holt, B. Kroon, Yunlei Li, Drs W. Meuleman, U.
Naci MSc, Ir. M.H. van Vliet, ir. R.P. Westerlaken
TUD-TNW-tn-qi
Delft University of Technology, Faculty of Applied Physics, Imaging Science & Technology,
Quantitative Imaging Group http://www.qi.tnw.tudelft.nl/
Prof.dr. I.T. Young, Prof.dr. L.J. van Vliet, Dr. P.P. Jonker, Prof.dr. A.M. Vossepoel, J. Caarls,
drs. F.G.A. Faas, B.E. TuanQuangPham, I.W.O. Serlie,ir.G.O.F. Parikesit, ir. C. van Wijk, B.J.
Vermolen
UL-LIACS/LERC
Leiden University, Faculty of Mathematics and Natural Sciences, Leiden Institute of Advanced
Computer Science (LIACS)
Computer & Software Systems Division- Leiden Embedded Research Center (LERC)
http://www.liacs.nl/research/CS/
Prof.dr. H.A.G. Wijshoff, Prof.dr. E.F. Deprettere, Prof.dr. F.J. Peters, Dr. M.S. Lew, Dr. A.A.
Wolters, Dr. D.P. Huijsmans, , Dr. E.M. Bakker, Dr.ir. T.P. Stefanov, Drs. J.T. Rijsdam, C.
Zissulescu-Ianculescu M.Sc., M. Haneda M.Sc., A. Turjan, drs.M.L. Cristea, drs. V. Zivkovic,
drs.I.Cimpian, Drs. Hui Li, H. Nikolov MSc, rs.ing. J.H.T. Rohling, Drs. Bin Jiang, J. Lemaitre,
Drs. S. Meijer, Drs. A.A.J. Oerlemans
UU-WI-ics
Utrecht University, Faculty of Science, Department of Information and Computing Sciences,
Center for Geometry, Imaging and Virtual Environments. http://www.give.nl
Prof.dr. M.H. Overmars, Dr. M. van Kreveld, Dr. F. van der Stappen, Dr. R. Veltkamp, Dr. R.W.
van Oostrum, Dr. P. Min, Dr. O. Grigore, M.Sc., Drs R. Geraerts, Drs. A. Kamphuis, dipl.ing.
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Research Themes
Iris Reinbacher, drs. J.P. van den Berg, drs. E.J. Moet, Dipl.Inform. R.Typke, O.C. Goemans
MSc. Ir. R. van Gulik, Drs. M. Bosma, Drs. F.B. ter Haar, Drs.R.H. van Leuken, M. Vahedi
TUD-L&R-frs
Delft University of Technology, Faculty of Aerospace Engineering
Department of Earth Observation and Space systems (DEOS)
Optical and Laser Remote Sensing Group
http://www.lr.tudelft.nl/olrs
Dr. B.G.H. Gorte, dr.ir. F. van den Heuvel, T.R. Shah M.Sc., F. Karimi Nejadasl
UG-CS-svcg
University of Groningen, Faculty of Mathematics and Physical Sciences, Institute of
Mathematics and Computing Science, Scientific Visualization and Computer Graphics.
http://www.cs.rug.nl/informatica/onderzoek/programmas/svcg
Prof.dr. J.B.T.M. Roerdink, Dr. G. Vegter, Dr. H. Bekker
UG-CS-IS
University of Groningen, Faculty of Mathematics and Natural Sciences, Institute of Mathematics
and Computing Science, Intelligent Systems.
http://www.cs.rug.nl/ Prof.dr. N. Petkov, Dr. M.H.F. Wilkinson
TUE-EE-dmes
Technische Universiteit Eindhoven, Faculty of Electrical Engineering, Design Methodology for
Electronic Systems
http://www.es.ele.tue.nl/es/ Prof.dr.ir. R.H.J.M.Otten, Dr.ir. T. Basten, Prof.dr. H. Corporaal,
Dr.ir.M.C.W. Geilen, Prof.dr.ir. G. de Haan, Dr.ir. J.P.M. Voeten, A. Beric M.Sc., S.H. Fatemi
M.Sc., S. Stuijk, M. Zhao M.Sc.; Dipl.Ing. O. Florescu, Dipl.Eng. S.V. Gheorghita, A.H.
Ghamarian Msc., H.Hu MSc.
TUE-WI-vis
Technische Universiteit Eindhoven, Department of Mathematics and
Computer Science, Visualization Group,
http://www.win.tue.nl/vis Prof.dr.ir. J.J. van Wijk, dr. R. van Liere, dr.ir. A.J.F. Kok, dr. A.C.
Telea, dr.ir. H.M.M. van de Wetering, ir. F.J.J. van Ham, A.J. Pretorius MSc, PD.Eng. S.L.
Voinea, ir. D. Reniers
TUE-BMT-bmia
Technische Universiteit Eindhoven, Department of Biomedical Engineering
Biomedical Image Analysis http://www.bmi2.bmt.tue.nl/image-analysis/
Prof.dr. B.M. ter Haar Romeny, Prof.dr.F.A. Gerritsen, Dr. L.M.J. Florack, Dr. A. Vilanova
Bartroli, dr.ir. J.M. Hofman, H. Bouma, dr.ir. R. Duits, F. Kanters, P. Sereda M.Sc., E.
Balmachnova MSc, ir. E.M. Franken, ir. T.H.J.M. Peeters, ir. B. Platel, ir. F. Kanters
UL-LUMC-lkeb
Leiden University Medical Center, division of Image Processing, laboratorium voor klinische en
Experimentele Beeldverwerking www.lkeb.nl Prof.dr.ir. Johan H.C. Reiber, dr.ir. Faiza Admira
Behloul, ir. Johan G. Bosch, dr.ir. B.P.F. Lelieveldt, Isabel Maria Adame MSc, Luca Ferrarini
MSc, drs Marijn van Stralen, drs. Avan Suinesiaputra, Drs.A.E.H. Scheenstra
UT-EEMCS-dacs
University of Twente, Faculty of Electrical Engineering, Mathematics and Computer Science,
Design and Analysis of Communication Systems
http://dacs.ewi.utwente.nl
prof.dr. B. Haverkort, Dr.ir. G.J. Heijenk,Dr.ir. A. Pras, Dr.ir. P.T. de Boer, Dr.ir. G. Karagiannis,
Ir. P. Goering, A. Jehangir MSc., Ir. M. Kamilova, Ir. Fei Liu, A. Remke Dipl.-Inf.
EUR-RMI-bigr
Erasmus MC, Departments of Radiology and Medical Informatics, Biomedical Imaging Group
Rotterdam http://www.bigr.nl/
Prof.dr. W.J. Niessen, Prof.dr.ir. A. Vossepoel, Dr.Ir. E. Meijering, Dr. J. Veenland, Dr.Ir. H.
Vrooman, Dr.ir. Th. van Walsum, Dr. R. Stokking, L. Alic MSc, Drs. F. van der Lijn, E. Rollano
MSc, I. Smal MSc
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1.3
ASCI Research Themes
In this report the scientific output of ASCI over the year 2004 has been collected and categorized along the two main
research lines of ASCI, Computing and Imaging.
These are divided into research themes (A,B,C and D – see matrix) of which the denomination has changed a bit.
ASCI research historically comprises two main themes: Computing and Imaging. Within these themes, activities can be
divided into methods & algorithms and systems & architecture. Methods & algorithms deals with the development of models
and tools for scientific and industrial applications.
Systems & architecture deals with the large scale integration in areas like telematics, embedded systems, communication
and networks. Both types of activity are targets for fundamental and applied research within ASCI.
These themes and target areas make it possible to construct the following matrix, in which four fields can are defined. These
fields are indicated as A, B, C and D and are made more specific in the following paragraphs.
Methods & Algorithms
Systems & Architecture
Computing
A
High Performance Computing
and Computational Science
B
Large scale distributed Information Systems
and Embedded Systems
Imaging
C
Image and Multimedia Sensing, Processing,
Interpretation and Visualisation
D
Multimedia Information Systems
A: High Performance Computing and Computational Science
A1: High Performance Computing
High Performance Computing (HPC) is the collective name of large scale and/or real-time calculations on state-of-the-art
computers. These computers are the very tools used in computational science to allow thrusting back the frontiers of
knowledge.
The Computing branch of ASCI is interested in HPC to develop, improve, and study program models and programming tools
for different HPC architectures. Of special interest to ASCI is research on distributed HPC architectures, which will form the
basis of future Grid computing. To this purpose ASCI has a research distributed HPC system available: the DAS (Distributed
ASCI Supercomputer). The research in distributed HPC comprises applications, algorithm design, languages and compilers,
run-time systems, and scheduling techniques.
A2: Computational Science
Besides theoretical and experimental research, modeling and simulation has become the powerful third paradigm of
scientific inquiry in the natural sciences. Here, models of natural phenomena are analyzed through (in many cases largescale) simulations executed on state-of-the-art computing system, ranging from desktop workstations to heterogeneous
distributed (grid-based) environments or massively parallel computers. Over the years, researchers have realized that
modeling and simulation has many generic elements, not connected to a specific application field. Furthermore, it became
clear that successful modeling and simulation requires multidisciplinary teams, where computer scientists, numerical
mathematicians and researchers from application fields work closely together. These developments led to the evolution of
the field of computational science. Here, research focuses on computational methods, models, and tools, using new insight
from computer science and (numerical) mathematics, with the goal to facilitate the study of processes, through simulation,
that was hitherto not possible.
Within ASCI a number of groups are active in the field of Computational Science. Their embedding in ASCI provides
necessary input from basic computer science, especially from the computing theme. Computational Science within ASCI is
basic research (as opposed to application driven computational science), focusing on generic models, enabling tools and
problem solving environments.
Generic Models : Capable to capture many natural systems, allowing for formal study (using e.g. concepts from theoretical
computer science), and preserving inherent parallelism. Examples include Cellular Automata, particle based models, and
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Research Themes
natural solvers. Also, study of fundamental issues related to e.g. synchronous vs. asynchronous execution in generic
(parallel) models.
Enabling Tools : Examples include Virtual labs, grid based computing environments, automatic load balancing and
scheduling systems, scientific visualization and virtual reality environments, data analysis and data retrieval systems (e.g. for
BioInformatics), web based computing, etc.
Problem Solving Environments : Tailored towards specific application fields (e.g. climate models) or generic environments for
e.g. interactive simulation.
The main challenge for computational science within ASCI lies in obtaining a true fundamental understanding of all issues
related to the modeling and simulation chain. This can be achieved by thorough study of generic models and execution
environments, and through detailed analysis of (possibly application oriented) case studies, in combination with realization of
specific tools and problem solving environments.
B: Large-scale Distributed Information Systems and Embedded Systems
With the advent of the Internet, a new dimension has been added to the notion of computing. Computing not only concerns
high-performance computations, but includes collecting, processing, and communicating information across large-scale
networks. These developments are leading to a next generation of distributed computer systems that are characterized by
their mixed scale, interconnectivity, and heterogeneity. Examples include traffic control systems and large-scale
computational grids. The number of embedded system applications is growing explosively and parallels the rapidly emerging
systems-on-silicon paradigm and the explosive expansion of networked applications, both wired and wireless.
Considerable research is needed by multidisciplinary teams of experts. Research topics include the following:
B1: Operating systems
Simply using existing operating systems to build the type of applications mentioned above will not do. Existing operating
systems are tailored for general use and often require significant CPU power and main memory. In addition, they are still
optimized for using local resources, and provide only traditional networking support. What is often needed are specialized
operating systems that exploit the available networking facilities such as programmable network interfaces. In addition, the
trend to customize operating systems to specific applications requires that new avenues to flexibility are explored.
B2: Distributed Systems
An important area of research covers middleware, also known as distributed systems. Middleware provides a layer of
abstraction by which the underlying network infrastructure is mostly transparent to applications. Such a layer handles issues
such as failure masking, resource management, caching and replication, automated storage, security, and so on. It provides
applications with a convenient communication interface while hiding the intricacies related to issues such as performance
and reliability. Developing scalable distributed systems is a major multifaceted research topic and includes subjects such as
adaptive large-scale replication, worldwide directory services, and high-performance communication infrastructures.
B3: Embedded systems
An embedded system is a (not self-contained) part of a larger unit that provides service(s) to, or controls that unit. It typically
consists of a heterogeneous collection of autonomous subsystems (ASICs, FPGAs, microcontrollers and DSPs) that require
co-operation to perform (complex) tasks. They can be part of a geographically distributed system, locally distributed systems
(in-home networks), or lumped systems (such as TV receivers). Reactive real-time embedded systems are becoming
ubiquitous. Such systems react continuously to their environment at the speed of the environment. Research in this area
ranges from the development of hardware and software components for digital signal processing to the development of
advanced communication software. Formal methods must be called for to guarantee time-to-market, correctness and safety.
However formal specifications, verifications and synthesis of software and hardware from high levels of abstraction have
been demonstrated only for small, specialized languages with restricted semantics. This is at odds with the complexity and
heterogeneity found in typical embedded systems of tomorrow.
One challenge is to base the approach of designing heterogeneous reactive embedded systems on the use of appropriate
formal models to describe the behavior of the system at a high level of abstraction, before a decision on its decomposition
into hardware and software components is taken. Another challenge is the systematic development of embedded
applications such as networked embedded applications. In the same way as embedded system design is a
hardware/software co-design effort, embedded application and embedded system should be specified and explored in
concert. Important issues here are scalability, robustness, re-use, quality of service, adaptive resource contracts, balancing
processing load and data allocation over available processing and storage resources, both local and distributed.
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C: Image and Multimedia Sensing, Processing, Interpretation, and Visualization
On the junction of Imaging and Methods and Algorithms we deal with the development and evaluation of generic models,
methods, algorithms and tools for image sensing, processing, interpretation, and visualization that can be used in many
concrete applications. The past decade has witnessed a huge increase in the amount of digital visual data that is generated,
processed, and stored. Because humans are good in the processing of visual information, and computers are strong in the
fast processing of huge amounts of data, the best of both worlds can only be combined if computers can adequately process
visual data for analysis and visualisation. Many theoretical and technological breakthroughs are required before we reach
that goal. New fundamental insight into the inherent complexity of problems, new algorithms with proven practical behaviour
are required.
Research topics include:
C1: Image and multimedia sensing
The sensing of the real world with satellites, cameras, all kinds of (medical) scanners etc. The resulting data streams are
typically large amounts of digital still images and video. Important aspects of research are the development of technology for
image acquisition, image sensors and other media, motion capturing, image filtering, image coding, restoration, high quality
image compression, and conversion.
C2: Image processing
Taking an image as input, process the digital image data, and output data either as an image, or as geometrical, numerical,
or statistical data. Fundamentally difficult issues are topics such as: representation of images, segmentation, digital
geometry, measurement, and mathematical morphology.
C3: Image interpretation
Classification and recognition of information in images. The problem is often ill-posed, and the image data often ambiguous.
Challenging research questions are the development of new models for sensor data fusion, parameter estimation, adaptive
control, statistical and geometrical pattern recognition, neuro computing, learning, goal directed computation, model-based
interpretation, image database techniques.
C4: Visualization and modeling
The (interactive) modeling of complex objects and whole scenes, and the generation of images from these descriptions.
Relevant research aspects are multi-modal data integration, 3D modelling and feature recognition, motion and path planning,
computational geometry, data and information visualisation, rendering, 3D interaction, virtual environments, levels of detail.
This list is not complete, and the classification of topics is not strict, there is much overlap between various topics. Each of
the techniques plays a natural role in many applications, including bio-medical imaging, industrial inspection, image and
video archiving and retrieval, document analysis, geographic information systems, earth observation, computer-aided design
and reverse engineering, robotics and manufacturing, robot vision and path planning. See also multimedia information
systems at the junction of Imaging and Communication and Systems.
D: Multimedia Information Systems
Multimedia systems are systems that are concerned with the handling of multimedia. It includes the acquisition,
representation, composition, interaction, architecture, analysis, retrieval and distribution of one or multiple information
streams like images, video, speech, sound, free text, language, and graphics. New uses of information require new ways of
representing the information, not only because of the availability of multiple information streams but also because of their
interaction and the way they can support one another. New methods, techniques and means for the manipulation and
architecture of the information are required. It will not only influence the user and the use of information, extensive use of
multimedia will also fire back at the internals of the computer, the computer organization and the networks connecting them.
Research topics include:
D1: Multimedia repositories
The processing of multimedia information relies on new designs of the system architectures. Research questions are directed
towards data and storage structures for multimedia data. Efficient use of storage space is necessary. Indexing multimedia
data based on a higher, more abstract level are to be investigated. New search techniques to handle the large databases
efficiently and to uncover information are to be developed.
D2: Image, video and audio compression
Although substantial progress has been achieved in efficient representation (compression) of images and video, it is no
longer studied as an isolated problem, but is considered as one of the components of an entire system. Compression
12
Research Themes
optimization is now investigated in relation with overall performance, including limited or adaptive bandwidth, quality of
service, scaling of information and the ability to analyze and to manipulate content in the compressed domain directly. To
interact with multimedia data, techniques are investigated to describe the data as coherent spatio-temporal objects.
D3: Multimedia understanding
At the multimedia level, understanding the information is reached by fusing the information of different modalities and
sources. The main issue is how to combine multiple information streams to facilitate a better understanding. Learning from
multimedia repositories is a challenging problem. Multimedia mining covers the conversion of the content of large databases
into generic rules on the content.
D4: Multimedia editing systems
For the design of multimedia products the availability of multimedia editing systems is indispensable. Research questions are
how to make these systems work on a sufficient level of abstraction in order not to obstruct the designer, but which are - at
the same time - intuitive to understand.
D5: Delivery
To secure multimedia data through e.g. the Internet, watermarking, security and encryption techniques are inevitable for copy
protection, authentication or hiding of data. Research issues are for instance the development of watermarking techniques
that are resistant to various deformations and privacy guaranteed exchange of multimedia data.
D6: Multi-modal man-machine interaction
The need grows for personalized video delivery, that is, for developing systems able to filter the incoming programs, to
analyze them and prepare them for retrieval according to user preferences. This is only possible if such systems are capable
of learning about the user profile. An important research issue here is to find ways of characterizing, quantifying and
measuring emotions.
D7:Multimedia applications
Multimedia applications are found in many different circumstances. To mention a few examples, disciplines such as the
textile branch, detective work and the medical profession drive on multimedia files. The management of data in bioinformatics, especially in the area of bio-diversity and microscopic analysis and the spatial location of metabolic processes
invariably are multimedia of nature. Exploring the depth of the content is an important task for the development of new
knowledge. In the Internet based tele-working and other aspects of professional life, multimedia transport of information to
escape human transportation is of great societal relevance.
13
Chapter 3: ASCI –wide Events
Chapter 2 Scientific Output along Research Themes
For each ASCI subtheme this chapter contains a subsection in which the contribution of the various research groups in ASCI
has been collected. The following scheme lists the enrollment of the groups with respect to the subthemes (x.y.z in a cell
(group, theme) refers to the section in which the scientific ouput of group with respect to theme is reported).
A
VU-WI-I
UvA-FdNWI-caps
UvA-FdNWI-scs
UvA-FdNWI-ias
UvA-FdNWI-isis
UvA-FdNWI-csa
TUD-EWI-st-pds
TUD-EWI-me-ce
TUD-EWI-mm-cgcc
TUD-EWI-mm-ict
TUD-TNW-tn-qi
UL-WI-I(LIACS)
UL-LUMC-lkeb
UU-WI-ics
TUD-L&R-frs
UG-CS-is
UG-CS-svcg
TUE-EE-dmes
TUE-WI-vis
TUE-BMT-bmia
UT-EEMCS-dacs
EUR-RMI-bigr
2.1
2.1.1
B
2.2.6
2.2.1
C
D
2.3.8
2.3.13
2.4.2
2.1.4
2.1.3
2.1.1
2.1.2
2.2.9
2.2.7
2.2.8
2.2.2
2.2.3
2.3.12
2.3.4
2.3.6
2.3.7
2.3.14
2.3.10
2.3.11
2.3.15
2.3.1
2.3.3
2.3.2
2.3.5
2.4.1
2.2.4
2.3.9
A: High Performance Computing and Computational Science
Contribution of TUD-TNW-tn-qi
Architectures and Algorithms, Embedded Imaging Systems
The work in 2005 encompassed projects on embedded systems that incorporate real-time computer vision subsystems.
The theoretical work was on the establishment of a parallel programming environment where heterogeneous architectures
can be programmed within a single parallel programming language but use various programming paradigms, such as
dataflow and data parallel. This is performed within the context of the Progress project SMARTCAM; with TUE, Philips
Research and Philips CFT as main industrial partners. Data-parallelism is hidden in “algorithmic skeletons, while task
parallelism is scheduled at run time over a Smartcam processor configuration incorporating TriMedia, Xetal-SIMD, FPGA
with embedded PowerPC; and controller PC. Hardware design space exploration is part of the project. A real-time stereo
vision camera was developed in cooperation with Philips Research and Philips Applied Technologies.
Equivalent problems, navigation using cameras and encoders, are encountered in augmented reality applications. Within the
Mobile & Wireless project of the Telematica Institute and with TUD-ITS, the positioning of virtual objects exactly in overlay
with the real world, is obtained by determining the position and orientation of the human head in relation with the real world.
An embedded imaging system closely coupled in a fast loop with the graphics animation system determines from visual
cues, fused with information from gyros, accelerometers, magnetometers and tilt sensors, the position and orientation in 3D
space with an update rate of 10ms. A demonstrator helmet was developed. A collaboration project with the Royal Academy
of Art in the Hague to require Augmented Reality content was successfully applied for (start in 2006).
A more or less equivalent problem can be found in the "ROBOCUP" project, in which two teams of four autonomous robots
play soccer on an indoor field of about 10x6 meter. Positioning of the robot, interception of the ball, and collision avoidance
of the other robots, is performed using odometry and real time image sensing and processing. This project was done in
cooperation with the TU-Eindhoven. Similarly robot soccer with Sony AIBO dogs is played in cooperation with the UvA, UU
and the Decis lab. A collaboration regarding humanoid robots is started up with the faculty of 3ME at the TU-Delft. A focus in
these projects is on reinforcement learning of robots to walk and dribble with the ball.
14
Much effort was put into the set-up of the Dutch Initiative for Cure and Care Technology, a 3TU- initiative together with
Erasmus MC, AMC and LUMC. Its focus is on the effectiveness of the entire cure and care chain as well as on automatic
systems that sense-think-act.
External projects
SmartCam
Period: 2002-2006; funding STW-Progress, with: TU/e Embedded Systems
Papers in international journals
Han, J., J. Gao, Y. Qi, P.P. Jonker, and J.A.B. Fortes; Toward Hardware-Redundant, Fault-Tolerant Logic for
Nanoelectronics, IEEE Design & Test of Computers, vol. 22, no. 4, 2005, 328-339.
Jonker, P.P.; Discrete topology on N-dimensional square tessellated grids, Image and Vision Computing, vol. 23, no. 2,
2005, Feb., 213-225.
Contributions to international conference proceedings
Broers, H., W. Caarls, P.P. Jonker, and R. Kleihorst; Architecture Study for Smart Cameras, Proc. EOS Conference on
Industrial Imaging and Machine Vision (Munich, Germany, June 13-15), European Optical Society, 2005, 39-49
Fatemi, H., H. Corporaal, T. Basten, R. Kleihorst, and P.P. Jonker; Designing Area and Performance Constrained
SIMD/VLIW Image Processing Architectures, in: J. Blanc-Talon, W. Philips, D. Popescu, P. Scheunders (eds.), Advanced
Concepts for Intelligent Vision Systems - ACIVS 2005 (Proc. 7th Int. Conf., Antwerp, Belgium, Sep.20-23), Lecture Notes in
Computer Science, vol. 3708, Springer Verlag, Heidelberg, 2005, 689-696.
Fatemi, H., H. Corporaal, T. Basten, R. Kleihorst, and P.P. Jonker; Parallelism Support in SIMD/VLIW Image Processing
Architectures, in: B.J.A. Krose, H.J. Bos, E.A. Hendriks, J.W.J. Heijnsdijk (eds.), ASCI 2005; Proceedings of the eleventh
annual conference of the Advanced School for Computing and Imaging (Heijen, NL, June 8-10), ASCI, Delft, 2005, 291-296.
Jonker, P.P., and H. Corporaal; Skeletons and Asynchronous RPC for Embedded Data- and Task Parallel Image
Processing, Proc. 9th IAPR Conference on Machine Vision Applications (Tsukuba Science City, May 16-18), Tokyo, 2005,
384-387.
Jonker, P.P., B. van Driel, J. Kuznetsov, and B. Terwijn; Algorithmic foundation of the Clockwork Orange Robot Soccer
Team, in: M.Erdmann, D. Hsu, M. Overmars, A.F. van der Stappen (eds.), Algorithmic Foundations of Robotics VI, STAR 17
(Proc. 6th Int. Workshop, Zeist/Utrecht, July 11-13 2004), Springer Tracts in Advanced Robotics, vol. 17, Springer Verlag,
Heidelberg, 2005 (@2004), 17-26.
Schuitema, E., D.G.E. Hobbelen, P.P. Jonker, M. Wisse, and J.G.D. Karssen; Using a controller based on reinforcement
learning for a passive dynamic walking robot, Humanoids2005, Proc. IEEE-RAS Int. Conf. on Humanoid Robots (Tsukuba,
Japan, Dec.5-7), IEEE, 2005, 1-6.
Cooperations within ASCI
TUE-EE-dmes
2.1.2
Contribution of UL-LIACS
Analysis and modeling of the circadian pacemaker at the cellular level
The project for developing computer models and performing large-scale simulation of the circadian pacemaker at the cellular
level started in 2004 as collaboration between the Leiden Institute of Advanced Computer Science (LIACS) and the Leiden
University Medical Center (LUMC). In 2005 a simulation model has been developed to investigate the effects of the single
unit activities (SUAs) on the activity of populations in the biological clock, more precisely the Suprachiasmatic Nuclei (SCN)).
The simulations use a limited number of neurons and contain different light-dark regimes.
Performance predictions and resource management in a Grid
To deliver nontrivial quality of service is one of the most challenging problems in the Grid. Specifically, mining performance
data on Grid resources to extract useful information, helps to improve performance or manage the system itself. The main
research questions are:
1. How to define a set of performance metrics and efficiently predict it using statistical data mining techniques?
2. How resource brokers can incorporate prediction information in an intelligent way to improve throughput and response
time on a meta-level?
3. How dynamic prediction information can be efficiently published or routed to the interested brokers/parties?
15
Another research topic is workload characterization and modeling in a Grid environment, specifically in Markov Arrival
Processes and Markov Modulated Poisson Processes (MMPP) in modeling job arrival patterns at the Grid level.
Cyttron Bio-Computing Search Project
The Cyttron (www.cyttron.nl) consortium wants to implement a comprehensive, integrated infrastructure for bio-imaging and
modeling cells down to atomic detail. We would like to provide a generic tool for identifying the molecular causes of disease,
essential for the prevention of disease and the development of new drug and therapies, and to establish a platform for
advanced diagnosis and tuning of individualized therapy, increasing effectiveness in health care. The consortium is highly
multidisciplinary including (bio-)physicists, chemists, mathematicians, bio-informatics and image processing specialists, cell
biologists, microscopists and medical researches from various research institutes. This sub-project of Cyttron focuses on
image search algorithms and methods for bio-image data bases.
HIRLAM on a grid environment
We investigate how the operational numerical weather forecast system HIRLAM could be made grid-enabled, meaning what
kind of adaptions are required to execute the system efficiently on a grid. As grid platform we use the DAS-2 system, which
consists of five clusters located on five different universities. For the experiments on a single cluster, we found that more
compute processors result in a better performance. However, we cannot obtain more improvement by only increasing the
number of computer processors due to communication overhead. We also found that an additional one or two IO processors
is an ideal number for the forecast model, more IO processors do not result in a better performance. For the experiment on a
multi-cluster, we varied the distribution of processors over two clusters to investigate the performance of the forecast model.
The distribution over two clusters increases the elapsed time: the more processors are distributed over the two clusters the
larger the elapsed time becomes. Our experiment shows that running the forecast model on a multi-cluster does not result in
a better performance than on a single cluster. However, using grid technology may give an advantage if the in- and output
files are not located on the main compute server.
Iterative Compilation
In iterative compilation we search for the best program transformations by profiling many variants and selecting the one with
the shortest execution time. Since this approach is extremely time consuming one has to incorporate static models. We show
that a highly accurate model as a filter to profiling can reduce the number of executions by 50%. We also show that using a
simple model to rank transformations and profiling only those with highest ranking can reduce the number of executions even
further, in case we have a limited number of profiles at our disposal. We conclude that a production compiler might perform
best using the last approach.
Exterrnal Projects
2004-2008, Bsik, 8.8 MEuro.
The Cyttron consortium wants to implement a comprehensive, integrated infrastructure for bio-imaging and modeling cells
down to atomic detail. We would like to provide a generic tool for identifying the molecular causes of disease, essential for
the prevention of disease and the development of new drug and therapies, and to establish a platform for advanced
diagnosis and tuning of individualized therapy, increasing effectiveness in health care.
Distributed ASCI Supercomputer 3 (DAS 3)
2005-2009, NWO-EW, 900 KEuro, cooperation with all partners of the ASCI graduate school.
Flexible Application Mapping Environments (FAME)
2002-2006, NWO-EW, 270 KEuro, TUE
The FAME project aims at developing a novel approach to program optimization, namely, iterative compilation in which the
transformation space is searched and profiling is used to measure the impact of transformations. One of the most important
goals of this project is to develop heuristics to control the complexity of the search by using analytical models and domain
specific knowledge.
Lateral boundary conditions for nested models – mathematical and computational aspects
2005-2009, NWO-ALW/EW, 300 KEuro.
The aim of this project is to formulate and implement good lateral boundary conditions, both mathematically ("well-posed")
and meteorologically (i.e., properly transferring information from the global into the local domain). The reseach should result
in a production code, implying that the code implements the developed algorithms efficiently on massively parallel and/or
GRID computers.
D. Cheresiz, B.H.H. Juurlink, S. Vassiliadis, and H.A.G. Wijshoff, The CSI Multimedia Architecture,
IEEE Trans. VLSI Syst. 13(1):1-13 (2005).
16
F.J. Cazorla, P.M.W. Knijnenburg, R. Sakellariou, E. Fernandez, A. Ramirez, and M. Valero, Architectural Support for RealTime Task Scheduling in SMT Processors, proceedings CASES, pp. 166-176, 2005.
F.J. Cazorla, P.M.W. Knijnenburg, R. Sakellariou, E. Fernandez, A. Ramirez, and M. Valero, Quality of service for
Simultaneous Multithreading Processors, proceedings Advanced Computer Architecture and Compilation for Embedded
Systems (ACASES), Poster Abstracts, pp. 67-70, 2005.
M. Haneda, P.M.W. Knijnenburg, and H.A.G. Wijshoff, Automatic Selection of Compiler Options using Non-Parametric
Inferential Statistics, proceedings PACT, pp. 123-132, 2005.
M. Haneda, P.M.W. Knijnenburg, and H.A.G. Wijshoff, Generating New General Compiler Optimization Settings,
proceedings ICS, pp. 161-168, 2005.
M. Haneda, P.M.W. Knijnenburg, and H.A.G. Wijshoff, Optimizing General Purpose Compiler Optimization,
proceedings Computing Frontiers, pp. 180-188, 2005.
Hui Li, David Groep, and Lex Wolters, Efficient Response Time Predictions by Exploiting Application and Resource State
Similarities, in proceedings of the 6th IEEE/ACM International Workshop on Grid Computing (Grid2005), Seattle,
Washington, USA, November 2005.
Hui Li, David Groep, and Lex Wolters, Workload Characteristics of a Multi-cluster Supercomputer, in D. Feitelson, L.
Rudolph, and U. Schiegelshohn (Eds.): proceedings of the 10th Workshop on Job Scheduling Strategies for Parallel
Processing (JSSPP 2004), LNCS 3277, pp. 176-193, 2005.
Experimental software
H. Li, Performance Data Miner (PDM): A Java Toolkit for Mining Performance Data in the Grid(www.liacs.nl/~hli/pdm/).
PDM is a Java-based toolkit for mining the performance data in distributed computing environments, or Grids. Its goal is to
extract useful information which can be used to improve performance or manage the Grid system itself.
Experimental hardware
DAS-2 & DAS-3
With research groups of prof.dr. H. Corporaal/ TUE, dr. D. Epema/ TUD, prof.dr. S. Vassiliadis/TUD
2.1.3
Contribution of TUD-EWI-me-ce
∆-iliad
The ∆-ILIAD research concerns with new computer architectural paradigms. The gamma of processor architectures
considered include general purpose, domain (e.g. media), vector processor extensions, polymorphic processing and nonconventional architectures. Furthermore, we perform some reality checks for existing processor implementations. More
specifically the Delta-Iliad team is currently working on the following research topics:
Vector Facility
Traditionally, vector processors are limited by memory accesses, sectioning, and simple-minded computations. The ∆-ILIAD
vector architecture eliminates sectioning, alleviates storage access overhead by overlapping accesses with computations
and merging both of them into a single instruction. In addition to traditional operations, ∆-ILIAD architecture includes new
instructions that perform complex multicycle latency operations. With the introduction of the ∆-ILIAD mechanism a
substantial code elimination is achieved. The specific dense and sparse architectural mechanisms of ∆-ILIAD include the
Complex Streamed Instruction Set (CSI) and the ∆-ILIAD sparse vector processing, which are described below.
CSI Media Architecture
The Complex Streamed Instruction Set Architecture (CSI) is a memory-to-memory vector architecture targeted at multimedia
applications. A single CSI instruction can process data streams of arbitrary length and, in addition to traditional arithmetic
and logical operations, performs data accesses, conversion between storage and computation formats (packing and
unpacking), and complex arithmetic hardwired computation. The main new features of the CSI are elimination of the vector
sectioning instructions, elimination of the packing/unpacking instructions, and introduction of new complex media related
arithmetic instructions.
17
Sparse Matrix Architectures
Vector processors are known for performing good on large amounts of regular data. However, when operating on sparse
matrices such as the one depicted here, the irregular structure induces a performance degradation. The main reasons are
the need for expensive indexed memory accesses and high vector startup overhead due to short vectors. Moreover, the
need for positional information when storing sparse matrices implies an extra storage overhead. The aim of this project is to
aleviate most of the aforementioned problems and increase the efficiency of vector processors on sparse operations. This is
achieved by introducing a new block based Sparse Martix format. In conjunction with a harware Vector ISA extension and
specialized hardware for sparse matrix computations we can aleviate the need for indexed memory accesses. Speedups of
4-5 times have been obtained for matrix-vector multiplication, an important kernel in sparse matrix processing.
Delft Sparse Architectures Benchmark
The Delft Sparse Architecture Benchmark (D-SAB) has been developed in the Computer Engineering Laboratory as a part of
the ∆-iliad project. Its purpose is the evaluation of novel architectures and techniques for processing Sparse Matrices. The
benchmark comprises two parts: The benchmark operations and the benchmark matrices.
Polymorphic processors
Current processor architectures force a complete separation of tasks between implementations (hardware-architectures),
which interpret an architecture, and the programmer targeting this architecture. Polymorphic processors eliminate the gap
between the (hardware) implementations and the programmer of the hardware. This is achieved using a new programming
paradigm and emulation on reconfigurable hardware.
Delft Linpack
The TOP500 Supercomputer Sites webpage ( http://www.top500.org/) presents the world best highperformance computers.
The LINPACK Benchmark is used as a yardstick for performance. Companies like IBM, HP, NEC and Intel (ASCI red) are
presented there with their top supercomputers. The interesting question is: Can a university student team with out of the
shelf inexspensive hardware components beat the industry supercomputers on Linpack? The DelftLinpack-1 processor uses
the power of reconfigurable hardware in order to attempt an answer of this question. Xilinx state of the art FPGA (XC2VP50)
incorporating reconfigurable logic and four PowerPC general purpose cores will be used to implement the DelftLinpack-1
machine.
Contributions to Books
D. Cheresiz, B.H.H. Juurlink, S. Vassiliadis, H. A. G. Wijshoff, The CSI Multimedia Architecture, IEEE Transactions on Very
Large Scale Integration (VLSI) Systems, pp. 1-13, January 2005, Vol. 13, No. 1
S. Vassiliadis, L. A. Sousa, G. N. Gaydadjiev, The Midlifekicker Microarchitecture Evaluation Metric, Proceedings of the IEEE
International conference on Application-Specific Systems, Architectures and Processors (ASAP05), pp. 92-97, Samos,
Greece, July 2005
B.H.H. Juurlink, A. Shahbahrami, S. Vassiliadis, Avoiding Data Conversions in Embedded Media Processors, Proceedings of
the 20th ACM Symposium on Applied Computing, pp. 901-902, Santa Fe, New Mexico, USA, March 2005
S. Suijkerbuijk, B.H.H. Juurlink, Implementing Hardware Multithreading in a VLIW Processor, Proc. 17th Int. Conf. on Parallel
and Distributed Computing and Systems, pp. 674-679, Phoenix, AZ, USA, November 2005
2.1.4
Contribution of UvA FdNWI-scs
Modelling and Simulation
Problem Solving Environments and Visualisation
Within each of the two main themes in our research, a number of projects are being pursued. Sometimes these projects
intersect both themes. We will start this section with the one thesis defended in 2005, by K.A. Iskra, and then move on to a
thematic report on the projects that were active in 2005. Besides the many projects that were active in 2005, a large number
of proposals were written in 2005 and granted in 2005 or early 2006. These include the EU projects Virolab, ACGT, and
QosCos, a project on Computational Finance an NWO STARE project..
Much of our research is performed in close international collaborations. Within the framework of a formal agreement between
the Universiteit van Amsterdam and the Saint Petersburg State University, Russian Federation, a joint laboratory for
computational science was established in Saint Petersburg. This lab works on problem solving environments and
applications. We formally collaborate with CYFRONET, Cracow, Poland, through joint Ph.D. students in the field of
monitoring and scheduling for scientific computing on the Grid. In the framework of a recently started NATO Science for
Peace program we collaborate with institutes of the Siberian Branch of the Russian Academy of Science in the field of
biomedical diagnostic systems. Finally, strong research cooperation is established with a number of USA based universities.
18
PhD Thesis
Kamil Iskra defended his thesis “Time Warp – from Cluster to Grid” in June 2005. In this thesis he investigates the behaviour
of the Time Warp optimistic parallel discrete event simulation strategy in high communication latency environments. Various
methods to reduce the impact of the high latency are studied.
Within each of the two main themes in our research, a number of projects are being pursued. Sometimes these projects
intersect both themes. We will start this section with the one thesis defended in 2005, by K.A. Iskra, and then move on to a
thematic report on the projects that were active in 2005. Besides the many projects that were active in 2005, a large number
of proposals were written in 2005 and honoured in 2005 or early 2006.
External Projects
Modelling and Simulation
AmCG
People involved J.A. Kaandorp, J. Cui, P.M.A. Sloot..
The bioinformatics group of Amsterdam Genomics Center (AmGC) is a collaboration between researchers from SILS-UVA,
IvI-UvA and Academic Medical Center Amsterdam working on bioinformatics. The bioinformatics group is coordinated by
Antoine H.C. van Kampen (Academic Medical Center Amsterdam) and Jaap Kaandorp (Section Computational Science,
UvA). One of the major current research themes within the AmGC is the analysis and modelling of biological networks. The
bioinformatics of biological networks involves a broad range of research and approaches. This research includes topics like
identification of common regulatory elements for genes in a pathway, the modelling and simulation of pathways, the
reconstruction of pathways from experimental data, the visualization of pathways, and the representation of pathways in
graphs and databases. To accelerate our understanding of the (dynamics of) biological networks, it is imperative that these
efforts are combined. Subsequently they have to be applied to real biological problems.
In 2004 three projects related to modelling and simulation of biological networks have been started up within the Section
Computational Science (Mesoscale simulation paradigms for biological systems, Simulation of developmental regulatory
networks, Mathematics and Computation for the System Biology of Cells). In May 2005 the bioinformatics group organised
the second international symposium on networks in bioinformatics in Amsterdam. In November 2005 the project Modelling
and inferring developmental regulatory networks was started up.
Mesoscale simulation paradigms for biological systems
People involved J.A. Kaandorp, J. Cui.
Project funded by the Applied Mathematics programme of the Dutch Science foundation, duration 2003 - 2007, total value
Eur 329000
In this proposed project we want to develop and compare computational models of parts of the living cell that can calculate in
detail system properties from experimentally obtained molecular and physical-chemical data. Such a model is as close as
possible to the biological experiments and therefore can be used not only for understanding the principles of function but also
to steer further biological experiments.
Simulation of developmental regulatory networks
People involved J.A. Kaandorp, Y. Fomekong Nanfack
Funded by Computational Life Sciences programme of the Dutch Science foundation, duration 2003 - 2007, total value Eur
328000
In this project we will develop a model for simulating regulatory networks that are capable of quantitatively reproducing
spatial and temporal expression patterns in developmental processes. The model is a generalization of the standard
connectionist model used for modelling genetic interactions. The model will be coupled with a biomechanical model of cell
aggregates and used to study the formation of spatial and temporal expression patterns of gene products during
development in cellular systems (sponges and scleractinian corals).
Mathematics and Computation for the System Biology of Cells (Cell.Math.)
People involved J.A. Kaandorp, J. Vidal Rodriguez, P.M.A. Sloot.
Project funded by Computational Life Sciences programme of the Dutch Science foundation, duration 2003 - 2007, total
value Eur 487000
The aim of the project is to develop, implement, and validate mathematical and computational techniques for the systems
biology of the cell. Biologists and mathematicians together will formulate realistic mathematical models of metabolic and
regulatory networks including intrinsic spatial non-homogeneity. Depending on the cellular phenomenon considered, models
and methods of appropriate temporal and spatial scales will be developed and can then be applied: models in the form of
ordinary differential equations and methods for system reduction; multi-adaptive computational methods for partial differential
equations (PDEs) for moderate spatial and temporal variability within a cell or an organelle; particle models describing the
interaction of individual molecules and computational methods for the evaluation of the dynamic behaviour; and methods for
integration of these different approaches into a single simulation.
19
Modelling and inferring developmental regulatory networks
People: J.A. Kaandorp, and Y. Fomekong Nanfack, P.M.A. Sloot.
Project funded by the Dutch Russian Research Cooperation 2004 (interdisciplinary mathematics),
Total value Eur 123000
The project is a collaboration with Prof. A. Samsonov (Ioffe Institute Russian Academy of Sciences, St Petersburg). And Prof.
M. Samsonava (St Petersburg State Polytechnical University) In this project we will develop mathematical models of
regulatory networks that are capable of quantitatively reproducing spatial and temporal expression patterns in developmental
processes. The second aim of the project is to develop new statistical techniques for the analysis of temporal and spatial
gene expression patterns, model driven optimization methods, based on simulated annealing in combination with semi
parametric statistical techniques, to infer regulatory networks from actual data sets. To demonstrate the effectiveness of our
models we are planning to apply these methods to analyze the developmental process in organisms with a relatively simple
body plan (for example sponges and scleractinian corals).
Virolab
People: P.M.A. Sloot et al. Funding EU, 3.5 MEuro, 1.0 MEuro (UvA)
Funding was obtained for Virolab in 2005; the actual project will start in 2006. In Virolab, the SCS group will extend their work
on the modelling of HIV infections started in the BMI project.
Nato SfP
People: A.G. Hoekstra, M Yurkin, K. Gilev, K. Semianov
In the context of the Science for Peace program of Nato we collaborate with institutes in Minsk (Belarus) and Novosibirsk
(Russian Federation) on new sensitive methods for cytological analysis of haematological samples. We concentrate on the
computational science aspects and HPC simulations in the field of computational electromagnetics of the project. We
delivered ADDA, a public domain code for Computational Light Scattering, capable to simulate scattering from particles as
large as real biological particles. In effect, this code is capable to solve sets of linear equations with O(107) unknowns. ADDA
is a highly efficient parallel code that was ported to many parallel computers, including the USA ASCI computers, and the
Dutch Asci Supercomputer DAS.
LBM
A.G. Hoekstra, L. Abrahamyan, P.M.A. Sloot
The work on mesoscopic modelling and simulation concentrated on adapting the LBM method, and specifically the L-BGK
method, for unsteady flow, and to apply this to modelling flow of blood during a full heart beat in the lower abdominal aorta.
We also initiated research to adapting the models to take advantage of state of the art (parallel) numerical algorithms (such
as multi grids). Moreover we studied fluid-structure interaction in LBM, and have demonstrated that for 2D time-harmonic
flow coupled to a simple elastic wall a theoretical expression for a dispersion relation is recovered, thus demonstrating the
correctness of our model. In collaboration with Prof. Reiber of LUMC we have developed a problem-solving environment for
image-based computational haemodynamics. Moreover, we have studied in detail the stability of time harmonic LBM
simulations and addressed the question of optimally choosing simulations parameters, by targeting at a specified wanted
accuracy and minimizing execution time. Finally, in collaboration with a number of German institutes, we have developed a
next generation LBM code capable of handling nested grids. We have realised a state-of-the-art decomposition tool to aid
parallelization of this unstructured LBM code. Part of this research is supported through the Token 2000 project ‘DIME’.
PECVD
Involved: V.K. Krzhizhanorskaya, P.M.A. Sloot
In this project a grid-based PSE to study the plasma enhanced chemical vapour deposition of thin films is being developed.
Internally funded project in close collaboration with the IHPCIS in St. Petersburg. The research was conducted with financial
support from the Dutch National Science Foundation NWO and the Russian Foundation for Basic Research under grants
number 047.016.007 and 047.016.018, and with partial support from the CrossGrid EU project IST-2001-32243.
Cluster of Grapes
People involved: S. Portegies Zwart, A. Gualandris, M.S. Sipior, E. Gaburov, B. Bastijns, P.M.A. Sloot, G.D. van Albada +
collaboration with the Pannekoek Astronomical Institute
One of the other research areas in which the SCS group is active, is computational astronomy. "A Cluster of Grapes", a joint
NWO proposal with the astronomical institute "Anton Pannekoek" to NWO was honoured in 2001. The research covers a
wide range of subjects on the boundary of Astronomy and Computational Science. As an example, Gualandris, TiradoRamos and Portegies Zwart studied the performance of a parallel astrophysical N-body solver on pan-European
computational grids. It was demonstrated that especially for large problems grids constitute a suitable computational
environment. Sipior is working to merge the “Kira integrator” with the GADGET tree code developed at MPI Garching. The
end result will allow us to make use of the unique advantages of each numerical approach – the high precision of Kira for
studying the dynamics of a large stellar cluster, and the computational speed of a tree code, used to simulate the galaxy in
which the cluster is embedded. The first stage of this effort is now completed and undergoing testing.
20
Dynamical evolution of dense star clusters
Portegies Zwart & McMillan considered the formation of the recently discovered ``hot Jupiter'' planet orbiting the primary
component of the triple star system HD 188753. The current outer orbit of the triple is too tight for a Jupiter-like planet to
have formed elsewhere and migrated to its current location, the binary may have been much wider in the past. We assume
here that the planetary system formed in an open star cluster, the dynamical evolution of which subsequently led to changes
in the system's orbital parameters and binary configuration. We calculate cross sections for various scenarios that could
have led to the multiple system currently observed and conclude that component A of HD 188753 with its planet was most
likely formed in isolation, to be swapped into a triple star system by a dynamical encounter in an open star cluster. We
estimate that within 500 pc of the Sun, there are about 1200 planetary systems that, like HD 188753, have orbital parameters
unfavourable for forming planets but still have a planet, making it quite possible that the HD 188753 system was indeed
formed by a dynamical encounter in an open star cluster. A press release was sent out and is available at:
http://www.uva.nl/onderzoek/ and articles about this work appeared in Noorderlicht, New Scientist and Der Spiegel. An
animation of the proposed encounter can be viewed at http://modesta.scienc.uva.nl.
Gualandris, Portegies Zwart and Sipior investigated the interplay between the supermassive black hole in the centre of the
Milky-way Galaxy and its local stellar cluster. They simulations the interactions between the black hole and other stars to
study the possibility that the hypervelocity star SDSS J090745.0+024507, found in the halo was initially ejected from this
region. The star currently has a velocity exceeding 700 km/s moving away from the Galactic centre. With the measured
radial velocity and the estimated distance to the star, they traced its trajectory backward in time in the Galactic potential.
Assuming it was ejected from the centre, they found that a proper motion of about 2 milli-arcseconds /yr is necessary for the
star to have come within a few parsecs of the SMBH. They conclude that this star is most likely ejected in a strong
dynamical interaction between the supermassive black hole and a tight binary, of which the currently observed star once was
a component. Such events should occur frequently enough that the Galactic halo should be populated with more than a
hundred hyper velocity stars.
Problem Solving Environments and Visualization
CrossGrid
People: A.G. Hoekstra, E.V. Zudilova, A. Tirado Ramos, R. Shulakov, D. Shamonin, P.M.A. Sloot, G.D. van Albada, M.
Scarpa
In the CrossGrid project, we participate in a large European collaboration of 21 partners in the development of interactive
applications in a Grid environment. These environments are characterized by the participation of multiple, geographically
distributed organizations, sharing computational resources and data. This gives an improved access to these resources and
data, at a cost in network and scheduling delays. In CrossGrid, we provide an application aiming to support vascular
surgeons in pre-operative planning. 2004 was a consolidation of a consortium-wide integration of grid support tools and
applications. The result is a fully integrated virtual vascular surgery on the grid, which was successfully demonstrated during
the European Grid Conference 2005 in Amsterdam. The CrossGrid project ended in March 2005, but its results will continue
to play an important role in our future research efforts.
Virtual Operation Theatre
Patient at MRI
scanner
MR image
MR image
Segmentation
(soon a GS!)
Shear stress,
velocities,
masses, etc.
I have no
GVK images,
ask Elena
se1 (e.g., Leiden)
ce (CrossGrid)
MD login and Grid
certificates
submission
Virtual Node
Creation
Bypass creation
LB mesh
generation
ce (CrossGrid)
Job submission
Job monitoring
Simulated flow
se2 (D-VRE machine)
Fig.1: CrossGrid
21
Token2000
People: A.G. Hoekstra, P.M.A. Sloot, E.V. Zudilova, M. Scarpa, L. Abrahamyan ASCI partner: LKEB/LUMC (P.I.: Reiber)
Token2000 is a nationally funded project (NWO), where we collaborate closely with the Universities of Leiden and Twente on
the development of an interactive medical application, somewhat similar to the work in CrossGrid. This application is
intended for training of surgeons. In collaboration with Leiden University Medical Centre we have created Hemosolve, a
problem-solving environment for image based computational Haemodynamics. Hemosolve includes our L-BGK solver, but
also a FEM Navier-Stokes solver. Moreover, it contains a 3D editing tool and powerful visualization modules.
High Performance Simulation on the GRID
Dutch-Russian project: NWO-RFBS-047.016.007
People: P.M.A. Sloot, A.V. Bogdanov.
In this project we study the use of Grid systems for High Performance Simulations. The project is a collaboration between
Amsterdam, St. Petersburg, Moscow and Novosibirsk.
Dynamite
People: K.A. Iskra, T. Gubala, B. Ó Nualláin, D.A. Kaarsemaker, G.D. van Albada, P.M.A. Sloot.
The Dynamite project (now internally funded) is the continuation of work on the dynamic scheduling and migration of tasks in
parallel programs started in the ESPRIT project Dynamite. In 2005 work continued on the single task checkpointer (ironing
out some smaller remaining defects) and on developing support for MPI and grid environments.
PDES
Involvement: K.A. Iskra, G.D. van Albada, P.M.A. Sloot.
This research on parallel discrete event simulation is a continuation of the work by Overeinder on the behaviour of optimistic
PDES, extended to grid-like environments. In 2005 further important results regarding the behaviour of PDES in a wide-area
distributed environment were obtained. Important strategies like dedicated routers, message aggregation and lazy
cancellation were studied and different methods of “global virtual time” evaluations were evaluated. The project culminated in
the PhD defence by K.A. Iskra in June 2005.
External Projects
Projectname
period
Funding agency
CrossGrid
A Cluster of
Grapes
2002 – 2006
2001 - 2005
Mesoscale
simulation
paradigms for
biological systems
Simulation of
developmental
regulatory
networks
Mathematics and
Computation for
the System Biology
of Cells
Token 2000
2003-2007
EU, 5th framework
NWO
Computational
Science
NWO
Applied
Mathematics
Total
funding
k€ 405
kf 690
partners in
ASCI
Brief description
Interactive Grid applications
N-Body simulations. P.I: E.van
den Heuvel, UvA Astronomy
k€ 329
See report
2003-2007
NWO
Computational Life
Sciences
k€ 328
See report
2003-2007
NWO
Computational Life
Sciences
k€ 487
See report
2002 – 2007
NWO - EW
k€ 150
LKEB/LUMC
(P.I.: Reiber)
Mesoscopic bloodflow
simulation
Doctoral Degrees
K.A. Iskra: Time Warp - from Cluster to Grid, PhD thesis, University of Amsterdam, Amsterdam, The Netherlands, (Promotor:
Prof. Dr. P.M.A. Sloot, Co-promotor: Dr. G.D. van Albada) June 2005. ISBN 90-5776-139-4, funded by University of
Amsterdam,. Virtual Laboratory for e-Science project,. Netherlands Organisation for Scientific Research . Massively Parallel
Programming programme (NWO.MPR),. European Union . ESPRIT project 23499 Dynamite.
Tirado-Ramos; D.P. Shamonin; R.M. Shulakov; D.J. Groen; A.G. Hoekstra; G.D. van Albada; E.V. Zudilova and P.M.A.
Sloot: Interactive Problem Solving Environments on the Grid for Image-based Computational Haemodynamics, in The
CrossGrid Book, (accepted 15 January 2004) The European CrossGrid Consortium, 2005.
22
A.M.M. Artoli; A.G. Hoekstra and P.M.A. Sloot: Optimizing lattice Boltzmann simulations for unsteady flows, Computers &
Fluids, vol. 35, nr 2 pp. 227-240. 2005.
K.A. Iskra; G.D. van Albada and P.M.A. Sloot: Towards Grid-Aware Time Warp, Simulation: Transactions of The Society for
Modeling and Simulation International, vol. 81, nr 4 pp. 293-306. April 2005.
J.A. Kaandorp; P.M.A. Sloot; R.M.H. Merks; R.P.M. Bak; M.J.A. Vermeij and C. Maier: Morphogenesis of the branching reef
coral Madracis mirabilis, Proc. Roy. Soc. B, vol. 272, nr 1559 pp. 127-133. January 2005.
O.V. Kaluzhnaya; S.I. Belikov; H.C. Schröder; S. Zapf; A. Borejko; J.A. Kaandorp; A. Krasko; I.M. Müller and W.E.G. Müller:
Dynamics of skeletal formation in the Lake Baikal sponge Lubomirskia baicalensis. Part I biological and biochemical studies,
Naturwissenschaften, vol. 92, pp. 128-133. 2005.
V.V. Krzhizhanovskaya; P.M.A. Sloot and Y.E. Gorbachev: Grid-based Simulation of Industrial Thin-Film Production,
Simulation: Transactions of the Society for Modeling and Simulation International, (Special Issue on Applications of Parallel
and Distributed Simulation) vol. 81, nr 1 pp. 77-85. January 2005.
K. Rycerz; M.T. Bubak; M. Malawski and P.M.A. Sloot: A Framework for HLA-Based Interactive Simulations on the Grid,
Simulation: Transactions of The Society for Modeling and Simulation International, (Special Issue on Applications of Parallel
and Distributed Simulation) vol. 81, nr 1 pp. 67-76. April 2005.
P.M.A. Sloot; A.V. Boukhanovsky; W. Keulen; A. Tirado-Ramos and C.A. Boucher: A Grid-based HIV Expert System, Journal
of Clinical Monitoring and Computing, vol. 19, nr 4-5 October 2005. ISSN: 11387-1307.
J.M. Voogd; P.M.A. Sloot and R. van Dantzig: Equilibrium spherically curved two-dimensional Lennard-Jones systems , J.
Chem. Phys., vol. 123, nr 084105 pp. 1-5. 2005. (DOI: 10.1063/1.2007707)
M.A. Yurkin; K.A. Semyanov; P.A. Tarasov; A.V. Chernyshev; A.G. Hoekstra and V.P. Maltsev: Experimental and theoretical
study of light scattering by individual mature red blood cells with scanning flow cytometry and discrete dipole approximation,
Applied Optics, vol. 44, pp. 5249-5256. 2005.
Z. Zhao; G.D. van Albada and P.M.A. Sloot: Agent-based flow control for HLA components, International journal of
simulation transaction, special issue Agent Directed Simulation, vol. 81, nr 7 pp. 487-501. 2005.
E.V. Zudilova and P.M.A. Sloot: Bringing Combined Interaction to a Problem Solving Environment for Vascular
Reconstruction, Int. J. Future Generation Computer Systems, vol. 21, nr 7 pp. 1167-1176. 2005.
A. Tirado-Ramos; D.P. Shamonin; R.M. Shulakov; D.J. Groen; A.G. Hoekstra; G.D. van Albada; E.V. Zudilova and P.M.A.
Sloot: Interactive Problem Solving Environments on the Grid for Image-based Computational Haemodynamics, in The
CrossGrid Book, (accepted 15 January 2004) The European CrossGrid Consortium, 2005.
L. Abrahamyan; J.A. Schaap; A.G. Hoekstra; D.P. Shamonin; F.M.A. Box; R.J. van der Geest; J.H.C. Reiber and P.M.A.
Sloot: A Problem Solving Environment for Image-Based Computational
Hemodynamics, in V.S. Sunderam; G.D. van Albada; P.M.A. Sloot and J.J. Dongarra, editors, Computational Science - ICCS
2005: 5th International Conference, Atlanta, GA, USA, Proceedings, Part I, in series Lecture Notes in Computer Science, vol.
3514, pp. 287-294. Springer, Berlin, Heidelberg, May 2005. ISBN 3-540-26032-3.
A.G. Hoekstra and P.M.A. Sloot: Introducing Grid Speedup Gamma: A Scalability Metric for Parallel Applications on the Grid,
in P.M.A. Sloot; A.G. Hoekstra; T. Priol; A. Reinefeld and M.T. Bubak, editors, Advances in Grid Computing - EGC 2005, in
series Lecture Notes in Computer Science, vol. 3470, pp. 245-249. Springer, Berlin, Heidelberg, February 14-16 2005. ISBN
3-540-26918-5.
A.G. Hoekstra: Image-based computational hemodyanamics with the Lattice Boltzmann Method, in K.J. Bathe, editor,
Computational Fluid and Solid Mechanics 2005, pp. 672-675. Elsevier Ltd, 2005.
K. Kruszynski; R. van Liere and J.A. Kaandorp: Quantifying performance of 3D skeletonization algorithms, in IASTED
International Conference on Visualization, Imaging, and Image Processing (VIIP 2005), Benidorm, Spain, September 2005.
T.A. Kvaløy; E. Rongen; A. Tirado-Ramos and P.M.A. Sloot: Automatic Composition and Selection of Semantic Web
Services, in P.M.A. Sloot; A.G. Hoekstra; T. Priol; A. Reinefeld and M.T. Bubak, editors, Advances in Grid Computing - EGC
23
2005, in series Lecture Notes in Computer Science, vol. 3470, pp. 184-192. Springer, Berlin, Heidelberg, February 14-16
2005. ISBN 3-540-26918-5.
K. Rycerz; M.T. Bubak; M. Malawski and P.M.A. Sloot: HLA Grid based support for simulation of vascular reconstruction, in
S. Gorlatch and M. Danelutto, editors, TR-05-22, Proceedings of the CoreGRID Workshop "Integrated Research in Grid
Computing", pp. 165-174. University of Pisa, Computer Science Department, Pisa, November 2005.
P.M.A. Sloot; A.V. Boukhanovsky; W. Keulen and C.A. Boucher: A Grid-based HIV Expert System, in Proceedings of the 5th
International Symposium on Cluster Computing and Grid, CCGrid, (IEEE product number: EX1055C) IEEE, Cardiff, Wales,
UK, May 2005. ISBN: 0-7803-9075-X.
P.M.A. Sloot; C.A. Boucher; M.T. Bubak; A.G. Hoekstra; P. Plaszczak; A. Posthumus; D. van de Vijver; S. Wesner and A.
Tirado-Ramos: VIROLAB - A Virtual Laboratory for Decision Support in Viral Diseases Treatment, in Cracow Grid Workshop
2005, (in press, best poster award) Cracow, Poland, November 2005.
A. Tirado-Ramos; D.J. Groen and P.M.A. Sloot: On-line Application Performance Monitoring of Blood Flow Simulation in
Computational Grid Architectures, in The 18th IEEE Symposium on Computer-Based Medical Systems, special track Grids
for Biomedicine and Bioinformatics, pp. 511-516. Trinity College Dublin, Ireland, June 23-24 2005. ISBN 0769523552.
A. Tirado-Ramos; G. Tsouloupas; M.D. Dikaiakos and P.M.A. Sloot: Grid Resource Selection by Application Benchmarking:
a Computational Haemodynamics Case Study, in V.S. Sunderam; G.D. van Albada; P.M.A. Sloot and J.J. Dongarra, editors,
Computational Science - ICCS 2005: 5th International Conference, Atlanta, GA, USA, Proceedings, Part I, in series Lecture
Notes in Computer Science, vol. 3514, pp. 534-543. Springer, Berlin, Heidelberg, May 2005. ISBN 3-540-26032-3.
A. Tirado-Ramos; D.J. Groen and P.M.A. Sloot: Exploring OGSA Interoperability with LCG-based Production Grids for
Biomedical Applications, in M.T. Bubak; M. Turala and K. Wiatr, editors, Cracow Grid Workshop 2005, pp. 367-374. Ekodruk,
Cracow, Poland, November 2005.
M.A. Yurkin; K.A. Semyanov; A.G. Hoekstra and V.P. Maltsev: Experimental and Theoretical Study of Light Scattering by
Individual Mature Red Blood Cells with Scanning Flow Cytometry and Discrete Dipole Approximation, in Proceedings of the
8th Conference on Electromagnetic and Light Scattering by Nonspherical Particles: Theory, Measurement and Applications,
pp. 333-336. Salobrena, Spain, May 2005.
M.A. Yurkin and A.G. Hoekstra: Capabilities of the discrete dipole approximation for simulation light scattering by biological
cells, in Proceedings of the NATO Advanced Research Workshop: Optics of Biological Particles, pp. 19-20.
Novosibirsk,Russia, October 2005.
M.A. Yurkin; D. de Kanter and A.G. Hoekstra: Applicability of effective medium approximation to light scattering by
granulated biological cells - first results, in Proceedings of the NATO Advanced Research Workshop: Optics of Biological
Particles, pp. 46-47. Novosibirsk,Russia, October 2005.
Z. Zhao; G.D. van Albada and P.M.A. Sloot: Rapid Prototyping of Complex Interactive Simulation Systems, in Proceedings of
the 10th IEEE International Conference on Engineering of Complex Computer Systems (ICECCS'05) , pp. 366-375. IEEE
Computer Society Press, Shanghai, China, June 2005.
Z. Zhao; A.S.Z. Belloum; H. Yakali; P.M.A. Sloot and L.O. Hertzberger: Dynamic Workflow in a Grid Enabled Problem
Solving Environment, in Proceedings of the 5th International Conference on Computer and Information Technology
(CIT2005), pp. 339-345 . IEEE Computer Society Press, Shanghai, China, September 2005.
Z. Zhao; A.S.Z. Belloum; A. Wibisono; F. Terpstra; P.T. de Boer; P.M.A. Sloot and L.O. Hertzberger: Scientific workflow
management: between generality and applicability, in Proceedings of the International Workshop on Grid and Peer-to-Peer
based Workflows in conjunction with the 5th International Conference on Quality Software, pp. 357-364. IEEE Computer
Society Press, Melbourne, Australia , September 19th-21st 2005.
Z. Zhao; A.S.Z. Belloum; P.M.A. Sloot and L.O. Hertzberger: Agent Technology and Generic Workflow Management in an eScience Environment, in Hai Zhuge and G.C. Fox, editors, Grid and Cooperative Computing - GCC 2005: 4th International
Conference, Beijing, China, in series Lecture Notes in Computer Science, vol. 3795, pp. 480-485. Springer, November 2005.
ISBN 3-540-30510-6. (DOI: 10.1007/11590354_61)
Z. Zhao; A.S.Z. Belloum; P.M.A. Sloot and L.O. Hertzberger: Agent technology and scientific workflow management in an eScience environment, in Proceedings of the 17th IEEE International conference on Tools with Artificial Intelligence (ICTAI05),
pp. 19-23. IEEE Computer Society Press, Hongkong, China, November 14th-16th 2005.
24
Software
The Dynamite software package for the checkpointing of PVM programs is available through
http://www.science.uva.nl/research/scs/Software
Development of "Roche" binary evolution web interface: http://carol.wins.uva.nl/~spz/act/roche/roche.html
Development of "McScatter" hybrid software package for Monte-Carlo dynamics with binary evolution.
http://manybody.org/McScatter.html
MODESTA is a dedicated parallel computer platform for MOdeling DEnse STellar systems in Amsterdam. The machine
became available for production on 2 October 2004 and is now working full time. Current performance is 1.01TFLOPs
sustained speed. MODESTA has a dedicated web site: http://modesta.science.uva.nl/
Cooperation within ASCI
The PhD thesis research by Iskra and many of our other research projects make heavy use of the DAS-2 supercomputer.
K. Kruszynski; R. van Liere and J.A. Kaandorp: Quantifying performance of 3D skeletonization algorithms, in IASTED
International Conference on Visualization, Imaging, and Image Processing (VIIP 2005), Benidorm, Spain, September 2005.
(TUE-W&I-vis)
L. Abrahamyan; J.A. Schaap; A.G. Hoekstra; D.P. Shamonin; F.M.A. Box; R.J. van der Geest; J.H.C. Reiber and P.M.A.
Sloot: A Problem Solving Environment for Image-Based Computational Hemodynamics, in V.S.
Sunderam; G.D. van Albada; P.M.A. Sloot and J.J. Dongarra, editors, Computational Science - ICCS 2005: 5th International
Conference, Atlanta, GA, USA, Proceedings, Part I, in series Lecture Notes in Computer Science, vol. 3514, pp. 287-294.
Springer, Berlin, Heidelberg, May 2005. ISBN 3-540-26032-3. (UL-LUMC-lkeb)
In the BSIK funded VL-e project we collaborate with a number of ASCI groups affiliated with VU and UvA.
In the NWO funded project DIME we collaborate with UL-LUMC-lked on a Problem Solving Environment for Computational
Hemodynamics, and its potential use in pre-operative planning and training.
25
2.2
2.2.1
B: Large scale distributed Information Systems and Embedded Systems
Contribution of UvA-FdNWI-caps
In the SNE group we work on different topics covered by Theme B2. In the following paragraphs we describe the research
carried out in the context of both Advanced Networking and Grid middleware and workflow
Advanced Networking
Optical networks modeling and brokering
In 2005 we focused on optical network modeling and resource brokering. In multi-domain optical networks the successful
setup of an end-to-end connection depends on the existence of a coherent view of the available resources and their interconnections. We researched suitable models for optical network description: we focused on extending the ITU G.805
standard and on semantic web techniques based on RDF. This latter model was used as basis for a prototype resource
brokering system based on web services. We also looked at the use of link-local addressing with Zero configuration
technology as a way to transparently setup the IP connectivity of end nodes in an optical environment. We participated to
both iGrid2005 and SC2005 with demonstrations and proof of concepts for the link-local addressing and the resource
brokering activities.
Network monitoring
In 2005 we pursued two main activities in the field of network monitoring and testing : network monitoring in Grids and
network monitoring on SURFnet6. In the Grid environment the traditional monitoring infrastructure and tools cannot be used
as is, given they must rely on direct access to the end hosts. We developed a test infrastructure for the DAS-2 cluster that
makes use of the Grid scheduling algorithms provided by MPICH-G2, the Globus variant of MPI. The periodic tests give
information on the network health among the Grid clusters. The SURFnet6 network, the new generation SURFnet network,
was installed and commissioned in 2005. We developed a suite of network performance tests to validate the performance of
this new network, in particular at the 10GE level.
Authorization Concepts and Architectures
Within the realm of our research into the concepts, feasibility and efficiency of Generic AAA based mechanisms, the focus in
the year 2005 was on the exploration of token-based sequences to manage and control network resources. The token
sequence is one of 3 fundamental authorization sequences described in RFC2904. This sequence allows separation
between acquiring and using an authorization, and therefore allows faster access enforcement. At SuperComputing ’05 we
were successful in demonstrating 2 implementations of this sequence. In one implementation, a network resource received a
token via a separate control channel. Within another implementation a token was embedded in the IP dataflow. With the first
implementation, a token was used to manage resource access to a transatlantic optical network link between Amsterdam
and Chicago using an Optical Cross Connect switch. The other implementation used special developed microcode within a
Network Processor Unit based network switch, which generated and recognized a token inside an IP packet. This switch was
used to provide both real time access control and path selection dependent on the presence of a valid token (Figure 1).
Both developments lead to publications.
Figure 1: Token-based architecture for Resource management, path selection, and access control
26
The results of SuperComputing 2004 were published, where our Generic AAA toolkit, in combination with a vendor based
Dynamic Operating Support System, implemented the concept of a Network Service Plane, capable of driving multiple
autonomous network control planes. Such concept is explored within the GGF GHPN group.
A prototype Role Based Access Control and Authorization mechanism based on the Generic AAA toolkit was finished within
the Collaboratory.nl project. This success resulted in our involvement in the follow-up project, CNL-III, which will make the
prototype ready for deployment.
Activities made several contributions towards the EU project EGEE where we were involved in developing mechanisms
enabling authentication and authentication in gLite (LCAS/LCMAPS). We performed architectural work and performed threat
analyses in the area of Grid Security. The group also contributed new authorization concepts within the EU Nextgrid project.
Based on experiences gained in a several projects, a GAP analyses was performed to identify new requirements for the
Generic AAA toolkit for Optical Light Path provisioning.
Based on our recognition in the area of AAA, we were asked to be involved in 3 EU project proposals to cover aspects of
authorization. One of these projects got selected for further negotiations.
Standards body activities: Within the Global Grid Forum, we established the Firewall Issues Research Group and a group
member acts as co-chair
Grid Middleware en Workflow Management
Grid-based Virtual Laboratory:
- Distributed Services Discovery
In the year 2005, we have started to investigate the Distributed Services Discovery of services for Grid-based Virtual
Laboratory based on Peer-to-Peer Networks, we started by looking into the problem of classifying the services that have to
be distributed and discovered by the targeted system. There are several ways to achieve the classification of the services
using pattern recognition, Natural Languages, or Ontology based classifiers. We have decomposed this work into a number
of steps: Survey the existing classifiers, model the targeted services, and evaluating the classifiers. Currently, we are
investigating the classification problem in both structured and unstructured network.
- Multi-layer Parameter sweep application
Parameter sweep application has recently acquired more attention from the grid computing community since it is the
potential candidate, which will require the non-trivial capabilities promised by the grid environment. As early experiment with
parameter sweep applications has shown that, some of these promises from grid environment are indeed carried into effect,
more demanding parameter sweep applications came into play such as parameter sweep workflows.
This research task will focuses on analyzing strategies for scheduling layers of parameter sweep tasks within a workflow of
parameter sweep into available resources on the grid. The approach will be to conduct simulation of selected algorithms for
scheduling parameter sweep applications to set of available grid resources. The goal of this task is to evaluate existing
strategy of scheduling parameter sweep workflow. Based on existing work on Critical-Path and Priority Based Algorithms for
Scheduling. Assumption used in this paper is that layers of parameter sweep applications in a workflow do not communicate.
Though it is indeed the case within one layer of parameter sweep task, it is no longer hold when we have layers of
parameter sweep task in a workflow.
- Agent Technology
We started also investigating how agent technology can be used in developing generic VL-e framework. Agent technology
provides a suitable way to decompose and encapsulate complex control intelligence. We will study how agent technology
facilitates the interoperability and integration among different workflow systems.
External Projects
VL-e 2004-2009 (Bsik project): WTCW, UvA, Amolf, Nikhef, CWI, SARA, VU, TUD, IBM, LigicaCMG, Philips, FEI
GigaPort (Bsik project): UvA, Telematica Instituut , TNO
StarePlane (NWO project, SURFnet and NORTEL):
Collaboratory.nl : UvA, Telematica Instituut, Philips, FEI Company, DSM
Lucifer: UvA, Surfnet, Sara
27
Papers in international Journals
Curti, C., Ferrari, T., Gommans, L., van Oudenaarde, S., Ronchieri, E., Giacomini, F., Vistoli, C.,
On Advance Reservation of Heterogeneous Network Paths Future Generation Computer Systems Journal Vol. 21 Issue 4
(2005), pp. 525-538
S.M.C.M. van Oudenaarde, Z.W. Hendrikse, F. Dijkstra, L.H.M. Gommans, C.T.A.M. de Laat, R.J. Meijer An Open Grid
Services Architecture Based Prototype for Managing End-to-End Fiber Optic Connections in a Multi-Domain NetworkHighSpeed Networks and Services for Data-Intensive Grids: the DataTAG Project, special issue, Future Generation Computer
Systems, volume 21 issue 4 (2005)
Robert Grossman, Yunhong Gu, Xinwei Hong, Antony Antony, Johan Blom, Freek Dijkstra, and Cees de Laat, Teraflows
over Gigabit WANs with UDTPublished in Future Generation Computer Systems, Vol. 21, Issue 4, pp.501-513, April 2005.
Bas van Oudenaarde, Zeger Hendrikse, Freek Dijkstra, Leon Gommans, Cees de Laat, Rob Meijer,
Dynamic paths in multi-domain optical networks for grids Published in Future Generation Computer Systems, Vol. 21, Issue
4, pp. 539-548, April 2005.
Catalin Meirosu, Piotr Golonka, Andreas Hirstius, Stefan Stancu, Bob Dobinson, Erik Radius, Antony Antony, Freek Dijkstra,
Johan Blom, Cees de Laat, Native 10 Gigabit Ethernet experiments over long distances Published in Future Generation
Computer Systems, Vol. 21, Issue 4, pp. 457-468, April 2005.
Freek Dijkstra, Jeroen van der Ham, Cees de Laat, Using Zero Configuration Technology for IP addressing in Optical
Networks In Press (accepted by Future Generation Computer Systems, Feature topic iGrid 2005), First draft submitted
October 2005, revision submitted February 2006.
Paola Grosso, Pieter de Boer, Linda Winkler, The network infrastructure at iGrid2005: lambda networking in action In Press
(accepted by Future Generation Computer Systems, Feature topic iGrid 2005), First draft submitted October 2005, revision
submitted February 2006.
Jeroen van der Ham, Freek Dijkstra, Franco Travostino, Bert Andree, Cees de Laat
Using RDF to Describe Networks", In Press (submitted for Future Generation Computer Systems, Feature topic iGrid 2005),
First draft submitted October 2005, revision submitted February 2006.
Leon Gommans, Bas van Oudenaarde, Freek Dijkstra, Cees de Laat, Tal Lavian, Inder monga, Arie Taal, Franco Travostino,
Alfred Wan Applications Drive Secure Lightpath Creation across Hetrogenous Domains In Press (accepted by IEEE
Communications Magazine, Feature topic Optical Control Planes for Grid Networks: Opportunities, Challenges and the
Vision), First draft submitted June 2005, revision submitted December 2005
Z. Zhiming, A.S.Z Belloum, Peter Sloot, and Bob Hertzberger Agent technology and scientific workflow management in an eScience environment The 17th IEEE international conference on Tools with Artificial Intelligence, Hong Kong, China, Nov. 14
-16, 2005.
Z. Zhiming, A.S.Z Belloum, Cees de Laat, and Bob Hertzberger Dynamic workflow in a Grid enabled Problem Solving
Environment, the 5th International Conference on Computer and Information technology (CIT2005), Shanghai, China, Sep.
21-23, 2005.
Z. Zhiming, A.S.Z Belloum, Adianto Wibisono, Frank Terpstra, Piter T. de Boer Peter Sloot, and Bob Hertzberger Scientific
workflow management: between generality and applicability The 5th international conference on quality software, (to
appear), Melbourne, Australia, Sep. 19 -20, 2005.
I. Morozov, I. Shoshmina, A. Evlampiev, E.Stankova, A. Bogdanov, A. Luzan, D. Malashonok, I. Valuev, V. Korkhov.
Experience in setting up an experimental Grid testbed for heavy scientific applications, All-Russian Scientific Conference on
Scientific Service in Internet: distributed computing technologies, Abrau-Durso, Sep. 19-24, 2005
S. de Ridder, A.S.Z Belloum, and L.O. Hertzberger “Grid Service based Collaboration for VL-e: Requirements, Analysis &
Design” European Grid Conference, February 14-16 2005, Science Park Amsterdam, The Netherlands
Morozov, I. Shoshmina, A. Evlampiev, E.Stankova, A. Bogdanov, A. Luzan, D. Malashonok, I. Valuev, V. Korkhov
Experience in setting up an experimental Grid testbed for heavy scientific applications, All-Russian Scientific Conference on
Scientific Service in Internet: distributed computing technologies, Abrau-Durso, Sep. 19-24, 2005.
28
Yuri Demchenko, Leon Gommans, Cees de Laat, Using VO concept for managing dynamic security associations, accepted
paper for 21st IFIP International Information Security Conference Security and Privacy in Dynamic Environments May 22 May 24, 2006 Karlstad University, Karlstad, Sweden
Demchenko, Y., L. Gommans, C. de Laat, B.Oudenaarde, A. Tokmakoff, M. Snijders, Job-centric Security model for Open
Collaborative Environment Proceedings 2005 International Simposium on Collaborative Technologies and Systems
(CTS2005 ) May 15-19, 2005, Saint Louis, USA. - IEEE Computer Society, ISBN: 0-7695-2387-0. - Page 69-77.
Yuri Demchenko, Leon Gommans, Cees de Laat, Bas Oudenaarde, Web Services and Grid Security Vulnerabilities and
Threats Analysis and Model Accepted paper to Grid 2005 - 6th IEEE/ACM International Workshop on Grid Computing. November 13-14, 2005.
Leon Gommans, Cees de Laat, Robert Meijer, Token Based path authorization at Interconnection Points between Hybrid
Networks and a Lambda Grid IEEE GRIDNETS2005 proceedings, ISBN 0-7803-9277-9.
Yuri Demchenko, Leon Gommans, Cees de Laat, Bas Oudenaarde, Andrew Tokmakoff, Martin Snijders, Rene van Buuren,
Security Architecture for Open Collaborative Environment Advances in Grid Computing EGC 2005: European Grid
Conference, Amsterdam, The Netherlands, February 14-16, 2005, Revised Selected Papers, LNCS, Springer Verlag,
Volume 3470, page 589, (2005)
Jos Vrancken, Karst Koymans Intelligent Complexity in Internet Addressing SchemesProceedings of the IEEE International
Conference on Systems, Man, and Cybernetics 2005
Experimental Software
This program has been designed to minimize the effort needed by scientists to develop Grid-enabled application GVLAM:
Data driven grid-enabled workflow management systems. 2000-2006: Java, C++, GT2.4, Web Services, Job Farming, Linux
OS.
This program has been designed to minimize to help the scientist to move file across geographically distributed storage
resource using a simple Graphical user Interaface. Vbrowser: Data driven grid-enabled workflow management systems.
2005-2006: Java, FTP, SRB, HTML
VL-e consortium include a number of ASCI members UvA, VU, TUD. We can consider the work developing the generic VL-e
middleware as a collaboration of ASCI members.
2.2.2
Integration, Analysis and Logistics (DIAL) project
Within the CMSB research groups from Leiden University, Leiden University Medical Center, TNO Prevention & Health, Vrije
Universiteit Amsterdam, Vrije Universiteit Medical Center, and Erasmus Medical Center common diseases, such as
cardiovascular disease, Alzheimer's, diabetes and rheumatism are studied. By combining the vast knowledge on a number of
disease areas with the latest research technologies including genomics and bioinformatics, the aim is to elucidate the causes
of various common diseases and apply these new insights in the development of new methods for diagnosis, new drugs and
new means for prevention.
During 2005 the main themes of DIAL were:
· Further development of the functionality of the DIAL CGH Database.
· Beta-testing of the database
· Initiating of research usage of the database.
External Projects
Integration, Analysis and Logistics (DIAL) project
2003-2007, the Netherlands Genomics Initiative.
Goals: To interface local databases; to establish a central database for experimental information; to develop biostatistics for
the interlinking of Epidemiological and Systems Biology approaches; to implement commercial and develop in-house
bioinformatics for the internal and external data mining and integration of all projects; to collaborate, within the BioASP
framework, on the development of biostatistics, bioinformatics and GRID-based Virtual Laboratory Software; to develop
education in biostatistics and bioinformatics.
29
E.M. Bakker & F.J. Sicking, DIAL CGH Database (www.liacs.nl/~sicking/dial/).
This database is a repository for storing raw MicroArray Data and quickly (re)calculating CGH Levels against the latest BAC
and Oligo Sets. The data can be annotated in a MIAME compliant fashion. In the underlying Oracle database each user has
a private database account, which means that data is private and not visible by others unless permitted.
Performance analysis and design space exploration of embedded multi-processor Systems-on-chip and large-scale
distributed embedded systems
Given a number of relevant industrial media applications, and a media platform of type on-chip networked heterogeneous
multiprocessor platform, model and program platform based architectures on a high level of abstraction, and with a high level
of confidence in a reasonable time.
External projects
Project Artemisia
2004-2008, PROGRESS, 132 K + AIO + PostDoc, UVA CSA, TUD EWI-CE, TUD EWI –ST, TUE E-ESA
The project includes the following: Firstly, translate given applications input-output equivalent process networks (an
automated translator does exist for a restricted class of applications and is called Compaan. Secondly, model the platform,
the architecture templates derived from it as well as the instantiation of these to architectures. Also on a high level of
abstraction.Thirdly, provide low-level performance/cost numbers for the processing units on the architecture so that highlevel performance/cost numbers are well calibrated and, hence, sufficiently accurate (a calibration tool/platform does exist for
a restricted class processing units and is called Laura. A more advanced calibration tool/platform is to be
developed/designed within Artemisia.
Project MASSIVE
2000-2007, PROGRESS, 242 K + 4 AIO
The aim of this project is to develop methods and tools to master the complexity of large scale embedded signal processing
systems. The dataflow part of such a system (in particular distributed radio telescopes), has been modeled and analyzed
with respect to performance in previous years. Currently the dataflow is modeled in an independent way, and the interfacing
between dataflow and control flow is being modeled.
Project Compaan and Laura
2001-2005, LIACS, 2 PHDs
Automatic parallelizing of sequential programs and mapping on homogeneous and heterogeneous multi-processor
embedded platforms. The parallelization is in terms of input-output equivalent Kahn Process Networks. Implementation is
in SW, in HW, or in HW/SW. The related tools are Compaan, Laura, and Espam.
Project Trader
2004-2008, ESI, 1 AIO, TUD EWI
Modern systems such as household appliances, DVD players, PCs, medical X-ray imaging systems, printers, advanced
vehicles, and airplanes rely increasingly on software, in particular for system integration. Embedded software monitors the
whole system taking care that the system accomplishes more than its parts would. In such software intensive systems,
reliability is of prime importance.
Project Neva
2005-2009, EU, 50K + 2 AIO
Is a European MEDEA+ collaboration between ACE, Bull Certess, LETI/CEA, Universiteit Leiden, Philips, Silicomp,
STMicroelectronics, TIMA/INPG, and VERIMAG/UJF (Project 2A703: Networks on Chip Design Driven byVideo and
Distribution Applications). Circuits for electronic devises are becoming so complex that they are expected to reach a billion
transistors by the end of 2008. Traditional silicon chip architectures are nearing the limit of their performance in such
applications, so the NEVA project was set up to introduce innovative network-on-chip designs, based on multiple processors
and asynchronous circuitry. The goal is to allow designers and application engineers to cope with emerging applications
resulting from multimedia/communications convergence. In first instance, datastream applications – mainly from video
environments – will be used as drivers, with a targeted computing power of around one-giga operations per second per chip.
Turjan, A, Kienhuis, B., and Deprettere, E. “Solving Out-of-Order Communication inKahn Process Networks”, In. Journal of
VLSI Signal Processing, Vol. 40, No. 1, pp. 7-18, May 2005
Nikolov, H., Stefanov, T., and Deprettere, E. “Modeling and FPGA implementation of Applications using parameterized
Process Networks with Non-Static Parameters", In Proc. "13th IEEE Symposium on Field-Programmable Custom Computing
Machines (FCCM'05)", pp. 255-263, Napa, California, USA, Apr. 18-20, 2005.
30
J. Lemaitre, Sylvain Alliot and Ed Deprettere Behavioral specification of control interface for signal processing applications
IEEE Intl Conf. on Application-Specific Systems, Architectures, and Processors (ASAP<92>05)Samos, Greece, July 2005
Claudiu, Z., Kienhuis, B., and Deprettere, E., “Communication Synthesis in a multiprocessor environment”, in Proc. FieldProgrammable Logic and Application Conference (FPL’05) Tampere, Finland, Aug. 24-26, 2005.
Claudiu, Z., Kienhuis, A., and Deprettere, E. “Expression Synthesis in Process Network generated by Laura”, In Proc. 16th
IEEE Int. Conf. on Application-specific, Systems, Architectures, and Processors (ASSAP’05), July 23-25, 2005.
.
Nikolov, H., Stefanov, T., and Huang, K.2005, Java, Linux
This is a tool suite for automatic platform synthesis and application mapping for multiprocessor Systems On-Chip.
Application and PlatformAre specified on a level of abstraction above the RTL level. The tool suit transforms both to the RTL
level in an automated way. Software and manual available.
2.2.3
Contribution of TUE-EE-dmes
Embedded multi-media systems: architectures, models, programming and design
The focus of our work is on mapping applications onto multiprocessor systems. System level design methods allow the
systematic development of abstract executable models. These models are used to verify correctness and performance
properties of the system. Based on the analysis results, system designers can take well-founded design decisions about the
architecture of the system, hardware/software partitioning, the choice of processors, etc.
operations-1
quality-1
quality-1
Multiprocessor implementation platforms also require novel programming techniques, and techniques to map executable
specifications
onto
multiprocessor
systems. These techniques must
optimize execution time, memory usage,
and energy usage and allow trade-offs.
The result is implementation-level code
for the application optimized towards the
intended multiprocessor platform. These
programming techniques build upon
compiler technology that covers the final
step to the hardware.
We set up an initial mapping trajectory
for multi-media applications targeting
multi-processor architectures. As a basic
model of computation, we take Kahn
process networks (KPN) and its
derivates such as synchronous dataflow (SDF). We developed efficient techniques for analyzing the throughput of SDF
graphs, and the entire Pareto space of throughput-buffer size trade-offs. We have identified the concept of application
scenarios that capture common execution modes of a system implementation from the resource usage point of view. The
mapping trajectory can use application scenarios to reduce energy consumption and to improve performance. We have also
developed a hybrid VLIW/SIMD processor template, and design-space exploration techniques for VLIW and SIMD
processors.
For the longer term, embedded systems will evolve into ambient systems. Ambient systems are in essence nothing but
networked embedded systems operating in a highly dynamic environment. More and more embedded systems have
communication capabilities. This networking dimension affects the architectures, the design flow, the run-time systems, and
the underlying computational models we are working on. We are looking at the integration of this dimension in our work.
External projects
Betsy: BEing on Time Saves energY
Continuous multimedia experiences on networked hand-held devices, 2004-2007. EU/IST/FP6, M€ 4.4, Philips research,
CSEM, IMEC, ISI, MDH/TU Kaiserslautern, Siemens C-lab, TUE, en de University of Cyprus
The aim of the BETSY project is to have multimedia streams on wireless hand-held devices seamlessly adapted to
fluctuating network conditions and available terminal resources while reducing the energy consumption of the stream
processing. This way the user can enjoy true multimedia experiences with freedom of movement in a networked home or at
31
any hot-spot. To achieve this, we need to be able to make trade-offs between the use and consumption of network and
terminal resources, such as bandwidth use, CPU consumption, memory needed and power consumption by the terminal,
while guaranteeing end-to-end timeliness - required for streaming data.
PreMaDoNa
Predictable Matching of Demands on Networked Architectures, 2004-2009, Progress/STW, M€ 1.97, Philips, CMG
The PreMaDoNa project focuses on the design and implementation of NoC-based platforms for multi-media applications.
The research challenges mainly originate from the increasing complexity of multi-media applications and the ever-shortening
design time to realise multi-media systems. The major research objective is the following: Being able to design NoC-based
real-time system in a predictable way such that non-functional properties can be guaranteed, while still being able to
dynamically match quality with the available resources.
PROgramming Multi-processor Embedded multi-media Systems (PROMES)
2002-2008, NWO, k€ 295 PROMES focuses on the development of both a sound theoretical framework and a programming
environment for multi-media applications building on top of multi-processor systems. Important is the study of task-level
analysis techniques that provide insight in concurrency-, timing-, and energy-related properties at the specification level
without fully implementing an application.
SmartCam
2002-2007. STW/progress, 1.4 M€, Philips Natlab, Philips CFT, TNO-FEL, In3D, HP Bristol labs, TUD-TNW-tn-ph
The SmartCam project investigates low-cost one-chip Smart Camera solutions, contributing to a quantitatively guided design
trajectory. In particular, we investigate the impact of current applications, and we try to define relevant architectural
parameters and to develop an architectural template. Other aims are to enhance and integrate existing application mapping
environments for SIMD and ILP processors.
Fexible Application Mapping Environment (FAME)
2003-2008, NWO, 250 k€, Leiden University, Delft University of Technology, TUD-ITS-me-ce
FAME aims to obtain low power solutions when mapping applications on processor platforms. We like to achieve this goal by
creating a compiler infrastructure capable of performing source-code transformations. We propose a dynamic approach in
combination with analytic pruning of the transformation search space in order to find the best low-power optimizations.
Beyond the Ordinary: Design of Embedded Real-time Control (BODERC)
2003-2008. Senter, 2.5 M€, Océ Technologies, Philips CFT, AAS, Imtech ICT, Chess iT, Katholieke Universiteit Nijmegen,
Universiteit Twente. The Boderc project focuses on distributed embedded real-time controllers of complex systems. An Océ
printer is taken as a case-study and acts as a driver for the project. The target is an integral approach for a systematic
architectural design, modeling, analysis, and validation methodology for such heterogeneous systems.
Bekooij, M. van; Meerbergen, J.L. van; Hoes, R.J.H.; Moreira, O.; Poplavko, P.; Pastrnak, M; Mesman, B.; Mol, J.D.; Stuijk,
S.; Gheorghita, V.S.: Dataflow Analysis for Real-Time Embedded Multiprocessor System Design. In Dynamic and robust
Streaming in and between Connected Consumer-Electronic Devices, Chapter 4. ISBN 1-4020-3453-9, ed. P. van der Stok;
Springer, Berlin, Germany, 2005, pp. 81-108.
Huang, J.; Voeten, J.P.M.; Florescu, O.; Putten, P.H.A. van der; Corporaal, H.: Chapter 8, Predictability in real-time system
development. Advances in Design and Specification Languages for SoCs, Chapter 8. ISBN 0-387-26149-4, ed. P. Boulet;
Kluwer Academic Publishers, 2005.
Aa, T. van der; Jayapala, M.; Barat, F.; Deconinck, G.; Lauwereins, R.; Corporaal, H.; Catthoor, F.: Instruction buffering
exploration for low energy embedded processors. JEC 1, nr. 3, 2005, pp. 341-351.
Ciordas, C.; Basten, T.; Radulescu, A.; Goossens, K.G.W.; Meerbergen, J.L. van: An Event-based Monitoring Service for
Networks on Chip. ACM Transactions on Design Automation of Electronic Systems 10, nr. 4, 2005, pp. 702-723.
Gheorghita, V.S.; Corporaal, H.; Basten, A.A.: Iterative Compilation for Energy Reduction. JEC 1, nr. 4, 2005.
Jayapala, M.; Barat, F.; Aa, T. van der; Catthoor, F.; Corporaal, H.; Deconinck, G.: Clustered Loop Buffer Organization for
Low Energy VLIW Embedded Processors. IEEE Transactions on Computers 54, nr. 6, 2005, pp. 672-683.
32
Aa, T. van der; Jayapala, M.; Barat, F.; Corporaal, H.; Catthoor, F.; Deconinck, G.: A High Level Memory Energy Estimator
based on Reuse Distance. Proceedings of 3rd workshop on Optimizations for DSP and Embedded Systems, ODES 2005
together with CGO 2005., 20-23 March 2005.
Aa, T. van der; Corporaal, H.; Catthoor, F.; Deconinck, G.: Combining data and instruction memory energy optimizations for
embedded applications. Proceedings of the 3rd workshop on Embedded Systems for Real-Time Multimedia 2005, 22-23
September 2005, ISBN 0-7083-9347-3, ed. M. Miranda; S. Ha; IEEE, 2005, pp. 121-126.
Avasare, P.; Nollet, V.; Mignolet, J.-Y.; Verkest, D.; Corporaal, H.: Centralized End-to-End Flow Control in a Best-Effort
Network-on-Chip. Proceedings of the EMSOFT conference 2005, ISBN 1-59593-091-4, IEEE, 2005, pp. 17-20.
Barat, F.; Aa, T. van der; Jayapala, M.; Deconinck, G.; Lauwereins, R.; Corporaal, H.: Methodology for building processor
design space exploration frameworks. Proceedings of 3rd Workshop on Optimizations for DSP and Embedded Systems
(ODES 2005), 20-20 March 2005.
Caarls, W.; Jonker, P.P.; Corporaal, H.: Skeletons and Asynchronous RPC for Embedded Data- and task Parallel Image
Processing. Proceedings of the 9th IAPR Conference on Machine Vision Applications 2005, 16-18 May 2005, ed. K Ikeuchi,
2005.
Fatemi, S.H.; Corporaal, H.; Basten, A.A.; Kleihorst, R.; Jonker, P.: Designing Area and Performance Constrained
SIMD/VLIW Immage Processing Architectures. Proceedings of the 7th Int. Conference of Advanced Concepts for Intelligent
Vision Systems. ACIVS 2005, 20-23 September 2005, ISBN 3-540-29032-X, ed. J. Blanc-Talon; W. Philips; D. Popescu; P.
Scheunders; Springer, Berlin, 2005, pp. 689-696.
Florescu, O.; Voeten, J.P.M.; Corporaal, H.: Property-Preserving Synthesis for Unified Control- and Data-Oriented Models.
Proceedings of the Forum on Specification & Design Languages (FDL) 2005, 27-30 September 2005.
Geilen, M.C.W.; Basten, T.; Theelen, B.D.; Otten, R.H.J.M.: An Algebra of Pareto Points. Proceedings of the 5th Application
of Concurrency to System Design 2005 conference, 6-9 June 2005, ISBN 0-7695-2363-3, ed. J. Desel; Y. Watanabe; IEEE
Computer Society Press, Los Alamitos, 2005, pp. 88-97.
Geilen, M.C.W.; Basten, T.; Stuijk, S.: Minimising Buffer Requirements of Synchronous Dataflow Graphs with Model
Checking. Proceedings of the 42nd Design Automation Conference, DAC 2005, 13-17 June 2005, ISBN 1-59593-133-3;
ACM Press, New York, 2005, pp. 819-824.
Gheorghita, V.S.; Stuijk, S.; Basten, T.; Corporaal, H.: Automatic Scenario Detection for Improved WCET Estimation.
Proceedings of the 42nd Design Automation Conference, DAC 2005, 13-17 June 2005, ISBN 1-59593-133-3; ACM Press,
New York, 2005, pp. 101-104.
Gheorghita, V.S.; Grigore, R.: Constructing Checkers from PSL Properties. Proceedings of the 15h Int. Conference on
Control Systems and Computer Science. 2, ISBN 973-8449-89-8, 2005, pp. 757-763.
Gheorghita, V.S.; Basten, T.; Corporaal, H.: Intra-task Scenario-aware Volgage Scheduling. Proceedings of CASES'2005,
24-27 September 2005, ISBN 1-59593-149-X; ACM Press, New York, 2005, pp. 177-184.
Heikkinen, J.; Cilio, A.; Takala, J.; Corporaal, H.: Dictionary-Based Program Compression on transport Triggered
Architectures. Proceedings IEEE Int. Symposium on Circuits and Systems, 23-26 May 2005, ISBN 0-7803-8835-6, 2005, pp.
1122-1125.
Heikkinen, J.; Takala, J.; Corporaal, H.: Dictionary-Based Program Compression on TTAs: Effects on Area and Power
Consumption. Proceedings of IEEE Workshop on Signal Processing Systems., 2-4 November 2005, ISBN 0-7803-9334-1,
2005, pp. 479-484.
Lambrechts, A.; Corporaal, H.; Robert, F.; Carrabina, J.; Raghavan, P.; Leroy, A.; Talavera, G.; Aa, T. van der; Jayapala, M.;
Catthoor, F.; Verkest, D.; Deconinck, G.: Power breakdown analysis for a Heterogeneous NoC Platform running a video
Application. Proceedings of IEEE 16th International Conference on Application-specific Systems, Architectures and
Processors ASAP 2005, IEEE 2005.
Lu, R.X.; Silva, C.; Ang, M.H.; Poo, J.A.N.; Corporaal, H.: A New Approach for Mechatonic System Design: Mechatronic
Design Quotient (MDQ). Proceedings of the 2005 IEEE/ASME International Conference on Advanced Intelligent
Mechatronics. 2005, pp. 911-915.
33
Marescaux, T.; Rangevall, A.; Nollet, V.; Bartic, A.; Corporaal, H.: Distributed congestion control for packet switched
networks on chip. Proceedings of Parallel Computing Conference PARCO'05, 25-25 January 2005.
Marescaux, T.; Bricke, B.; Debacker, P.; Nollet, V.; Corporaal, H.: Dynamic Time-Slot Allocation for QoS Enabled Networks
on Chip. Proceedings of the 3rd Workshop on Embedded Systems for Real-Time Multimedia 2005; IEEE, 2005, pp. 47-52.
Ovadia, I.; Ha, Y.; Corporaal, H.: Using Multiple Paths in NoCs for Guaranteed Resource Allocation and Improved Best Effort
Performance. Proceedings of ProRISC 2005, 2005.
Palkovic, M.; Corporaal, H.; Catthoor, F.: Global memory optimisation for embedded systems allowed by code duplication.
Proceedings of International Workshop on Software and Compilers for Embedded Systems, SCOPES 2005, 2005, pp. 7279.
Palkovic, M.; Corporaal, H.; Catthoor, F.: Scenario creation for low power embedded systems. Proceedings of Architectures
and Compilers for Embedded Systems ACES 2005, 2005, pp. 26-29.
Palkovic, M.; Brockmeyer, E.; Vanbroekhoven, P.; Corporaal, H.; Catthoor, F.: Systematic preporocessing of data dependent
constructs for embedded systems. Proceedings of 15th international workshop Integrated Circuit and System Design. Power
and Timing Modeling Optimization and Simulation, PATMOS 2005, 2005, pp. 88-99.
Seneclauze, M.; Blanch, C.; Bormans, J.; Geilen, M.C.W.; Basten, T.; Theelen, B.D.; Koulamas, C.; Papadopoulos, G.;
Prayati, A.; Fohler, G.; Isovic, D.; Decotignie, J.D.; Papadopoulos, G.A.; Cheng, P. et.al.: The BETSY Project on Timeliness
and Energy Aspects of Wireless Video Streaming. Proceedings of the International Workshop on Wireless Ad-hoc Networks.
Electronic proceedings, 2005.
Stuijk, S.; Basten, T.; Mesman, B.; Geilen, M.C.W.: Predictable embedding of large data structures in multiprocessor
networks-on-chip. Proceedings of he 8th EUROMICRO Conference on Digital System Design, 30 August - 3 September
2005, ISBN 0-7695-2433-8, ed. C. Wolinski; IEEE Compuer Society Press, Los Alamitos, 2005, pp. 388-395.
Terechko, A.; Garg, M.; Corporaal, H.: Evaluation of Speed and Area of Clustered VLIW Processors. Proceedings of the 18th
Int. Conference on VLSI Design and the 4th Int. Conference on Embedded Systems Design, 3-7 January 2005, ISBN 07695-2264-5; IEEE Computer Society, 2005, pp. 557-563.
Voeten, J.P.M.; Huang, J.; Florescu, O.; Theelen, B.D.; Corporaal, H.: Towards predictability in real-time embedded system
design. Invited presentation. Proceedings of the Lorentz-ARTIST (Network of Excellence on Embedded Systems Design)
Workshop Embedded Systems. 22-22 November 2005.
Ykman-Couvreur, Ch.; Brockmeyer, E.; Nollet, V.; Marescaux, T.; Catthoor, F.; Corporaal, H.: Design-Time Application
Exploration for MP-SoC Customized Run-Time Management. Proceedings of Systems on Chip Conference (SoC '05), ISBN
0-7803-9294-9, 2005, pp. 66-69.
Abstracts
Poplavko, P.; Basten, T.; Pastrnak, M; Meerbergen, J.L. van; Bekooij, M. van; With, P.H.N. de: Extended Abstract:
Estimation of Execution Times of On-chip Multiprocessors Stream-oriented Applications. Formal Methods and Models for
Codesign, 3rd ACM & IEEE Int. Conference, MEMOCODE 2005, proceedings., 11-14 July 2005, ISBN 0-7803-9227-2; IEEE
Computer Society Press, Los Alamitos, 2005, pp. 251-252.
Stuijk, S.; Basten, T.; Mesman, B.; Geilen, M.C.W.: Predictable embedding of large data structures in multiprocessor
networks-on-chip (extended ebstract). Proceedings of DATE 2005, 7-11 March 2005, ISBN 0-7695-2288-2, ed. N. Wehn;
Benini; IEEE Computer Society Press, Los Alamitos, 2005, pp. 254-255.
Fatemi, H; Caarls, W; SmartCam Image Processing Library
2003 - 2005, C/Unix, C++/MPI/Linux, 1DC/IMAP, XTC/Xetal, StreamC/kernelC/Imagine.
The library is based on algorithmic skeletons for image processing operations (low, intermediate and high level). By using
this library, the programmer of an image processing application can easily parallelize the application and s/he does not have
to handle the problems related to communication and synchronization.
Stuijk, S; Multiprocessor design flow
2002 - now , C++/JAVA/Linux/Windows.
Next-generation embedded multi-media systems will often be built on multi-processor systems to obtain high compute power
at relatively low energy cost. Work is ongoing to implement a design flow to map streaming applications specified as
34
synchronous dataflow (SDF) graphs to a heterogeneous multi-processor systems. We aim at predictability with respect to
timing behavior, while minimizing energy consumption. An important component of this design-flow is a tool to analyze SDF
graphs, called SDF3. The tool also allows the generation of random test graphs, and it supports the visualization of graphs.
The tool is available via http://www.es.ele.tue.nl/sdf3.
Products of cooperation within ASCI
Caarls, W.; Jonker, P.P.; Corporaal, H.: Skeletons and Asynchronous RPC for Embedded Data- and task Parallel Image
Processing. Proceedings of the 9th IAPR Conference on Machine Vision Applications 2005, 16-18 May 2005, ed. K Ikeuchi,
2005.
Fatemi, S.H.; Corporaal, H.; Basten, A.A.; Kleihorst, R.; Jonker, P.: Designing Area and Performance Constrained
SIMD/VLIW Immage Processing Architectures. Proceedings of the 7th Int. Conference of Advanced Concepts for Intelligent
Vision Systems. ACIVS 2005, 20-23 September 2005, ISBN 3-540-29032-X, ed. J. Blanc-Talon; W. Philips; D. Popescu; P.
Scheunders; Springer, Berlin, 2005, pp. 689-696.
Fatemi, H; Caarls, W; SmartCam Image Processing Library 2003 - 2005, C/Unix, C++/MPI/Linux, 1DC/IMAP, XTC/Xetal,
StreamC/kernelC/Imagine.The library is based on algorithmic skeletons for image processing operations (low, intermediate
and high level). By using this library, the programmer of an image processing application can easily parallelize the
application and s/he does not have to handle the problems related to communication and synchronization.
2.2.4
Contribution of UT- EEMCS-dacs
Management and measurement of operational networks
In this activity, we work on methods and techniques to improve network performance and dependability, based on
measurements taken in a life network. Today, the network we focus on is primarily the fixed internet. Using active and
passive measurement techniques, critical network parameters are derived (using statistical techniques). Simple models are
fed with these parameters; model evaluations help in decision making in order to imrove network performance and
dependability. Decisions are put into effect using network management techniques (e.g. SNMP or web-services based).
Intrusion detection (anomaluy based) is a new activity we are starting in this field.
Mobile and wireless communications
This activity focuses on the development of architectures, protocols, and algorithms for future wireless networks. Aspects
that play a role here are for instance access mechanisms, routing, service discovery, and all kinds of traffic control aspects,
such as scheduling, congestion control, power control, etc. New mechanisms are designed, and the design in analyzed using
analytical models, simulation models, and prototype implementations. The current work concentrates on self-organizing ad
hoc networks, that optimize their operation based on information regarding other nodes in the network and the environment.
Design and analysis of networked embedded systems
Networked embedded systems are starting to appear as real systems. Networked embedded systems typicallly have to
operate under severe resource constraints; furthermore, best effort services are typically not appropriate. Hence, new
lightweight protocols have to be designed and validated for their correctness and performance and dependability properties.
Our research in this area primarily focusses on specifications of such systems, followed by numerical evaluation of critical
performance and dependability parameters. Our specification and evaluation techniques use classical techniques known
from queueing theory, but also more advanced techniques pairing stochastic analysis with model checking. We started work
on using the DAS machine for distributed evaluation of these very large models.
External projects
MC
MC, 2004-2008, NWO, 350 kEU, -.This project focusses on specification and numerical evaluation of infinite-state systems,
using stochastic model checking technique. Techniques known for finite-state systems model checking, will be adapted and
enhanced for infinite-state systems. This is a cooperation project between the FMT group (Brinksma) and DACS, both at the
UT.
VOSS2
2005-2007, NWO, 55 kEU, -.This project facilitates the cooperation between two universities in the Netherlands (UT
(Haverkort, Katoen), RUN (Vaandrager)) and 3 universities in Germany (Bonn (Baier), Saarbruecken (Hermanns) and
Muenchen (Siegle)).
35
MoQS
2006-2008, NWO, 500 kEU, -. Cooperation project (NWO/FOCUS) with the FMT group (Stoelinga) at UT, in which work on
component-based design and evaluation of large systems is being performed. Tool support for that purpose is being
developed as well.
VeriGRID
2006-2008, NWO, 500 kEU, -.Cooperation project (NWO/FOCUS) between TU/e (Groote), CWI (Van der Pol) and UT, in
which large-scale distributed algorithms are developed for model checking purposes, in order to increase the size of the
systems that can be practically analysed with these techniques by at least one order of magnitude. Use of the ASCI DAS-3 is
foreseen.
QoSPN@Home
2004-2008, EZ/Senter, 400 kEuro (DACS budget), -. Cooperation project between TUDelft (Niemegeers/Van Mieghem) and
UT, on the design and analysis of QoS-aware personal networks. Such networks are overlay networks consisting of ad hoc
nodes (such as in a personal area network) and potentially fixed nodes.
Freeband/Awareness
BSIK, 500 kEuro (DACS). Cooperation project between UT and Lucent Tehnologies, Telematica Instituut, Ericsson,
Roessingh R&D, Yucat, TMS, and WMC, researching and developing context-aware services and networks. The DACS
group investigates context discovery for ad hoc networks in this project.
Freeband/PNP2008
SIK, 500 kEuro (DACS) . Cooperation project between UT and TUDelft, Philips, KPN, WMC,and TNO, to research and
develop a Personal Network, focussing on the prototyping of a Personal Mobile Gateway.
Gigaport NG
Research on Networks, 2005-2007, BSIK, 150KE, UvA & TUD. Within this project the UT investigates self-management of
hybrid IP/ Optical networks, and the measurement of traffic flows within such networks. The project is managed by
SURFnet, and supports the introduction of SURFnet6.
Emanics
2006-2009, EU, 310 KE, -.European Network of Excellence (NoE) for the Management of Internet Technologies and
Complex Services. This NoE addresses the scalability, dynamics, security and automation challenges that emerge towards
the management plane of the future Internet and complex services running on top of it. UT
coordinates the research within this NoE.
Parhonyi, R., Nieuwenhuis, L.J.M., Pras,A. The rise and fall of micropayment systems. In T. Lammer (Ed.), Handbuch EMoney,E-Payment & M-Payment (pp. 343-361). Heidelberg: Springer Verlag (ISBN
3-7908-1651-5).
Ait Yaiz, R., Heijenk,G.J. Providing QoS in Bluetooth. Cluster computing, (ISSN 1386-7857), 8, 223-231. Baier, C.,
Hermanns, H., Katoen, J.P., Haverkort, B.R.H.M. Efficient computation of time-bounded reachability probabilities in uniform
continuous-time Markov decision processes. Theoretical computer science, (ISSN0304-3975), 345, 2-26.
Baier, C. , Haverkort, B.R.H.M., Hermanns, H., Katoen, J.P. Model Checking meets Performance Evaluation. Performance
evaluation review,(ISSN 0163-5999), 32, 10-15.
Bell, A., Haverkort,B.R.H.M. Sequential and distributed model checking of Petri nets. International journal on software tools
for technology transfer, (ISSN 1433-2779), 7(1), 43-60.
Boer, P.T. de, Kroese,
D.P., Mannor, S., Rubinstein, R. A Tutorial on the Cross-Entropy Method. Annals of operations research, (ISSN 0254-5330),
134, 19-67.
Boer, P.T. de. Rare-event simulation of non-Markovian queueing networks using a state-dependent change of measure
determined using cross-entropy. Annals of operations research, (ISSN 0254-5330), 134, 69-100.
Clemm, A., Festor, O., Pras, A. A Report on IM 2005. Journal of network and systems management, (ISSN 1064-7570),
13(3), 351-354.
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Haverkort, B.R.H.M., Katoen, J.P. Performance and Verification. Performance evaluation review, (ISSN 0163-5999), 32(4),3.
Karagiannis, G., Fu, X., Schulzrinne, H., Bader, A., Hogrefe, D., Kappler, C., Tschofenig, H., & Bosch, S. van den. NSIS: A
New Extensible IP Signaling Protocol Suite. IEEE communications magazine, (ISSN 0163-6804), 43(10), 133-141.
Niemegeers, I.G.M.M., Heemstra de Groot, S.M. FEDNETS: Context-aware Ad-hoc Network Federations. Wireless personal
communications, (ISSN 0929-6212), 33, 319-325.
Pavlou, G., Pras, A. Introducing the Series on Network and Service Management. IEEE communications magazine, (ISSN
0163-6804), 43(10), 60-60.
Bader, A., Karagiannis, G., Westberg, L., Kappler, C., Phelan, T., Tschofenig, H., & Heijenk, G.J. QoS Signaling Across
Heterogeneous Wired/Wireless Networks: Resource Management in Diffserv Using the NSIS Protocol Suite. In S. Shen
(Ed.), Proceedings of QShine 2005 .Orlando, Florida USA: IEEE Communications Society (ISBN 0-7695-2423-0).
Bomhoff, M.J., Eyckelhof, C.J., Meent, R. van de , & Pras, A. Quarantine Net: design and application. In Application session
proceedings of the 9th IFIP/IEEE Int. Symposium on Integrated Network Management . Nice: IEEE (ISBN 0-7803-9088-1).
Brandhorst, C.J., & Pras, A. DNS: a statistical analysis of name server traffic at local network-to-Internet Connections. In C.
Delgado Kloos & et al. (Eds.), Proceedings of the 11th Open European Summer School and IFIP WG6.4/6.6/6.9 Workshop
(pp. 72-78) (ISBN 84-89315-43-4).
Cloth, L. , & Haverkort, B.R.H.M. Hyperbolic PDE's for CSRL Model Checking: A Deja Vu. In Proceedings of the 7th Int.'l
Workshop on Performability Modeling Computer and Communication Systems (pp. 19-22). Torino, Italy.
Cloth, L. , Katoen, J.P., & Khattri, M. Model Checking Markov Reward Models with Impulse Rewards. In A. Dr. Bondavalli,
B.R.H.M. Haverkort, & D. Prof. Tang (Eds.), Proceedings of the Int.'l Conference on Dependable Systems and Networks
(pp. 722-731). Yokohama, Japan: IEEE Computer Society (ISBN 0-7695-2282-3).
Cloth, L. , & Haverkort, B.R.H.M. Surviving Survivability Specifications. In A. Dr. Bondavalli, B.R.H.M. Haverkort, & D. Prof.
Tang (Eds.), Supplemental Volume of the 2005 Int.'l Conference on Dependable Systems and Networks (pp. 70-71).
Yokohama, Japan:IEEE Computer Society.
Heijenk, G.J. , & Liu, F. (2005). Interference-based Routing in Multi-hop Wireless Infrastructures. In T. Braun, G. Carle, Y.
Koucheryavy, & V. Tsaoussidis (Eds.), Proceedings WWIC 2005, 3rd Int.'l Conference on Wired/Wireless Internet
Communications Vol. 3510. Lecture notes in computer science, (pp. 117-127). Xanthi, Greece: Springer Verlag (ISBN 3-54025899-X).
Jacobsson, M., Hoebeke, J., Heemstra de Groot, S.M., Lo, A., Moerman, I., Niemegeers, I.G.M.M., Munoz, L., Alutoin, M.,
Louati, W., & Zeghlache, D. A Network Architecture for Personal Networks. In P. Herhold & R. Schlager (Eds.), Proceedings
of the 14th IST Mobile and Wireless Communication Summit . Dresden, Germany.
Jehangir, A. , Heemstra de Groot, S.M. A Secure and Lightweight Ad-hoc Routing Algorithm for Personal Networks. In L.
Heinzl & N.R. Prasad (Eds.), Proceedings of the Int.'l Conference on Wireless Personal Multimedia Communications (pp.
1998-2002). Aalborg, Denmark (ISBN87-90834-79-8).
Karagiannis, G. , Hancock, R., Loughney, J., & Bosch, S. van den. Next Steps in Signaling: Framework. In Proceedings
IETF'63 . Paris, France:IETF.
Karagiannis, G. , Manner, J., Bosch, S. van den, & McDonald, A. NSLP for Quality-of-Service signalling. In Proceedings
IETF'63 . Paris, France: IETF.
Karagiannis, G. , Bader, A., Westberg, L., Kappler, C., & Phelan, T.. RMD-QOSM - The Resource Management in Diffserv
QoS model. In Proceedings IETF'63 . Paris, France: IETF.
Karagiannis, G. , Bader, A., & Westberg, L. Using IP as Transport Technology in Third Generationand Beyond Radio Access
Networks. In H. de Meer & N. Bhatti (Eds.), Proceedings of 13th IEEE Int.'l Workshop on Quality of Service (IWQoS2005)
Vol. 3552. Lecture notes in computer science, (pp. 372-375). Passau, Germany: Springer Verlag (ISBN 3-540-26294-6).
Lo, A., Heijenk, G.J. , Niemegeers, I.G.M.M.. Evaluation of MPEG-4 Video Streaming over UMTS/WCDMA Dedicated
Channels. In Proceedings of the 1st Int.'l Conference on Wireless Internet . Budapest, Hungary.
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Lo, A., Heijenk, G.J. , Niemegeers, I.G.M.M. Performance Evaluation of MPEG-4 Video Streaming over UMTS Networks
using an Integrated Tool Environment. In M.S. Obaidat, L. Marchese, J.L. Marzo, & F. Davoli (Eds.), Proceedings of the
Symposium on Performance Evaluation of Computer and Telecommunication Systems . Philadelphia, USA: The Society for
Modeling and Simulation Int.'l (SCS) (ISBN 1-56555-300-4).
Parhonyi, R., Nieuwenhuis, L.J.M. , Pras, A. . Second generation micropayment systems: lessons learned. In M. Funabashi
& A. Grzech (Eds.), Proceedings: Challenges of expanding Internet: E-commerce, E-business and E-government (pp. 345359). Springer (ISBN 0-387-28753-1).
Prasad, V., Jacobsson, M., Lo, A., Niemegeers, I.G.M.M., Heemstra de Groot, S.M. Architectures for Intra-Personal Network
Communication. In M.M. Buddhikot & Lo R. Cigno (Eds.), Proceedings of the Third ACM Int'.l Workshop on Wireless Mobile
Applications and Services on WLAN Hotspot . Cologne, Germany: Springer Verlag.
Remke, A.K.I., Haverkort, B.R.H.M. Beyond Model-Checking CSL for QBDs: Resets, Batches and Rewards. In Proceedings
of the 7th Int.'l Workshop on Performability Modeling Computer and Communication Systems (pp. 23-26). Torino, Italy:
University of Torino.
Remke, A.K.I. , Haverkort, B.R.H.M. , Cloth, L. Model Checking Infinite-State Markov Chains. In N. Halbwachs & L.D. Zuck
(Eds.), Tools and Algorithms for the Construction and Analysis of Systems Vol. 3440. Lecture notes in computer science,
(pp. 237-252). Edinburgh, UK: Springer Verlag (ISBN 10-3-540-25333-).
Vulic, N, Heemstra de Groot, S.M., Niemegeers, I.G.M.M. 802.11 Modifications for WLAN-UMTS Integration at Radio
Access. In L. Heinzl & N.R. Prasad (Eds.), Proceedings of the Int.'l Conference on Wireless Personal Multimedia
Communications (pp. 1206-1210). Aalborg, Denmark (ISBN87-90834-79-8).
Vulic, N, Heemstra de Groot, S.M., & Niemegeers, I.G.M.M. A Comparison of Interworking Architectures for WLAN
Integration at UMTS Radio Access Level. In Proceedings of the First Int.'l Workshop on Convergence of Heterogeneous
Wireless Networks, Budapest, Hungary.
Vulic, N, Heemstra de Groot, S.M., & Niemegeers, I.G.M.M. Common radio resource management for WLAN-UMTS
integration Radio Access Level. In P. Herhold & R. Schlager (Eds.), Proceedings of the 14th IST Mobile and Wireless
Communication Summit, Dresden, Germany.
Vulic, N, Heemstra de Groot, S.M., & Niemegeers, I.G.M.M.. UMTS-based Architectures for UMTS-WLAN Integration. In van
W.C. Etten & R. Srinivassan (Eds.), Proceedings of the IEEE 12th Symposium on Communications and Vehicular
Technology in the Benelux SCVT 2005 . Enschede: IEEE.
Wanrooij, W. van, & Pras, A. Data on Retention. In J. Schoenwaelder & J. Serrat (Eds.), Proceedings of the 16th IFIP/IEEE
Int.'l Workshop on Distributed Systems: Operations and Management (DSOM 2005) Vol. 3775. Lecture notes in computer
science, (pp. 60-71). Barcelona, Spain: Springer Verlag (ISBN 3-540-29388-4).
Wanrooij, W. van, & Pras, A. DNS Zones Revisited. In C. Delgado Kloos & et al. (Eds.), Proceedings of the 11th Open
European Summer School and IFIP WG6.4/6.6/6.6/6.9 (pp. 84-92). Colmenarejo, Spain (ISBN 84-89315-43-4).
Highlight
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As highlight from the publication list, we would like to put forward the paper: Alexander Bell, Boudewijn R.H.M. Haverkort,
Sequential and distributed model checking of Petri nets. International Journal on Software Tools for Technology Transfer,
7(1), 43-60 (Springer-Verlag).
This paper, in essence, reports about a PhD project that was completed while I was still working at the RWTH; in fact, the
PhD project finished in november 2003, the paper ws finalized in the beginning of 2004, and published in 2005.
The paper describes an application /from computer science/ for large-scale parallel/distributed computing. What we see most
often in computational science, is that clusters and grids are being used to solve problems in the physical sciences, like
geology, astrology, or the engineering sciences, like aerodynamics, mechanics, and so on. Here, instead, we use a cluster of
26 dual processor nodes to attack large-scale model checking problems. Model checking is an exhaustive search and proof
technique to verify the validity of formally specified properties in the context of a formally described system description. It is
currently seen as one of the most promising automated correctness proof systems and is, for instance, widely employed in
the context of embedded software and communication protocol design. However, "production model checking" does not
emply parallel and distributedalgorithms so far.
In our work, we developed parallel/distributed algorithms to verify correctness properties specified in a temporal logic called
CTL (computational tree logic). The system is described using Petri nets (but other description formalisms could be use
equally well). The real problem in disitributed model checking is that the state space of the system being described as Petri
net is a priori unknown, and in any case, unstructured. Furthermore, the state space may easily contain many millions of
states, so that it cannot be stored in main memory; this counts even more for the state-transition relation, which is, typically,
10 to 20 times larger than the state space itself. The unstructuredness of the state space makes the work division strategy
very difficult. We developed a probabilistic work division concept based on hashing functions. We dealt with the enormous
memory requirements by using disk-based techniques, as well as on-demand recomputation techniques; given a state, its
possible predecessors are re-computed whenever necessary, instead of storing them. The algorithms have been
implemented on the PARSECS cluster, a machine we built ourselves in 2000, for slightly less than DM 200.000,- (less than
100.000,- Euro). Cooling and appropriate power supply accounted for another DM 10.000,-. This Linux cluster comprises 26
dual Pentium III nodes (500 MHz), equipped with 512 MB main memory and a 40 GB local disk per node, connected via a
switched 100 Mbps Erhernet (see figure); early in 2006, the cluster was put out of operation. The algorithms we developed
scale surprisingly well: we achieved efficiencies of around 90% for small processor numbers, around 80% for26 processors,
going down to some 70% for 52 prcoessors (probably due to intra-node bus contention). The larger the problems we
addressed, the better the speed-ups and efficiencies.
Using the same cluster, and similar algorithms, we recently also developed numerical solution procedures for Markov chains
based on Petri net models. We were able to solve Markov chains with close to a billion states, meaning that we solve linear
systems with up to a million unknowns, in a distributed, disk-based fashion. These are the largest Markov chains known
publicly tohave been solved; Google might solve larger Markov chains in the context of their pagerank computations, but
they did not (yet) report about that in the open literature.
2.2.5
Contribution of VU – WI
Research in the group is concentrated in three areas, Large-Scale distributed Systems, Security, as well as Cluster and Grid
computing.
Large-Scale Distributed Systems
We are concentrating on three strongly interrelated subareas. First, we are putting effort into developing a fully decentralized
user-centric content delivery networks, called Globule. Globule handles automatic and adaptive replication of Web pages for
the sake of performance and availability. A first version of Globule was
released in December 2003. Various Web sites are currently hosted by Globule software. The current version is 1.3.2 and
supports Windows as well as UNIX platforms. In 2005, we have been concentrating on research aimed at service-oriented
architectures, replication of dynamically generated documents, and automated resource provisioning.
Second, we are increasing our efforts concerning large-scale epidemic-based systems, covering wired as well as wireless
networks. In particular, attention has been paid to protocols for decentralized membership management for very large
networks, allowing nodes to regularly join and leave the system. Also, we have been looking at using epidemics for efficiently
monitoring systems. These efforts are now leading to solutions for large-scale sensor networks, where we concentrate on
debugging, monitoring, and security with emphasis on local-only solutions.
Security
This work concerns reliability and security in various forms. One area is building a new operating system with as goal high
reliability. Current operating systems are structured as large monolithic lumps of code and a bug in any component,
especially in a device driver, can bring down the entire system. The goal of this subproject is to compartmentalize the
39
components of the system so that bugs and security breaches in one compartment cannot spread to other ones.
Another area is that of ubiquitous computing, including sensor networks and RFID. Consider a network of sensors deployed
in a forest with the intention of detecting fires. A malicious person who looks for an finds a sensor can put a match near it and
set off a false alarm. Worse yet, he can do it repeatedly. Using the (software) concept of one-time sensors, we hope to make
this problem more manageable. This work is applicable to any sensor network used for safety purposes.
Another area of research is RFID security and privacy. RFID tags are being place on many products, on clothes, and
passports, and elsewhere. The European bank is thinking of putting them on euro banknotes. Anyone with an easilyavailable RFID reader can read these tags at a distance. We are looking at ways to guard people's privacy in an RFIDenabled world.
Part of our security work focuses on detecting intrusions and blocking malware. We implemented very accurate intrusion
detection technology for next-generation honeypots. The system, known as Argos, is based on an hardware emulator which
keeps track of what data comes the network and triggers an alert when such data is used in ways that violate the security
policy. The system is intended to not just detect the attack, but also generate signatures of the attack. The signatures
generated by ourselves and others are used for blocking malicious traffic. For this purpose, we have taken the notion of a
distributed firewall to its extreme, whereby an intrusion prevention system is implemented on a programmable network card,
close to the wire. The prototype card, known as the CardGuard, may be plugged into an end-user's PC, or, more likely, in the
edge router or switch. We are currently developing a more advanced version of CardGuard, known as SafeCard, which
applies several different intrusion prevention techniques in low-level hardware. As a result, we expect to offer sophisticated
protection at gigabit rates.
Finally, we are looking at secure peer-to-peer content distribution networks in which people who buy digital content can be
authorized by the owner to resell the content in a secure way.
Cluster and Grid Computing
Part of this effort is the Ibis project. Ibis is a Java-centric programming environment for writing distributed supercomputing
applications. The Ibis project integrates results from earlier projects in this group, including Manta (a Java compiler and fast
communication library) and Albatross (which studied parallel programming on wide-area systems, so-called distributed
supercomputing). Since 2004, the Ibis project takes place in the context of the BSIK project "Virtual Laboratory for eScience" (VL-e).
The key idea behind Ibis is to benefit from Java's high portability (write once, run anywhere), making it possible to run parallel
applications on heterogeneous large-scale systems (Grids). Ibis provides a range of communication primitives (Remote
Method Invocation, group communication, divide-and-conquer, replicated objects, message passing) implemented in a
portable and efficient fashion. The divide-and-conquer system implemented with Ibis (called Satin) also is fault-tolerant, so it
recovers transparently from processor crashes.
The core of Ibis has been implemented in pure Java, allowing it to run on any platform that provides a Java Virtual Machine.
We have also developed a peer-to-peer called Zorilla that can be used to deploy Ibis (and other) applications on a largescale system, using locality-aware scheduling.
Ibis applications have access to Grid resources (like files or computer nodes) using the Grid Application Toolkit (GAT), for
which we have developed a Java-based version within the EC-funded project GridLab. The GAT provides a set of simple
APIs for Grid-aware applications, allowing to dynamically bind to proxies that give access to actual resources, services, and
protocols.
Many large-scale experiments have been performed with Ibis, on the Distributed ASCI Supercomputer (DAS) as well as on a
testbed of the EC GridLab project and on the French Grid'5000 system. The experiments have shown that Ibis makes it
possible to run a single parallel Java application on a very heterogeneous, European-scale grid and obtain high speedups.
For example, we have won an award at the N-Queens Challenge of the Grid Plugtests (Nice, France, Oct. 2005) for using
the largest number (961) of CPUs in a single Grid application. Several applications have been developed with Ibis, including
automated protein identification (with AMOLF), electromagnetic simulation (JEM3D, with researchers from the French
ProActive project), processing of MEG scanner data (with VUmc), and grammar induction (with the University of
Amsterdam).
In high-speed computing, we also address the issue of processing traffic at truly high link rates (multiple gigabits per
second). In this area we are developing the FFPF/Streamline framework. By means of aggressive copy avoidance, minimal
context switching, and judicious use of the cache, Streamline significantly improves performance of modern operating
systems. In addition, Streamline takes a 'structured operating systems' whereby simple components can be clicked together
in straightforward way in order to build complex applications. As a result, the architecture offers more flexibility to the end-
40
user, and facilitates incorporation of advanced hardware (such as network processor boards, or FPGAs). The framework is
sufficiently flexible to allow for distributed traffic processing whereby a high-speed link is split among several nodes (perhaps
on several levels) which each perform part of the processing. As the two-level hierarchy easily extends to more levels, the
system is inherently scalable.
External projects
Industrial cooperations have been set up with Philips Research Laboratories (Eindhoven) and Chess embedded Technologies
(Haarlem). In addition, we are heavily involved in DevLab, and Dutch consortium of SMEs aiming to apply wireless sensor
technology. Efforts continue in the Bsik IShare project, in which the TU-Delft and VU jointly work on the Tribler .
Papers in International journals
Aline Baggio and Maarten van Steen. Distributed Redirection for the World-Wide Web. Computer Networks 49 (6), page 743765, December, 2005
Rob V. van Nieuwpoort, Jason Maassen, Thilo Kielmann and Henri E. Bal. Satin: Simple and Efficient Java-based Grid
Programming. Scalable Computing: Practice and Experience 6 (3), page 19-32, September, 2005
Spyros Voulgaris, D. Gavidia and Maarten van Steen. CYCLON: Inexpensive Membership Management for Unstructured
P2P Overlays. Journal of Network and Systems Management 13 (2), page 197-217, June, 2005
M.L. Boonk, D.R.A. de Groot, F.M.T. Brazier and A. Oskamp. Agent Exclusion on Websites. Proceedings of The 4th
Workshop on the Law and Electronic Agents (LEA 2005), page 13-20, 2005
G. Allen, K. Davis, T. Goodale, A. Hutanu, H. Kaiser, T. Kielmann, A. Merzky, Rob V. van Nieuwpoort, A. Reinefeld,
Schintke F., T. Schuett, E. Seidel and B Ullmer. The Grid Application Toolkit: Towards Generic and Easy Application
Programming Interfaces for the Grid. Proceedings of the IEEE 93 (3), page 534-550, 2005
K. Bicakci, Crispo B. and A. S. Tanenbaum. How to Incorporate Revocation Status Information into the Trust Metrics fro
Public-Key Certification. International Journal for Infonomics I (2), page 1-10, 2005
Gabrielle Allen, Kelly Davis, Tom Goodale, Andrei Hutanu, Hartmut Kaiser, Thilo Kielmann, Andre Merzky, Rob van
Nieuwpoort, Alexander Reinefeld, Florian Schintke, Thorsten Sch?tt, Ed Seidel, Brygg Ullmer.The Grid Application Toolkit:
Towards Generic and Easy Application Programming Interfaces for the Grid. Proceedings of the IEEE, Vol. 93, No. 3, pp.
534-550, March 2005.
Ronald Veldema, Ceriel J. H. Jacobs, Rutger F. H. Hofman, Henri E. Bal: "Object combining: a new aggressive optimization
for object intensive programs Concurrency and Computation: Practice and Experience", Concurrency & Computation:
Practice & Experience, Vol. 17, No. 5-6, pp. 439-464, April/May 2005
Rob V. van Nieuwpoort, Jason Maassen, Gosia Wrzesinska, Rutger Hofman, Ceriel Jacobs, Thilo Kielmann, Henri E. Bal:
"Ibis: a Flexible and Efficient Java-based Grid Programming Environment", Concurrency & Computation: Practice &
Experience, Vol. 17, No. 7-8, pp. 1079-1107, June/July 2005
Contribution to international conference proceedings
Mathijs den Burger, Thilo Kielmann, and Henri Bal: "BalancedMulticasting: High-throughput Communication for Grid
Applications", SC'05, Seattle, WA, 12-18 Nov. 2005.
C. van Reeuwijk, Rob van Nieuwpoort, and Henri Bal: "Developing JavaGrid Applications with Ibis", Euro-Par 2005, Lisbon,
Portugal, August 2005.
Olivier Aumage, Rutger Hofman, and Henri E. Bal: "NetIbis: An Efficient and Dynamic Communication System for
Heterogeneous Grids", CCGrid05, Cardiff, UK, 9 - 12 May 2005.
Gosia Wrzesinskan, Rob van Nieuwpoort, Jason Maassen, and and Henri E. Bal: "Fault-tolerance, Malleability and
Migration for Divide-and-Conquer Applications on the Grid", IPDPS 2005, Denver, Colorado, 3-8 April 2005.
Spyros Voulgaris and Maarten van Steen. Epidemic-style Management of Semantic Overlays for Content-Based Searching.
In: 11th International Conference on Parallel and Distributed Computing (Euro-Par) , Lecture
Notes on Computer Science vol. 3648, page 1143-1152, Berlin, September, 2005
Markus Bornemann, Rob V. van Nieuwpoort and Thilo Kielmann. MPJ/Ibis:a Flexible and Efficient Message Passing
Platform for Java. In: EuroPVM/MPI 2005, page 217-224, September, 2005
41
H. J. Bos and Huang K. Towards software-based signature detection for intrusion prevention on the network card. In: Eighth
International Symposium on Recent Advances in Intrusion Detection (RAID2005), September, 2005
P. Garbacki, D. Epema and Maarten van Steen. A Two-Level Semantic Caching Scheme for Super-Peer Networks. In: 10th
Intl Workshop on Web Content Caching and Distribution, September, 2005
Mihai Lucian Cristea, Claudiu Zissulescu, Ed Deprettere and Herbert Bos. FPL-3E: towards language support for
reconfigurable packet processing. In: SAMOS V: Embedded Computer Systems: Architectures MOdeling, and Simulation,
July, 2005
W. de Bruijn, Herbert Bos and Henri E. Bal. Robust distributed systems: achieving self management through inference. In: 1st
International Workshop on Autonomic Communications and Computing, June, 2005
Pietro Mazzoleni, Bruno Crispo, Swaminathan Sivasubramanian and Elisa Bertino. Efficient Integration of Fine-grained
Access Control in Large-scale Services. In: Service Computing Conference, page 77-86, June, 2005
Swaminathan Sivasubramanian, Guillaume Pierre and Maarten van Steen. Autonomic Data Placement Strategies for
Update-intensive Web Applications. In: International Workshop on Advanced Architectures and Algorithms for Internet
Delivery and Applications, June, 2005
Mihai Lucian Cristea, W. de Bruijn and H. J. Bos. FPL-3: towards language support for distributed packet processing. In: IFIP
Networking 2005, May, 2005
Swaminathan Sivasubramanian, Gustavo Alonso, Guillaume Pierre and Maarten van Steen. GlobeDB: Autonomic Data
Replication for Web Applications. In: 14th International World-Wide Web Conference, page
33-42, New York, NY, May, 2005
B.C. Popescu, J. Sacha, Maarten van Steen, Bruno Crispo, A. S. Tanenbaum and Ihor Kuz. Securely Replicated Web
Documents. In: 19th International Parallel & Distributed Processing Symposium, LosAlamitos, CA., April, 2005
Giovanni Russello, M.R.V. Chaudron and Maarten van Steen. Dynamically Adapting Tuple Replication for High Availability in
a Shared Data Space. In: 7th Intl Conf. on Coordination Models and Languages, April, 2005
Michal Szymaniak, Guillaume Pierre and Maarten van Steen. Latency-driven Replica Placement. In: Symposium on
Applications and the Internet, Los Alamitos, CA., January, 2005
C. Gamage, J. Leiwo, K. Bicakci, Crispo B. and A. S. Tanenbaum. A Cost-Efficient Counter-Intrusion Scheme for One-Time
Sensor Networks. In: 2nd International Conference on Intelligent Sensors, Sensor Networks and Information Processing,
page 45-50, 2005
K. Bicakci, C. Gamage, Crispo B. and A. S. Tanenbaum. One-Time Sensors: A Novel Concept to Mitigate Node-Capture
Attacks. In: 2nd European Workshop on Security and Privacy in Ad-Hoc and Sensors Networks, page 80-90, 2005
K. Bicakci, Crispo B. and A. S. Tanenbaum. Counting Abuses Using Flexible Off-line Credentials. In: 10th Australiasian
Conference on Information Security, page 548-559, 2005
Crispo B., Swaminathan Sivasubramanian, Pietro Mazzoleni and Elisa Bertino. P-Hera: Scalable fine-grained access control
for P2P. In: 11th International Conference on Parallel and Distributed Systems, page 585-591, 2005
K. Bicakci, Crispo B. and A. S. Tanenbaum. How to Incorporate Revocation Status Information into the Trust Metrics for
Publik-Key Certification. In: 20th Annual ACM Symposium on Applied Computing,page 1594-1598, 2005
Herbert Bos, Lai Xu, Kees van Reeuwijk, Mihai Lucian Cristea. Network intrusion prevention on the network card. In: IXA
EDU Summit, 2005 Giovanni Russello, M.R.V. Chaudron and Maarten van Steen. Adapting Strategies for Distributing Data
in Shared Data Space. In: Intl Symp. on Distributed Objects and Applications, page 1225-1242, 2005
Experimentele software
Gobule: a user-centric Content Delivery Network. Java. Solaris/Linux. For description: see above.
The work on Globule and other peer-to-peer related research is done a cooperation between the VU-WI-i and TUD-ti-ki.
42
2.2.6
Contribution of TUD-EWI-ST-pds
Parallel and Distributed Systems
Our work in this area covers grids, peer-to-peer systems, wireless sensor networks, and embedded systems. In the area of
grids, we have completed the design and implementation of a first version of our KOALA grid scheduler, we have deployed it
for general use in the Distributed ASCI Supercomputer, and we have done numerous experiments with it. In addition, we
have designed the Grenchmark tool for grid benchmarking. In peer-to-peer systems, we have created a first version of the
Tribler p2p client as an extension to Bittorrent with as a final goal TV distribution across the Internet, which includes a novel
buddycast algorithm for peer and content discovery, and we have researched semantic-based caching in p2p systems. In the
area of wireless sensor networks we participated in the first large-scale (100 nodes) out-door deployment in precision
agriculture in The Netherlands in cooperation with Wageningen UR. This pilot showed the large gap between simulations
and reality, and produced some detailed RSSI data that we plan to use to redesign our MAC and localization protocols. In
the area of embedded systems, we have developed a design of a programming environment and a performance tool for
high-performance streaming applications for consumer electronics applications.
Cooperative Agent-Based Systems
The major effort of the CABS project is directed towards the development of methods and tools for the modelling and
implementation of information systems supporting independent, autonomous agents or agent organisations in mutual
competition or group-wise cooperation.
External Projects
Two-level Peer-to-Peer Systems
2003-2007, NWO, EURO 147.000, ASCI partner VU-EW-cs-i.
This project aims at exploring the notion of superpeers in p2p systems in order to improve the performance of such systems.
Virtual Laboratory for e-Science (VL-e)
2004-2008, EZ (BSIK program), EURO 1.000.000 (TUD-EWI-st-pds part), ASCI partners TUD-EWI-mm-cgcc, VU-EW-cs-I,
UvA-FdNWI-caps, UvA-FdNWI-scs.This projects aims at designing and implementing grid technology (schedulers,
communication libraries, problem-solving and visualization environments, etc) for virtual laboratories (e.g., for simulations in
the sciences) on top of the basic grid fabric.
CoreGRID
2004-2008, EU (Network of Excellence), EURO 38.000, ASCI partners VU-EW-cs-i.
This network integrates the grid research of 42 universities in Europe.
I-SHARE (part of Freeband)
2004-2008, EZ (BSIK program)
EURO 800.000, ASCI partners TUD-EWI-mm-ict, VU-EW-cs-i.
This projects researches sharing technology in distributed systems, particularly for video. As a research vehicle, we have
chosen P2P-TV, a system for sharing live and recorded TV programs of 10,000+ TV channels and web cams among millions
of users.
SCALP
2004-2008, STW, EURO 220.000, ASCI partners VU-EW-cs-i.
This project deals with high-productivity methods for programming parallel systems on a chip.
CONSENSUS
2002 – 2006, NWO, Euro 155.000.
The CONSENSUS project will develop collaborative algorithms for Wireless Sensor Networks to overcome the limited
capabilities of individual sensor nodes. TUD focuses on algorithms for communications and networking, including distributed
wireless access, ad-hoc routing protocols, and reliable end-to-end transport.
MilSens
2003 – 2007, TNO-FEL (AIO fonds), Euro 160.000.
The key objective is to develop an integrated approach to operate large ad-hoc networks of wireless sensor nodes. We will
take a practical approach and start from some well-defined application scenarios (to be developed at the start of the project),
derive the requirements on the network, and integrate and develop the necessary algorithms.
Smart Surroundings
2004 – 2008, EZ (BSIK program), Euro 800.000.
43
The overall mission of the Smart Surroundings project is to investigate, define, develop, and demonstrate the core
architectures and frameworks for future ambient systems. TUD focuses on two important aspects at the middleware layer:
service discovery and localization. These two are related through the ServiceGRID approach, in which location serves as an
index in a database of cached service providers.
LOFAR-agro
2004 - 2008, NN (Stichting Samenwerking Noord Nederland), Euro 200.000.
The LOFAR-Agro project carries out a pilot project in which ensor nodes will measure the conditions in a potato field; this
detailed information (1 reading per 150m2) will be used to improve the advice on how to fight the fungous Phytophtora
infestans disease within a crop.
RELATE
2005-2008, EU (FP6-IST), EURO 400.000
This project will investigate an approach wherein spontaneously networked mobile objects perform collaborative sensing and
communication tocollectively determine their relative positions and spatial arrangement.
Feldman, AB ,Gemund, AJC van, & Bos, A . A hybrid approach to hierarchical fault diagnosis. In R Dearden & S Narasimhan
(Eds.), Proceedings of DX'05 (pp. 101-106). Pacific Grove, CA, USA: NASA AMES.
Pietersma, J,Gemund, AJC van, & Bos, A . A model-based approach to sequential fault diagnosis. In S Karlovic & D
Wallhermfechtel (Eds.), Autotestcon 2005 Proceedings (pp. 621-627). Piscataway: IEEE.
Garbacki, PJ,Epema, DHJ, & Steen, M van . A two-level semantic caching scheme for super-peer networks. In s.n. (Ed.),
Proceedings of the 10th International Workshop on Web Content Caching and Distribution (WCW'05) . Piscataway: IEEE.
(TUD)
Mors, AW ter,Valk, JM, & Witteveen, C . An event-based task framework for disaster planning and decision support. In B van
de Walle & B Carle (Eds.), Proceedings of ISCRAM2005 - Second international ISCRAM conference (pp. 151-153).
Brussels, Belgium: KVAB. (TUD)
Iosup, A,Garbacki, PJ,Pouwelse, JA, & Epema, DHJ . Analyzing BitTorrent: Three lessons from one-peer level view. In BJA
Kröse, HJ Bos, EA Hendriks, & JWJ Heijnsdijk (Eds.), ASCI 2005 Proceedings of the eleventh annual conference of the
Advanced School for Computing and Imaging (pp. 96-103). Delft: ASCI.
Ditzel, M, & Langendoen, KG . D3: Data-centric data dissemination in wireless sensor networks. In s.n. (Ed.), European
Microwave Week 2005 Conference Proceedings (pp. 185-188). London: Horizon House Publications Ltd.
Mors, AW ter, & Witteveen, C . Coordinating non cooperative planning agents: Complexity results. In B Werner (Ed.),
Proceedings of the 2005 IEEE/WIC/ACM International Conference on Intelligent Agent Technology (pp. 407-413).
Piscataway: IEEE.
Wang, J,Reinders, MJT,Lagendijk, RL, & Pouwelse, JA . Distributed collaborative filtering for peer-to-peer file sharing
systems. In BJA Kröse, HJ Bos, EA Hendriks, & JWJ Heijnsdijk (Eds.), ASCI 2005 - Proceedings of the eleventh annual
conference of the advanced school for computing and imaging (pp. 34-40). Delft, The Netherlands: Advanced School for
Computing and Imaging (ASCI).
Mohamed, HH, & Epema, DHJ . Experiences with the KOALA co-allocating scheduler in multiclusters In s.n. (Ed.),
Proceedings of the 5th International Symposium on Cluster Computing and Grid, CCGrid05 (pp. 784-791). Piscataway:
IEEE. (TUD)
Mohamed, HH, & Epema, DHJ . Experiences with the KOALA co-allocating scheduler in multiclusters. In BJA Kröse, HJ Bos,
EA Hendriks, & JWJ Heijnsdijk (Eds.), ASCI 2005 Proceedings of the eleventh annual conference of the Advanced School
for Computing and Imaging (pp. 104-111). Delft: ASCI. (TUD)
Haratcherev, IJ,Taal, JR,Langendoen, KG,Lagendijk, RL, & Sips, HJ . Fast 802.11 link adaptation for real-time video
streaming by cross-layer signaling. In s.n. (Ed.), Proceedings of IEEE international symposium on circuits and systems
(ISCAS 2005) (pp. 3523-3526). Piscataway: IEEE. (TUD)
Parker, TEV, & Langendoen, KG . Guesswork: Robust routing in an uncertain world. In P Krishnamurthy (Ed.), Conference
proceedings of the 2005 IEEE Conference on Mobile Adhoc and Sensors Systems (pp. 1-9). Piscataway: IEEE. (TUD)
44
Haratcherev, IJ,Langendoen, KG,Lagendijk, RL, & Sips, HJ . Link adaptation and cross-layer signaling for wireless videostreaming in a shared medium. In s.n. (Ed.), Proceedings of the 2005 International Conference on Wireless Networks,
Communications and Mobile Computing (pp. 1-5). Piscataway: IEEE. (TUD)
Pouwelse, JA, Slobbe, M van,Wang, J,Reinders, MJT, & Sips, HJ . P2P-based pvr recommendation using friends, taste
buddies and superpeers. In M Setten, S McNee, & J Konstan (Eds.), Proceedings of the workshop beyond personalization
2005 - A workshop on the next stage of recommender systems research (IUI2005) (pp. 66-71). s.l.: s.n.. (TUD)
Roos, N, & Witteveen, C . Problem solving in a computational society. In HR Arabnia & R Joshua (Eds.), Proceedings of the
2005 International Conference on Artificial Intelligence (pp. 764-770). Las Vegas: CSREA Press. (TUD)
Thelen, J, Goense, D, & Langendoen, KG . Radio wave propagation in potato fields. In s.n. (Ed.), Proceedings of the
WINMEE, RAWNET and NETCOD 2005 workshops: Measurements, resource allocation and network coding in wireless
networks (pp. 1-5). s.l.: ICST. (TUD)
Thelen, J, Goense, D, & Langendoen, KG . Radio wave propagation in potato fields. In BJA Kröse, HJ Bos, EA Hendriks, &
JWJ Heijnsdijk (Eds.), ASCI 2005 Proceedings of the eleventh annual conference of the Advanced School for Computing
and Imaging (pp. 344-349). Delft: ASCI. (TUD)
Wang, J,Reinders, MJT,Lagendijk, RL, & Pouwelse, JA . Self-organizing distributed collaborative filtering. In G Marchionini, A
Moffat, J Tait, R Baeza-Yates, & N Ziviani (Eds.), Proceedings of the 28th Annual International ACM SIGIR Conference on
Research and Development in Information Retrieval (pp. 659). New York: ACM.
Garbacki, PJ,Epema, DHJ, & Steen, M van . Two-level semantic caches in super-peer networks. In BJA Kröse, HJ Bos, EA
Hendriks, & JWJ Heijnsdijk (Eds.), ASCI 2005 Proceedings of the eleventh annual conference of the Advanced School for
Computing and Imaging (pp. 26-33). Delft: ASCI.
Wang, J,Reinders, MJT,Pouwelse, JA, & Lagendijk, RL . Wi-Fi Walkman: a wireless handhold that shares and recommends
music on peer-to-peer networks. In S Sudharsanan, S Bove, & S Panchanathan (Eds.), Proceedings of SPIE -IS&T
Electronic Imaging 2005 Vol. 5683. Proceedings SPIE (pp. 155-163). Bellingham: SPIE.
Papers in international Journal
Reeuwijk, C van, & Sips, HJ . Adding tuples to Java: a study in lightweight data structures Concurrency and computationpractice & experience, 17(5-6), 423-438.
Haratcherev, IJ,Taal, JR,Langendoen, KG,Lagendijk, RL, & Sips, HJ . Automatic IEEE 802.11 rate control for streaming
applications Wireless communications & mobile computing, 5(4), 421-437.
Halkes, GP, Dam, T van, & Langendoen, KG . Comparing energy-saving MAC protocols for wireless sensor networks Mobile
networks & applications, 10(5), 783-791.
Mors, AW ter,Valk, JM, & Witteveen, C . Complexity of task coordination for non cooperative planning agents. In M
Pechoucek, P Petta, & LZ Varga (Eds.), Multi-agent systems and applications IV Vol. 3690. Lecture notes in artificial
intelligence (pp. 600-603). Berlin: Springer.
Valk, JM,Weerdt, MM de, & Witteveen, C . Coordination in multi-agent with an application in logistics. In I Vlahavas & D
Vrakas (Eds.), Intelligent techniques for planning (pp. 194-224). Hersey: IDEA Group Publishing.
Witteveen, C, & Roos, N . Diagnosis of plan execution and the agent. In U Furbach (Ed.), KI 2005: Advances in artificial
intelligence Vol. 3698. Lecture notes in artificial intelligence (pp. 161-175). Berlin: Springer. (TUD)
Roos, N, & Witteveen, C . Diagnosis of plans and agents. In M Pechoucek, P Petta, & LZ Varga (Eds.), Multi-agent systems
and applications IV Vol. 3690. Lecture notes in computer science (pp. 357-366). Berlin: Springer.
Pouwelse, JA,Garbacki, PJ,Epema, DHJ, & Sips, HJ . The Bittorrent P2P file-sharing system: Measurement and analysis.
Lecture notes in computer science, 3640, 205-216.
Mohamed, HH, & Epema, DHJ . The design and implementation of the KOALA co-allocating grid scheduler. Lecture notes in
computer science, 3470, 640-650.
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Verwer, SE,Weerdt, MM de, & Witteveen, C . Timed automata for behavorial pattern recognition. In K Verbeeck, K Tuyls, A
Nowé, B Manderick, & B Kuijpers (Eds.), BNAIC 2005 - Proceedings of the seventeenth Belgium-Netherlands conference on
artificial intelligence (pp. 291-296). Brussels, Belgium: KVAB.
Garbacki, PJ, Biskupski, B, & Bal, H . Transparent fault tolerence for grid applications. Lecture notes in computer science,
3470, 671-680. Goense, D, Thelen, J, & Langendoen, KG . Wireless sensor networks for precise Phytophthora decision
support. In JV Stafford (Ed.), Precision agriculture '05 (pp. 573-581). Wageningen: Wageningen Academic Publishers.
Mohamed, H.H. and Epema, D.H.J.; The KOALA Grid Scheduler
2002-2005, Java, Linux.
This scheduler has been designed and implemented for scheduling jobs across multicluster systems and grids. It smain
features are its support for co-allocation, i.e., for jobs that can be split up into components across multiple clusters, and its
support for load-balancing across clusters. It has been deployed for general use on the DAS in sept. 2005.
G.P. Halkes, MAC simulator
2004-2005, OMNeT++, Linux
The simulation framework used for our MAC layer publications has been made available for public use in 2004, and was
actively supported in 2005. It currently includes models of four energy-efficient protocols for use in Wireless Sensor
Networks: S-MAC, T-MAC, B-MAC, and LMAC.
Varbanescu, A.L., Sips H.J. and van Gemund A.J.C.; PamSoc 2005-2005, C, Linux PamSoc is a semi-static perforrmance
analysis tool for MPSoC systems. It takes as input a program and a parallel machine description and generates a symbolic
cost model of an application.
2.2.7
Contribution of TUD-me-ce
Arachne
The general goal of the project is to investigate novel processor architectures that enables a ubiquitous (i.e., anywhere
and anytime) and unobtrusive (i.e., without much user intervention) communication environment. In order to achieve this, we
focus on the following (intertwined) research topics:
Arachne network processor
This entails the specification of the Arachne network processor. In a truly ubiquitous communication environment, the
communication devices are not located in a fixed geographical location and therefore may encounter different
communication settings during their utilization. For example, moving from a GSM/UMTS network to a Wi-fi network to a
Bluetooth network. Instead of incorporating a multitude of heterogeneous and application-specific network processors, we
seek to provide a single solution that adapts itself depending on its surroundings in order to lower design complexity and
costs of such devices. Herein, we focus on the design of complex hardware units that are able to perform the required
functions and on the utilization of reconfigurable hardware technologies, e.g. field-programmable gate arrays (FPGAs).
Furthermore, we focus on low-power implementations of the Arachne network processor that are intended to be incorporated
in battery-powered handheld devices. Finally, the research in this project also focus on other communication devices other
than wireless handheld devices as suggested previously. Examples of such devices include wireless base stations, network
routers, network gateways, etc.. Therefore, we investigate the possibility of a single and scalable solution that can be
incorporated in these devices. This means covering bandwidths from several kilobits to several tens of Gigabits.
Internet and protocol processing
This entials the investigation into the functional and temporal requirements of Internet-related applications, such as webbased databases, database mining, content-based processing (e.g., multimedia stream processing), voice-over-IP,
videoconferencing, e-learning. In addition, we investigate the requirements associated with the processing of protocols, e.g.,
IPv4/IPv6, TCP, RTP/RTCP, SIP, etc. and their derivatives that govern and enable the previously mentioned applications on
top of the internet. The research performed entails ranging from the modeling and profiling of applications to modeling of the
Arachne processor to the design of specialized hardware units.
Software and design tools
The research performed entails the development of software tools that allow (faster) modeling and profiling of Internet
applications and the Arachne network processor with the purpose of investigating the attainable performance and power
requirements/consumption. Related research topics include: simulation tools development, benchmarking, application and
processor modeling. In addition, special attention must be paid in the integration of these tools as they provide a valuable
source of information prior to the definition of the Arachne network processor (targeting a specific network environment or
46
application set) or to the actual design of specialized hardware units. Finally, design tools must be developed that
incorporate the earlier determined profiling information.
Molen
The MOLEN proposition is that reconfigurable processors, i.e. processors that adapt (dynamically or statically) their
microarchitecture to fit application "design requirements", are the answer to the processor (embedded or not) hardware
design challenges. To prove the viability of the proposition, we are working on multiple design aspects of (single and multi)
processors on a chip using reconfigurable fabric. More specifically our team is working on the following:
The MOLEN reconfigurable microcoded processor
The main idea for the MOLEN reconfigurable processors is to utilize microcode and custom configured hardware to improve
embedded system computing. The reconfigurable hardware execution of code (ranging from a single instruction to a piece of
application code) is divided into two logical phases. In the first phase the reconfigurable hardware is being configured. In the
second phase the execution of the code is being performed. In both phases, microcode is utilized to perform both the
reconfiguration process and the execution of the code. Frequently utilized microcode resides permanently within the fixed
part of an on-chip storage facility and non-frequently utilized microcode are paged into the pageable part of the same or
another storage facility. The approach is generic, therefore, different applications can utilize the proposed processing
capabilities. Our experimentation thus far has involved multimedia operations. In the multimedia experimentation, we
investigate processing elements that are capable of performing operations and algorithms found in generating, coding, and
displaying multimedia formats, i.e., pictures, video, audio, and graphics. At the current stage, the multimedia processor
architecture has targeted multimedia standards including JPEG, MPEG-1/2, MPEG-4, and H.261. Currently, we consider
graphic operations and power consumption. We have implemented a Molen processor prototype on the Virtex-II Pro FPGA
family from Xilinx Corp. The Virtex-II Pro devices incorporate up to four PowerPC 405 GPP cores, FPGA reconfigurable
fabric hardware, dedicated RAM blocks, and dedicated high-speed I/O blocks. In the future of the project we intend to
consider lossless compression.
Reconfigurable arithmetic and logic processor units
The first basic goal is to speed up scientific (mostly vector based) code. Arithmetic (mostly complex to design in hardware)
units normally are not present in general purpose processor instruction sets. Such operations include matrix multiplication,
sparse matrix operations (such as transpose) etc. They can be implemented in reconfigurable hardware speeding up the
execution of scientific programs. A second goal is to design a router and network related reconfigurable hardware.
Reconfigurable processor units can be added to general purpose processors for domains (such us switches, networks,
packet processing, protocols), that have not been envisioned for the general purpose processor paradigm providing
substantial speed-ups.
Embedded IP execution units
We analyze embedded system computational requirements in order to determine the feasibility of hardwired accelerator units
and propose implementations for such units. We have considered JPEG, MPEG-1/2, MPEG-4, H.261, and lossless
compression algorithms and we have proposed numerous specialized units including DCT/IDCT, sum of absolute differences
(SAD), variable length decoding (VLD), Paeth encoding for portable network graphics (PNG), filters, entropy decoders,
repetitive padding units, saturated arithmetic units, accepted quality function (AQF), color space convertors. For our
experimentation, we have utilized various FPGA technologies and applied the Molen processor framework to the Philips
Trimedia, the IBM's PowerPCs (processors integrated on the Xilinx Virtex-II Pro devices) and the ARM (processors integrated
on the Altera Excalibur devices). We will keep on exploring embedded applications for potential hardwired IP units.
Memory architecture and implementations
Multimedia and embedded processing has specific requirements for memory accesses. For high performance processing, it
is required that the memory is accessed in a rectangular manner implying that to be efficient, mechanisms are needed that
access memory in a two-dimensional manner. We propose mechanisms for media reconfigurable processors utilizing special
addressed memory organizations and an implementation of two-dimensional memory cores that substantially improve the
memory performance of the Molen FPGA implemented processor. In addition, because memory may require a significant
amount of power, we propose a cache organization that reduces the number of off-chip accesses thus decreasing main
memory power consumption of the reconfigurable processor architecture.
Compiler and design space exploration tools
We have defined a programming paradigm that target the Molen reconfigurable microcoded processor engine and we are
developing a backend compiler and a design space exploration toolset. The programming paradigm is based on sequential
consistency. It provides mechanisms for parallel and concurrent hardware execution and it is intended (currently) for single
program execution. In order to conform to the Molen programming paradigm, an existing compiler has been extended to
support the required instruction set and register set extensions. Moreover, a specific mechanism has been developed for
passing parameters/results in the case of parallel executions. The compiler and the design space exploration tools are
developed in the project The Delft Workbench.
47
Low-Power High-Performance Graphics Architectures
We are designing a low-power 2D/3D graphics hardware accelerator for mobile terminals equipped with an ARM processor
core. The purpose of using a graphics accelerator is to move some of the graphics-related computations, in particular the
rasterization, from the CPU to this dedicated hardware device in order to improve the rendering speed for graphics
applications. One important concern for a graphics accelerator meant to be employed in mobile terminals is a low power
consumption figure since the most current graphics accelerators are notorious for their high power consumption. Therefore,
algorithmic- and circuit-level techniques for low-power graphics need to be studied and evaluated.
GraalBench Low-Power Graphics benchmark.
The GraalBench is a 3D graphics benchmark suite suitable for 3D graphics on low-power mobile systems, in particular
mobile phones. These benchmarks were collected to facilitate our studies on low-power 3D graphics accelerators in the
Graal (GRAphics AcceLerator) project. It includes traces of several games as well as virtual reality applications such as 3D
museum guides. Applications were selected on the basis of several criteria such as resolution, polygon count, pixel rate, and
relevance to mobile devices. For example, 3D FPS games or 3D virtual guides were considered relevant while CAD/CAM
applications, such as contained in the Viewperf package, were excluded because it is unlikely that they will be offered on
mobile devices (they often have high polygon count and require high resolution). More information and downloads can be
found in The GraalBench Benchmark Suite.
System on Chip (SoC).
Clustered Torus
The underlining assumption of this research is that entire systems are migrating onto single chips and that a single chip
incorporates numerous heterogeneous IPs. We further assume that the entire system comprises of a network that provides
communications among chiplet IPs (processors). In essence, we consider embedded multiprocessor systems and networks
on a chip (NoC). We believe that for such systems the interconnection networks have to be regular, expendable, and that
they have to provide fast interconnections for some but not all communications between processors. Additionally, networks
have to be reliable and avoid lifelock and deadlocks. In our research, we have been proposing a network topology, denoted
as the clustered torus, having the properties discussed above and we examine the properties, performance, design issues,
and feasibility of such a network.
The Delft Java processor
We have developed a processor which is a parallel multi-threaded engine optimized for the Java language. Since Java
bytecodes are interpreted, the interpretation of the program achieves a performance level that meets or exceeds natively
compiled code. The multi-threaded processor architecture is currently being utilized by Sandbridge Technologies to develop
cost-effective low-power broadband wireless processor technology. The processor, a 3G digital wireless multi-threaded
processor architecture, is intended to meet demands for services such as web browsing, MP3 audio, MPEG-4 video, and
video telephony for handheld devices.
T. Hamalainen, A. D. Pimentel, J. Takala, S. Vassiliadis, Embedded computer systems: architectures, modeling and
simulation, Springer Verlag, pp. 476, July 2005
G.K. Kuzmanov, S. Vassiliadis, J.T.J. Eijndhoven, Hardwired MPEG-4 Repetitive Padding, IEEE Transactions on Multimedia,
pp. 261--268, April 2005, vol. 7, issue 2
M. Sima, S. D. Cotofana, J.T.J. Eijndhoven, S. Vassiliadis, L.J. Visser, IEEE-Compliant IDCT on FPGA-Augmented
TriMedia, Journal of VLSI Signal Processing, pp. 195-212, March 2005, vol. 39, No. 3
G.K. Kuzmanov, G. N. Gaydadjiev, S. Vassiliadis, The Molen Media Processor: Design and Evaluation, Proceedings of the
International Workshop on Application Specific Processors, WASP 2005, pp. 26--33, New York Metropolitan Area, USA,
September 2005
I. Sourdis, D.N. Pnevmatikatos, S. Wong, S. Vassiliadis, A Reconfigurable Perfect-Hashing Scheme for Packet Inspection,
proceedings of 15th International Conference on Field Programmable Logic and Applications (FPL 2005), pp. 644-647,
Tampere, Finland, August 2005
G.N. Gaydadjiev, S. Vassiliadis, Flux Caches: What Are They and Are They Useful?, Proceedings of the 5th International
Workshop on Computer Systems: Architectures, Modelling, and Simulation (SAMOS 2005), pp. 93-102, Samos, Greece,
July 2005, LNCS 3553
48
E. Moscu Panainte, K. Bertels, S. Vassiliadis, Interprocedural Optimization for Dynamic Hardware Configurations,
Proceedings of SAMOS 05, pp. 2-11, Samos, Greece, July 2005, Springer-Verlag Lecture Notes in Computer Science
(LNCS)
C.J. Glossner, S. Dorward, S. Jinturkar, M. Moudgill, E. Hokenek, M. J. Schulte, S. Vassiliadis, Sandbridge Software Tools,
Proceedings of SAMOS 05, pp. 269-278, Samos, Greece, July 2005, Springer-Verlag Lecture Notes in Computer Science
(LNCS)
E. Moscu Panainte, K. Bertels, S. Vassiliadis, Instruction Scheduling for Dynamic Hardware Configurations, Proceedings of
Design, Automation and Test in Europe 2005 (DATE 05), pp. 100-105, Munich, Germany, March 2005
Y. Dou, S. Vassiliadis, G.K. Kuzmanov, G. N. Gaydadjiev, 64-bit Floating-Point FPGA Matrix Multiplication, ACM/SIGDA
Thirteenth International Symposium on Field Programmable Gate Arrays (FPGA 2005), pp. 86--95, Monterey, CA, USA,
February 2005
2.2.8
Contribution of UvA-FdNWI-csa
Microgrids
In CSA we are developing new microprocessor architectures that are completely scalable in area, performance and power.
These are based on a process of code fragmentation, we call microthreads. Each code fragment is managed in the hardware
with minimal and above all scalable structures. Along with the concept of microthreading we are exploring microcontexts and
microgrids in order to provide complete solutions to the problems of the highly concurrent microprocessors we expect to see
in the near future, i.e. 100s of processors in the next generation and perhaps 100,000 by 2020, by which time CMOS will be
at its limit of scaling.
System-on-Chip & SoC Design
Designers of System-on-Chip (SoC) based embedded systems are typically faced with conflicting design requirements
regarding performance, flexibility,, power consumption, and cost. As a result, SoC-based embedded systems often have a
heterogeneous system architecture, consisting of components that range from fully programmable processor cores to fully
dedicated hardware blocks. Programmable processor technology is used for realizing flexibility, for example to support
multiple applications and future extensions, while dedicated hardware is used to optimize designs in time-critical areas and
for power and cost minimization. System-level design should be accompanied by a proper methodology for effective and
efficient design space exploration. Due to the systems' complexity, it is imperative to have good (performance evaluation)
tools for exploring a wide range of design choices, especially during the early design stages where the design space is at its
largest.
External projects
Microgrids
NWO, jaartallen : 2005-2009, EURO 250 k
Microgrids is an NWO project funded under the Glance program. This project investigates a novel approach to microarchitecture that supports massive on-chip concurrency, which is scalable, flexible and amenable to analysis. It has the
potential to provide for the management of on-chip resources (processors etc.) so as to autonomously configure a system for
performance, power dissipation or fault tolerance.
Artemis
STW/Progress,2005-2009, Euro 500K
is a cooperation between the University of Amsterdam, Leiden University, Delft University of Technology and Philips
Research, studies the design of Network-on-Chip (NoC) based MP-SoCs. Our role in this project constitutes of developing a
high-level modeling and simulation framework for system-level design space exploration of these NoC-based MP-SoCs.
Papers in International Journals
A. D. Pimentel, ``The Artemis Workbench for System-level Performance Evaluation of Embedded Systems’’, in the Int.
Journal of Embedded Systems, Vol. 1 (No. 7), 2005.
A. D. Pimentel, C. Erbas, and S. Polstra `À Systematic Approach to Exploring Embedded System Architectures at Multiple
Abstraction Levels’’, in IEEE Transactions on Computers, pp. 99-112, Vol. 55 (No. 2), Feb. 2006, Electronic publication:
December 2005.
K. Bousias, N.M. Hasasneh and C.R. Jesshope, `Ìnstruction- level parallelism through microthreading - a scalable
Approach to chip multiprocessors’’, The Computer Journal, published online in December, 2005.
49
Contributions to International Conference Proceedings
C.R. Jesshope, ``Micro-grids - the exploitation of massive on- chip concurrency’’, pp 203-223 (Invited paper, HPC 2004
Cetraro, June 2004), In Grid Computing: A New Frontier of High Performance Computing, 14, pp. 203-223, (ed. L.
Grandinetti, Elsevier, Amsterdam, 2005).
K. Bousias and C.R. Jesshope, ``The Challenges of Massive On- Chip Concurrency’’, in Proc. of ACSAC, Lecture Notes in
Computer Science, Volume 3740, pp157 – 170, 2005.
I. Bell, N. Hasasneh, and C.R. Jesshope, ``Microgrids and Micro- contexts: Support Structures for Microthread Scheduling
and Synchronisation’’, in Proc. 1st MicroGrid Conference, Amsterdam, July
2005
A. D. Pimentel, `À Case for Visualization-integrated System- level Design Space Exploration’’, in the Proc. of the 5th Int.
Workshop on Embedded Computer Systems: Architectures, MOdeling, and Simulation (SAMOS 2005), pp. 455-464, LNCS,
Samos, Greece, July, 2005.
Books
T. D. Hämäläinen, A. D. Pimentel, J. Takala, and S. Vassiliadis, editors, Proceedings of the 5th Int. Workshop on Embedded
Computer Systems: Architectures, MOdeling, and Simulation (SAMOS 2005) , LNCS 3553, Samos, Greece, July, 2005.
2.3
2.3.1
C: Image and Multimedia Sensing, Processing, Interpretation and Visualisation
Contribution of UG-CS-svcg
3D Morphological shape analysis
We continued work on multi-scale methods based on mathematical morphology to be used in segmentation, classification
and object recognition tasks, in particular morphological hat-transform scale spaces and connected operators. An algorithm
was developed to compute Euclidean skeletons of 3D data sets in linear time by the integer medial axis transform.
The robust method for solving systems of polynomial equations, as developed last year, has been used to analyse
Minkowski-sum based similarity measures of 3D objects. This opens up the way to efficiently calculate this type of similarity
measure.
Surface and volume visualization
In the project ‘Particle systems for image segmentation and visualisation’ work was carried out on a novel, physicallymotivated method for surface reconstruction that can recover smooth surfaces from noisy and sparse data sets, without
using orientation information. The technique involves a new volumetric technique based on regularised-membrane potentials
for aggregating the input sample points and a mesh-smoothing paradigm based on a mass-spring system.
Perception-based visualisation
A common approach for visualising data sets is to map them to images in which distinct data dimensions are mapped to
distinct visual features, such as colour, size and orientation. Many of the end user tasks performed on these images involve
a form of visual search. There is evidence for perceptual dependencies when simultaneously presenting multiple features.
Such dependencies could potentially affect information visualisations that contain combinations of features for encoding
information. Perceptual dependencies in information visualisation were assessed by a complex visual search task. The most
relevant findings are that for low-contrast displays colour and size are features that can be used independently to represent
information, and feature hierarchies are flexible and accurately controllable by manipulating feature contrasts.
Visualisation in functional neuroimaging
A review of recent wavelet denoising techniques for medical ultrasound and for (functional) magnetic resonance images was
completed and potential applications in the clinical investigations of the brain were discussed.
A new approach to the visualisation of time-varying multichannel EEG data was developed, based on an extension of the
parallel coordinate method. The method, referred to as tiled parallel coordinates (TPC), can be applied to an arbitrary
number of time steps, handling the maximum number of channels currently in use. We also designed and carried out an
extensive user evaluation, showing that, for a typical EEG assessment task, data evaluation by the TPC method is faster
than by an existing clinical EEG visualisation method, without loss of information.
50
Gene regulatory network identification and visualization
Further work on the {multiple ontology visualisation and exploration, system was carried out, based upon an existing opensource graph visualisation framework. This framework supports several basic modules for input, graph management,
transformations, metrics, layout, and interactive display, and allows for integrated network visualisation of genomic,
metabolic and proteomic information. A prototype application is under construction, based on the use of open source
components for data input, filtering, layout and network visualisation.
Together with the Molecular Genetics group (RUG) we also redesigned FIVA (Functional Information Viewer and Analyzer)
which is capable of processing information contained in clusters of genes exhibiting similar gene expression patterns,
thereby constructing functional profiles. The new version supports multiple view types, and uses focus and context
techniques. A usability study has been conducted, and results are being analysed.
Computational Geometry and Object Modeling
We introduced envelope surfaces, a new class of tangent continuous surfaces based on finite collections of balls. Our results
generalise earlier work Edelsbrunner on skin surfaces for modelling macromolecules. Envelope surfaces are more flexible
than skin surfaces: they allow for local control with an arbitrary number of degrees of freedom, whereas skin surfaces have
only a single global control parameter.
Earlier work on certified meshing was extended to the context of excursion sets, where a whole family of isosurfaces can be
meshed, with little overhead compared to the cost of meshing a single isosurface. This meshing algorithm is currently being
implemented. We also obtained preliminary results on approximating smooth curves by biarc- and conic splines. In
particular, we derived the complexity (number of elements) of such a spline in terms of the Hausdorff distance between the
curve and the approximating spline.
External projects
Visualization of regulatory gene networks
NWO-CW, 2002-2005, 239 keuro, 1 PhD and 1 Postdoc, part of the project Computational Genomics of Prokaryotes, NWOBMI program (Biomolecular Informatics). Partners: WU, RU, RUG-Molecular Biology, RUG-Computing Science.
Certified Shape Reconstruction
NWO-EW, 2005-2009, 90 kEuro, 1 PhD.
Interactive morphological and wavelet-based volume processing and visualisation
NWO-EW, 2005-2009, 500 kEuro, 2 PhD and 1 Postdoc, part of the NWO program VIEW (Visual Interactive Effective
Worlds).
Pathway and Network Visualisation
Bioinformatics Centre (NBIC), 2005-2008, 175 kEuro (excluding matching of 50% by the University of Groningen), 1 postdoc.
Part of the SPX - Project Integrative Bioinformatics of the BioRange program.
Algorithms for Complex Shapes with certified topology and numerics (ACS)
EU, 2005-2008, 246 kEuro, 1 PhD and 1 postdoc. Vegter is coordinator of this project, in which seven European universities
and research institutes and one industrial partner participate.
Muresan, L., Renken, R., Roerdink, J. B. T. M., and Duifhuis; H. Automated correction of spin-history related motion artefacts
in fMRI: Simulated and phantom data. IEEE Transactions on Biomedical Engineering 52, 8, 2005, 1450–1460.
Roerdink, J. B. T. M.; Morphological pyramids in multiresolution MIP rendering of large volume data: Survey and new results;
Journal of Mathematical Imaging and Vision 22, 2/3, 2005, 143–157.
Jalba, A. C., Wilkinson, M. H. F., Roerdink, J. B. T. M., Bayer, M. M., and Juggins, S.; Automatic diatom identification using
contour analysis by morphological curvature scale spaces. Machine Vision and Applications 16, 4, 2005, 217–228.
H. Bekker, E. P. Braad, B. Goldengorin; Selecting the roots of a small system of polynomial equations by tolerance based
matching, 4th International Workshop on Efficient and Experimental Algorithms, WEA 2005, LNCS 3503, 610-613, SpringerVerlag.
H. Bekker, E. P. Braad, B. Goldengorin; Using bipartite and multidimensional matching to select the roots of a system of
polynomial equations, International Conference on Computational Science and its Applications, ICCSA 2005, LNCS 3483,
397-406, Springer-Verlag.
51
Hesselink, W. H., Visser, M., and Roerdink, J. B. T. M. Euclidean skeletons of 3D data sets in linear time by the integer
medial axis transform. In Mathematical Morphology: 40 Years On (Proc. 7th Intern. Symp. on Mathematical Morphology, April
18-20), C. Ronse, L. Najman, and E. Decenci‘ere, Eds. Springer, Wien, New York, 2005, pp. 259–268.
ten Caat, M., Maurits, N. M., and Roerdink, J. B. T. M. Tiled parallel coordinates for the visualization of time-varying
multichannel EEG data. In Proc. Eurographics – IEEE VGTC Symposium on Visualization, June 1-3, Leeds, United
Kingdom, K. W. Brodlie, D. J. Duke, and K. I. Joy, Eds. The Eurographics Association, 2005, pp. 61–67.
N. G. H. Kruithof and G. Vegter, Meshing skin surfaces with certified topology, Computer Aided Design and Computer
Graphics, Hong Kong, China, pag. 287--292, 2005.
High-lights
Multiscale visualisation based on morphological pyramids
We developed a multiresolution approach based on morphological pyramids for multiscale maximum intensity projection
(MIP) volume rendering, often used in visualisation of medical angiography data, which allows integrated filtering and fast
data exploration (based on reduced pyramid data). Such user interaction may take the form of setting window and level, a
common practice in a medical setting, or rendering only thin slices of data, as in sliding thin slab visualisation. Special care is
required in choosing the morphological operators to ensure that (i) the MIP operation can be carried out in the transformed
domain; (ii) the expand operations are only carried out in the 2D image plane; (iii) detail coefficients can be efficiently coded
(only nonzero voxels should be coded, which may save up to 95% of memory for sparse data). Further improvements are
possible by using morphological connectivity preserving filters in the construction of the pyramid. The best results so far
have been obtained by streaming MIP-splatting, which resorts all detail coefficients in decreasing magnitude and projects
only those coefficients needed to attain a user-defined accuracy, see Fig. 1.
(a)
(b)
(c)
Fig. 1 Multiresolution MIP reconstruction from a 2-level morphological pyramid. (a): full-scale MIP;
(b) level-1 MIP; (c) streaming MIP. The absolute errors are 0.676 for (b) and 0.301 for (c). The fraction of
nonzero detail coefficients taken into account is 3.4% in both cases (from Roerdink, J. B. T. M.;
Morphological pyramids in multiresolution MIP rendering of large volume data: Survey and new results; J. of
Mathematical Imaging and Vision 22, 2/3, 2005, 143–157).
2.3.2
Contribution of TU/e-vis
Information visualization
Our research in information visualization has led to new methods for the visualization of various aspects of software systems,
including dynamic behaviour, state spaces and metrics. New results were achieved in our Virtual Reality track, especially
concerning interaction and modeling to support interaction.
External projects
GraphVis
2001-2005, NWO, 100KE This project aims at the visualization of large graphs, with thousands to millions of nodes and
edges, for applications such as software engineering and web visualization. Solutions are sought in interaction, clustering
and above all, effective visual representations.
SMARTER
2002-2007, NWO, 572 KE The aim of the project is to develop new methods and techniques for the simulation of anisotropic
turbulent transport. These new methods are based on Local Defect Correction (LDC). This project is a collaboration between
four research groups at TU/e. Our contribution concerns the development of new visualization methods.
52
VOLTS
2004-2008, NWO, 315 KE
The aim is to develop new methods to gain insight in large state transition graphs, such as produced when formal methods,
i.e. process algebra, is applied to model dynamic systems. The project is a collaboration with the group Design and Analysis
of Systems at TU/e.
MULTISKEL
2005-2008, NWO, 110KE The aim is to develop new methods for the skeletonization of high-dimensional data-sets.
RECONSTRUCTOR
2005-2008, NWO, 1,290 KE Development of new methods for the analysis and understanding of large software systems.
Collaboration with the Software Engineering group of prof. dr. A. van Deursen, TU Delft.
Doctoral degrees
Ham, F.J.J. van; November 21 2005; Interactive visualization of large graphs.TU Eindhoven, Eindhoven 2005, iv+189 pp.,
ISBN 90-386-0704-0,
Telea, A.C.; An open architecture for visual reverse engineering. K. Khan & Y. Zhang (eds.); Managing Corporate
Information Systems Evolution and Maintenance. Hershey PA, USA, 2005, Idea Group Publishing, pp. 211-227.
Frasincar, F., Telea, A.C. & Houben, G.J.; Adapting Graph Visualization Techniques for the Visualization of RDF Data.
Geroimenko, V. and Chen, C. (eds.); Visualizing the Semantic Web, 2nd edition, Springer, ISBN: 1-85233-976-4, pp. 99-116.
Pranovich, S., Achten, H.H., Vries, B. de, and Wijk, J.J. van; Structural Sketcher: representing and applying well-structured
graphic representations in early design. International Journal of Architectural Computing, volume 3, 2005, (1), pp. 75-92.
Maubach, J. & Telea, A.; The NumLab Numerical Laboratory for Computation and Visualisation. Computing and
Visualisation in Science, volume 8, 2005, 1, pp. 1-17.
Pretorius, A.J.; Visual analysis for ontology engineering. Journal of Visual Languages and Computing, volume 16, 2005, 4,
pp. 359-381.
Rushmeijer, H., Wijk, J.J. van, & Turk, G.; Guest editors' introduction: Special section on IEEE Visualization.
IEEE Transactions on Visualization and Computer Graphics, volume 11, 2005, 4, pp. 353-354.
Broersen, A., & Liere, R. van; Transfer functions for imaging spectroscopy data using principal component analysis.
Eurographics/IEEE VGTC Symposium on Visualization (EuroVis 2005), Leeds, UK, June 1-3, 2005,
In Proceedings Eurographics/IEEE VGTC Symposium on Visualization, D. Fellner & S. Spencer (eds.), Aire-la-Ville,
Switzerland, 2005: Eurographics Association, pp. 117-123.
Broersen, A., Liere, R. van & Heeren, R.M.A. (2005); Comparing three PCA-based Methods for the 3D Visualization of
Imaging Spectroscopy Data. Proceedings Visualization, Imaging, & Image Processing (VIIP 2005), J.J. Villanueva (ed.),
Benidorm, Spain, September 7-9, 2005, IASTED, ACTA Press, pp. 540-545.
Holten, D.H.R., Vliegen, R., & Wijk, J.J. van (2005); Visual realism for the visualization of software metrics.
VISSOFT 2005, Budapest, Hungary, September 25, 2005, Proceedings 3rd IEEE International Workshop on Visualizing
Software for Understanding and Analysis, S. Ducasse & et al. (eds.), IEEE Computer Society, pp. 27-32.
Huizing, C., Kuiper, R., Punter, H.T., & Serebrenik, A.; Looking for stability. DDoPS-05, San Diego CA, USA, June 27-28,
2005, Proceedings of Development and Deployment of Product Software 2005, P. Dey, M. Amin, & S. Brinkkemper (eds.),
2005, pp. 291-304.
Huizing, C., Kuiper, R., Punter, H.T., & Serebrenik, A.; Looking for stability. 6th Net.Object Days, Erfurt, Germany,
September 19-22, 2005B. Proceedings 6th Net.Object Days, Franczyk & et al. (eds.), 2005, pp. 575-585.
Kruszynski, K.J, Liere, R. van & Kaandorp, J. ; Quantifying Differences in Skeletonization Algorithms: A Case Study.
Proceedings Visualization, Imaging, and Image Processing (VIIP 2005), J. J. Villanueva (ed.), Benidorm, Spain, September
7-9, 2005, IASTED, ACTA Press, pp. 666-673.
53
Kok, A. & Liere, R. van; A Multimodal Virtual Reality Interface for VTK. Multimodal Interaction for the Visualization of
Scientific Data, E.V. Zudilova-Seinstra, T. Adriaansen (eds.). Trento, Italia, October 2005, pp 35-42.
Liere, R. van , Kok, A., Martens, J-B, Tienen, M. van; Interacting with Molecular Structures: User Performance versus
System Complexity.
Proceedings IPT / EGVE 2005, In R. Blach, E. Kjems (eds.), Aalborg, Denmark, October 2005, pp. 147-156.
Lommerse, G., Nossin, F., Voinea, S.L., & Telea, A.C.; The Visual Code Navigator: an interactive toolset for source code
investigation. IEEE Information Visualization 2005, Minneapolis MN, USA, October 23-25, 2005, Proceedings IEEE InfoVis
2005, IEEE Computer Society, pp. 24-31.
Middelkoop, R., Huizing, C., Kuiper, R. & Luit, E.; Cooperation-Based Invariants for OO Languages. Proceedings of the
International Workshop on Formal Aspects of Component Software (FACS'05), Luis Barbosa and Zhiming Liu (eds), Macau,
October 24-25, 2005, number 333 in UNU-IIST Reports, P.O.Box 3058, Macau, pp. 85-99.
Moberts, B., Vilanova, A., & Wijk, J.J. van; Evaluation of fiber clustering methods for diffusion tensor imaging.
IEEE Visualization 2005, Minneapolis MN, USA, October 23-28, 2005, Proceedings IEEE Visualization 2005, C. Silva, E.
Gröller, & H. Rushmeier (Eds.), pp. 65-72.
Pretorius, A.J., & Wijk, J.J. van; Multidimensional visualization of transition systems.
9th International Conference on Information Visualisation IV'05, London, UK, July 6-8, 2005, Proceedings 9th International
Conference on Information, IEEE Computer Society, pp. 323-328.
Rhijn, A. van, Liere, R. van & Mulder, J.; An Analysis of Orientation Prediction and Filtering Methods for VR/AR. IEEE Virtual
Reality 2005, Bonn, Germany, March 2005, Proceedings IEEE Virtual Reality 2005, B. Froehlich, S. Julier, H. Takemura
(eds.), 2005, pp. 67—74.
Sillanpää, M., & Telea, A.C. (2005); Demonstration of the SoftVision software visualization framework.
CSMR 2004, Tampere, Finland, March 24-26, 2004, Tools for Software Maintenance and Reengineering (Proceedings 8th
European Conference on Software Maintenance and Reengineering, CSMR 2004), M. Di Penta & M. Harsu (eds.), pp. 88108.
Schindler, E., Kok, A. J.F. & Terken, J.M.B. ; Evaluation of Input Modalities for Interaction Tasks Supporting 3D Object
Manipulation. Proceedings Multimodal Interaction for the Visualization of Scientific Data, E.V. Zudilova-Seinstra & T.
Adriaansen (eds.), Trento, Italia, October 2005, pp. 35-42.
Telea, A.C., & Voinea, S.L.; Interactive visual mechanisms for exploring source code evolution. VISSOFT 2005, Budapest,
Hungary, September 25, 2005, Proceedings 3rd IEEE International Workshop on Visualizing Software for Understanding and
Analysis, S. Ducasse & et al. (eds.), IEEE Computer Society, pp. 52-57.
Termeer, M., Lange, C.F.J., Telea, A.C., & Chaudron, M.R.V.; Visual exploration of combined architectural and metric
information. VISSOFT 2005, Budapest, Hungary, September 25, 2005, Proceedings 3rd IEEE International Workshop on
Visualizing Software for Understanding and Analysis, S. Ducasse & et al. (eds.), IEEE Computer Society, pp. 21-26.
Voinea, S.L., Telea, A.C., & Wijk, J.J. van; CVSscan : visualization of code evolution. SoftVis'05, Saint Louis MO, May 14-15,
2005, Proceedings 2005 ACM Symposium on Software Visualization, New York NY, USA: ACM Press, pp. 47-56.
Voinea, S.L., Telea, A.C., & Chaudron, M.R.V.; Version-centric visualization of code evolution. EuroVis 2005, Leeds, UK,
June 1-3, 2005, Proceedings Eurographics/IEEE VGTC Symposium on Visualization, D. Fellner & S. Spencer (Eds.), Aire-laVille, Switzerland: Eurographics Association, pp. 223-230,331.
Voinea, S.L., & Telea, A.C.; Visual assessment techniques for component-based framework evolution.
Euromicro-SEAA'05, Porto, Portugal, August 30-September 3, 2005, Proceedings of the 31st Euromicro Conference on
Software Engineering and Advanced Applications, pp. 168-179.
Wijk, J.J. van; The value of visualization. IEEE Visualization 2005, Minneapolis MN, USA, October 23-28, 2005, Proceedings
IEEE Visualization 2005, C. Silva, E. Gröller, & H. Rushmeier (eds.), pp. 79-86.
Wijk, J.J. van, & Cohen, A.M.; Visualization of the genus of knots. IEEE Visualization 2005, Minneapolis MN, USA, October
23-28, 2005, Proceedings IEEE Visualization 2005, C. Silva, E. Gröller, & H. Rushmeier (eds.), pp. 567-574).
54
Voinea, L., Telea, A.C., G., Nossin, F.; Visual Code Navigator. 2004-2006 C++, MS Windows The Visual Code Navigator is
an open toolset for software visualization. The tools implement various visual techniques for getting interactive insight into
large software repositories. See http://www.win.tue.nl/~lvoinea/VCN.html
Wijk, J.J. van; SeifertView. 2004-2005, Delphi, MS-Windows. SeifertView enables a user to define and visualize Seifert
surfaces: Oriented surfaces that are bound by a knot or link. See www.win.tue.nl/~vanwijk/seifertview
Collaboration with BioMedical Image Analysis group, TU/e
Moberts, B., Vilanova, A., & Wijk, J.J. van; Evaluation of fiber clustering methods for diffusion tensor imaging. IEEE
Visualization 2005, Minneapolis MN, USA, October 23-28, 2005, Proceedings IEEE Visualization 2005, C. Silva, E. Gröller, &
H. Rushmeier (Eds.), pp. 65-72.
2.3.3
Contribution of TUE-EE-dmes
Video processing: algorithms and architectures
The focus of our video processing research is targeted on high-end consumer applications. The current activities fall into two
categories, format conversion and video enhancement. The emphasis of both research activities is shifting with the start of
new PhD-students.
The format conversion activities have so far been focused on improving the cost/performance ratio, through algorithmarchitecture co-design of a motion estimation/compensation unit for picture rate up-conversion. This year the emphasis will
shift to performance enhancement of the motion estimation unit. The study has led to initial proof that the algorithmarchitecture co-design methodology, for motion estimation, yields up to an order of magnitude reduction in area and power
dissipation compared to mapping of the algorithms to a fixed though flexible architecture. In 2004, the design was extended
to include picture rate up-conversion and in 2005 the algorithm/architecture co-design of an advanced de-interlacing method
based on generalized sampling and directional interpolation was completed. Finally a start has been made extending the
design with an extremely flexible video enhancement module applying structure-controlled LMS-filters that emerged from the
research in the video enhancement area.
The focus of the video enhancement activities shifts from resolution up-conversion, necessary since modern displays have
more pixels than the video signal contains, to the enhancement of compressed video.
The study has led to a thorough benchmarking of the available video-enhancement algorithms, including classification-based
filters and neural networks. Furthermore various innovative algorithms, for de-interlacing, coding artefact reduction and
colour enhancement, resulted from this work. Particularly, the gained insight of classified filters was found to enable
substitution of time-consuming heuristic optimization procedures by classified mixing. The new research, aimed at
compressed video enhancement, continues in this direction and has already resulted in a very effective algorithm capable of
boosting fine details while suppressing coding artefacts. In subjective tests this, purely spatial, method outperformed
competing designs of much higher complexity. An invention disclosure has been submitted and papers are to follow.
External projects
Video Enhancement
2001-2005, Philips research, 180 k€ The purpose of video enhancement is to improve the subjective picture quality.
Conventional focus in this field was mainly on sharpness, contrast, and colour reproduction improvement, as well as on noise
reduction. The purpose of this project is to evaluate what has been achieved in this area, and to propose an optimal
technique of SD (standard-definition video) to HD (high-definition video) conversion.
Design of systems on silicon for video enhancement and format conversion
2002-2006, Philips Research, 180 k€The goal of this research project is the design of a system on silicon for video
enhancement and format conversion, aiming at the joint optimisation of algorithms and architecture for a single chip video
converter/enhancer. Fields of interest are motion estimation and compensation, picture rate conversion, de-interlacing,
resolution enhancement, noise reduction, power optimisation, VLSI design.
Video coding artefact reduction
2005-2009, Philips research, 180 k€ The aim of this project is to gather and evaluate what has been achieved
(benchmarking) in the area of coding artifact reduction and to propose (synthesize) some optimal techniques for coding
artifact reduction, taking into account constraints of implementation in current technologies and keeping in mind the
developments in the area of digitally transmitted video.
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Beric, A.; Haan, G. de; Sethuraman, R.; Meerbergen, J.L. van:An Efficient Picture-Rate Up-Convertor. Journal of VLSI Signal
Processing 2, june 2005.
Peters, H.; Meerbergen, J.L. van; Haan, G. de; Sethuraman, R.; Beric, A.; Meeuwissen, P.; Balakrishnan, S.; Alba Pinto,
C.A.; Kruijtzer, W.; Ernst, F.; Alkadi, G.:Application specific instruction-set processor template for motion estimation in video
applications. IEEE Transactions on Circuits and Systems for Video Techniques 15, nr. 4, 2005, pp. 508-527.
Beric, A.; Haan, G. de; Sethuraman, R.; Meerbergen, J.L. van: Algorithm/Architecture Codesign of the Generalized Sampling
Theorem Based De-Interlacer. Proceedings of IEEE/ISCAS Conference, May 2005, 2005, pp. 2943-2946.
Beric, A.; Sethuraman, R.; Meerbergen, J.L. van; Haan, G. de: Memory-Centric Motion Estimator. Proceedings IEEE
Conference on VLSI Design, January 2005, pp. 816-819.
Ciuhu, C.; Haan, G. de: Motion Estimation on Interlaced Video. Proceedings of SPIE, Image and Video Communications and
Processing, January 2005.
Heesch, F.; Klompenhouwer, M.A.; Haan, G. de: Masking Noise in Up-scaled Video on Large Displays. IEEE Digest of the
ICCE'05, Session 11.3, paper 4, 2005.
Hu, H.; Hofman, M.; Haan, G. de: Content-adaptive neural filters for image interpolation using pixel classification.
Proceedings of SPIE, Applications of Neural Networks and Machine Learning in Image Processing IX, January 2005.
Zhao, M.; Ciuhu, C.; Haan, G. de: Classification based data mixing for hybrid de-interlacing techniques. Proceedings of the
13th European Signal Processing Conference, EUSIPCO 2005. (pdf-file, 348 kB), 2005.
Zhao, M.; Haan, G. de: Content adaptive vertical temporal filtering for de-interlacing. Proceedings of the 9th INternational
Symposium on Consumer Electronics, 2005 ISCE 2005 (pdf-file 493 kB), 2005, pp. 69-73.
Zhao, M.; Haan, G. de: Subjective evaluation of de-interlacing techniques. Proceedings of SPIE, Image and Video
Communications and Processing, January 2005.
Zhao, M; Resolution Up-Conversion
2003 - 2005, C++/Windows XP.
Content-adaptive vertical temporal de-interlacing: De-interlacing of video data using adaptive vertical temporal filters.
Classification based data mixing for hybrid de-interlacing techniques: based on classification and Least Mean Square
filtering, we can achieve better data mixing results for hybrid de-interlacing. Subjective optimal Least Mean Square filtering
for up-scaling: Using the inverse relationship between sharpen and blur, we designed content adaptive up-scaling techniques
with build-in sharpness enhancement, thus improving the perceived up-scaling image quality.
Experimental hardware
Beric, A; Sethuraman, R; A motion compensated picture-rate up-converter
2003 – 2005
This design concerns a VLIW-based ASIP for motion estimation used in picture-rate up-conversion. The ASIP meets lowpower and low-cost requirements apart from providing flexibility for the application domain. It consumes 27 mW and takes an
area of 1.1 mm2 in 0.13 µm technology for delivering motion estimation functionality for standard definition (SD) sequences
at 140fps. The designed hardware was synthesized and tested up to the pre-layout netlist level.
Patent
Haan, G. de: A unit for and method of image scaling. Philips, EP1547378 A1, 29 June 2005.
Haan, G. de: A unit for and method of image conversion. Philips, EP1554874 A1, 20 July 2005.
Haan, G. de: A unit for and method of image conversion. Philips, EP1565878, 24 August 2005.
Haan, G. de: Gamma correction. Philips, EP1570651 A1, 7 September 2005.
Haan, G. de: Method for image scaling. Philips, EP1540593, 15 June 2005.
Haan, G. de; Bellers, E.B.: Chrominance signal interpolation. Philips, US6498609, 24 December 2005.
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Haan, G. de; Biezen, P.W.A.C.; Wittebrood, R.B: Image processing unit with fall-back. Philips, EP1557037, 27 July 2005.
Haan, G. de; Klompenhouwer, M.A.: Anti motion blur display. Philips, US6930676, 16 August 2005.
Haan, G. de; Klompenhouwer, M.A.: Method of and unit for processing images. Philips, US6501446, 31 December 2005.
Haan, G. de; Klompenhouwer, M.A.; Velthoven, L.J.: A unit for and method of sharpness enhancement.
Philips, EP1512120, 9 March 2005.
Haan, G. de; Pelagotti, A.: Problem area location in an image signal. Philips, EP1048170, 11 February 2005.
Haan, G. de; Wittebrood, R.B: Recognizing film and video objects occurring in parallel in single television signal fields.
Philips, US6937655, 30 August 2005.
Klompenhouwer, M.A.; Haan, G. de; Velthoven, L.J.: Unit and method of calculating a sharpened edge. Philips, EP1512120,
9 March 2005.
Riemens, A.K.; Dommisse, A.; Haan, G. de: Recognizing film and video occurring in parallel in television fields. Philips,
EP1574055 A1, 14 September 2005.
Velthoven, L.J.; Klompenhouwer, M.A.; Haan, G. de: Edge dependent motion blur reduction. Philips, EP1509881, 26 January
2005.
Wesenbeeck, J.M.A. van; Haan, G. de; Klompenhouwer, M.A.; Krijn, M.P.C.M.: CRT with enhanced vertical resolution.
Philips, EP1540689, 15 June 2005.
Wittebrood, R.B; Haan, G. de: Unit for and method of estimating a motion vector. Philips, EP1514241, 9 March 2005.
Wittebrood, R.B; Haan, G. de: Unit for and method of estimating a motion vector. Philips, EP1514242, 16 March 2005.
Wittebrood, R.B; Haan, G. de: Image segmentation using template prediction. Philips, EP1565879 A2, 24 August 2005.
2.3.4
Contribution of TUD-mm-ict
Pattern Recognition
A typical human ability is the recognition of patterns in the world around us. It constitutes the basis of each natural science:
the laws of physics, the description of species in biology or the analysis of human behavior; they are all based on seeing
patterns. Also in daily life pattern recognition plays an import role: reading texts, identifying people, retrieving objects or
finding the way in a city. Once patterns are established, learned from some examples or from a teacher, we are able to
classify new objects or phenomena into a class of known patterns.
The study of automatic pattern recognition has two sides, one purely fundamentally scientific and one applied. By trying to
build a system with pattern recognition capabilities more will become clear about the human ability to learn, recognize and
classify. At the same time, systems are constructed that may be applied in various areas of science as well as in many
places in society to assist human decision making.
In our research, both aspects are treated. There are two projects focusing on the foundations of pattern recognition:
representation and generalization, in which new ways of describing objects and learning from examples are studied. In
addition, there are several applied projects focusing on the recognition of spectra. Like images and time signals, spectra
constitute a pattern domain with an unsolved problem: how to represent patterns in their entirety, when only a set of samples
(pixels or bins) is available.
The research makes clear that automatic pattern recognition systems may successfully be applied in several places but that
an understanding of the human ability of recognizing patterns is still in its early days.
Bioinformatics
Knowledge discovery and machine learning play an increasingly important role in biomolecular science, now that micro-array
technology reaches maturity and genomes of different organisms are being published with increasing frequency. As a
consequence, massive amounts of data are being (and will be) produced that contain important facts about the "Book of Life"
of living organisms. These measurements have opened new avenues to discover novel functionalities within cells (e.g.
function of genes and gene pathways).
Although molecular biologists are extremely enthusiastic about these developments, they are confronted with the availability
of enormous amounts of data about a very complex (many genes, hence many parameters) and heterogeneous (many
elements such as genes, proteins metabolites etc.) system. Traditional ways to study biological phenomena in a gene-by-
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gene approach (reductionism) are no longer adequate. Instead, the cell should be studied as a network of complex
interactions. This systems view, coupled with the integration of already available knowledge, defines the core of our
approach to biomolecular knowledge discovery.
External projects
ALL-AGE ("Analysis of gene expression profiles of children with acute lymphomatic leukaemia by bioinformatics")
2004-2008, EUR, 280 k€. The ALL-AGE project is a co-operation with the Department of Immunology of the Erasmus
University Medical Center in Rotterdam. Jointly, we apply, evaluate and develop techniques for the analysis of microarray
data and other molecular measurements. Applications include: basis molecular biology, molecular diagnosis and gene
therapy.
Improving endoscopic detection of lung cancer using autofluorescence spectroscopy analyzed by a neural network
2001-2005, STW, 100k€.This project, a cooperation with the Daniel den Hoed Hospital in Rotterdam, in which we
participated by studying the data-analysis. We found that by combining a set of spectral classifiers, each based on a different
excitation wavelength a significant improvement of the recognition performance may be reached. However, the size of the
dataset collected over the years is still too small for an advanced development of classifiers. The project has been finished
in 2005.
The analysis of spatial structures in hyperspectral images
2003-2007, STW, 470 k€.The construction of an initial toolbox for hyperspectral image recognition was finalized. We are now
focusing on applications in various areas like agriculture, mining, paper production and infra-red imaging for microscopic
particle analysis. On a more fundamental level we study procedures fo the selection of subbands, good for classification.
One-Class Classifiers
2001-2005, NWO 250 k€. In cooperation with some other projects like the characterization of interstitial lung disease and
mineral spectral analysis a set of advanced applications has been studied, resulting in a better understanding of performance
estimation of one-class classifiers. In addition we studied techniques for active and semi-supervised learning. The project
has been finished in 2005 and concluded by a PhD thesis, defended in 2006.
Proximity-based representations for pattern learning
2004-2008, NWO, 370 k€. The essential difference between proximity representations and kernel approached has been
studied and resulted in understanding of the possible advantage of non-Euclidean object representations. Further the
construction of augmented representation spaces and the application for invariant representations has been studied.
Computer-aided detection and characterization of interstitial lung disease
2004-2008, STW, 200 k€.This project started as a cooperation with the Image Science Institute in Utrecht. We intend to
make use of the one-class classifier technique and study the use of spatial data-connectivity for improved recognition.
Mineral spectral analysis
2003-2005, DeBeers, 90 k€ This project aims at a robust spectral recognition of multi-class minerals for changing class
distributions. Extensive experiments have been performed in which many classification techniques have been evaluated.
Unknown priors, novelty detection and changing class distributions are the challenges for this real world application.
ITB, "Innovative therapies for bone recovery"
2004-2007, Senter/Organon, 290 k€. Due to the continuous increase of people's life expectancy, there is an urgent need for
effective therapies for the recovery and prevention of bone loss due to osteoporosis. In this project, the newest
developments in genomics are integrated with the latest techniques in pathway discovery and pattern recognition. This will
lead to a faster and novel approach to discover and functionally characterize genes involved in bone development.
REGNET
"Unravelling the hierarchy of transcriptional regulation in chemostat cultures of Saccharomyces cerevisiae: a bioinformatics
approach", 2004-2008, NGI/Kluyver Centre for Genomics of Industrial Fermentation, 230 k€.The Kluyver Center generates
large transcriptome datasets of Saccharomyces cerevisiae grown under a wide range of carefully defined, industrially
relevant, cultivation conditions in steady-state chemostat cultures. These different environmental conditions lead to widely
differing physiological responses. The general objective of this project is to implement and develop bioinformatics
approaches to unravel the underlying transcriptional regulation networks. Special emphasis will be placed on the hierarchy of
transcriptional regulation, i.e., the quantitative analysis of how the (simultaneous) action of different transcription factors
acting at the same promoter region determine the transcriptional response of a promoter.
Analysis of regulatory networks in Saccharomyces Cerevisiae
2004-2008, NGI/Kluyver Centre for Genomics of Industrial Fermentation, 150k€.
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The overall aim of this project is to investigate genome-wide regulatory circuitry (transcription and signal transduction), by
concurrently developing and performing bioinformatic analyses of various genome-scale data sets: expression microarray
data; chromosome localization microarray data; protein-protein interaction data; high throughout phenotype data; sequence
data as well as data currently stored in databases.
METNET
" Data-driven discovery of metabolic and regulatory network structure", 2004-2008, Delft Research Center Life Science and
Technology, 210 k€.
This project is collaboration with the Bioprocess Technology Group at the TUDelft that studies mathematical techniques to
accurately model metabolic reactions using metabolic control analysis when the structure of networks of such reactions is
assumed to be known. In this project, tools developed for genetic network discovery will be adapted and extended to allow
ab initio metabolic network structure discovery, facilitating detailed modeling by the Bioprocess Technology Group. These
models will subsequently be extended to incorporate regulatory mechanisms at the genomic and proteomic level. Such
models will allow targeted interference at the genomic level to obtain certain desired metabolic behaviour.
BioRange-SP121, “Unifying framework for data-driven pathway discovery”
2004-2009, NBIC-BioRange, 350 k€ Together with the Radboud University Nijmegen, the University Medical Center Utrecht
and the Dutch Cancer institute we study the integration of various genomic sources to arrive at novel pathways. In particular
we look at the development of a unifying framework to integrate this data and at the analysis of insertion sites in retroviral
insertional mutagenesis screens and relate them to onco-genetic events.
BioRange-SP132, “Developing clinical predictors based on high-dimensional genomics data, pathway information
and directed experimentation”
NBIC-BioRange, 350 k€. Together with the Leiden University Medical Center and the Dutch Cancer institute this project
studies data-driven approaches based on genomics data to construct predictors for diagnosis and prognosis in human
disease. We will develop statistical techniques which regulate the gene selection strategy such that it takes particular known
relationships between genes, defining e.g. a particular pathway, into account.
In addition, we explore how predictors based on gene expression data can be augmented with prognostic predictors derived
from proteomics data originating from the same patient series.
BioRange-SPHGL
Bioinformatics, NBIC-BioRange, 450 k€. This project concerns funding by NBIC-BioRange for the chair of Prof. Reinders in
Bioinformatics.
CANCER
"Molecular Classification of Cancer", 2002-2007, NKI, 300 k€. This project is conducted in close collaboration with the Dutch
Cancer Institute (NKI). Central to the program lies the prediction of prognosis and optimal treatment choice for cancer
patients, which is dependent on correct disease classification. Our goal within this program is to perform computational
analysis of all information sources to construct a taxonomy of breast cancer (sub-)types, such that the classes correlate
strongly with survival and response to radio- or chemotherapy.
Doctoral Degrees
Pekalska, E.M.; January 17, 2005 Dissimilarity representations in pattern recognition. Concepts, theory and applications. TU
Delft, Delft 2005, 116 pp., ISBN 90-9019021-X, external project
Books
Pekalska, E.M., Duin, R.P.W.; Dissimilarity representation for pattern recognition: foundations & applications. Singapore,
2005, 636 pp., World Scientific, ISBN 981-256-530-2, Series in Machine Perception and Artificial Intelligence, vol. 64, 1st
edition.
Duin, R.P.W., Tax, D.M.J.; Statistical Pattern Recognition. Chen, C.H., Wang, P.S.P.; Handbook of Pattern Recognition and
Computer Vision.Singapore, 2005, 967 pp., World Scientific, ISBN 981-256-105-6, pp. 3-24, 3rd edition.
Kranenburg, P. van, Backer, E.; Musical Style Recognition – A Quantitative Approach. Chen, C.H., Wang, P.S.P. (eds.);
Handbook of Pattern Recognition and Computer Vision, 3rd ed. Singapore, 2005, 967 pp., World Scientific Press, ISBN 981256-105-6, pp. 583-600.
Bard, M.P.L., Amelink, A., Skurichina, M., Bakker, M. den, Burgers, S.A., Meerbeeck, J.P. van, Duin, R.P.W., Aerts, J.G.J.V.,
Hoogsteden, H.C., Sterenborg, H.J.C.M.; Improving the specificity of fluorescence bronchoscopy for the analysis of
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neoplastic lesions of the bronchial tree by combination with optical spectroscopy: preliminary communication. Lung Cancer,
Elsevier, ISSN 0169-5002, vol. 47, no. 1, pp. 41-47.
Beers, E.H. van, Welsem, T. van, Wessels, L.F.A., Li, Y., Oldenburg, R.A., Devilee, P., Cornelisse, C.J., Verhoef, S.,
Hogervorst, F.B.L., Veer, L.J. van 't, Nederlof, P.M.; Comparative genomic hybridization profiles in human BRCA1 and
BRCA2 breast tumors highlight differential sets of genomic aberrations. Cancer Research, ISSN 0008-5472, vol. 65, no. 3,
pp. 822-827
Dik, W.A., Pike-Overzet, K., Weerkamp, F., Ridder, D. de, Haas, E.F.E. de, Baert, M.R.M., Spek, P. van der, Koster, E.E.L.,
Reinders, M.J.T., Dongen, J.J.M. van, Langerak, A.W., Staal, F.J.T.; New insights on human T cell development by
quantitative T cell receptor gene rearrangement studies and gene expression profiling.
The Journal of Experimental Medicine, Rockefeller University Press, ISSN 0022-1007, vol. 201, no. 11, pp. 1715-1723.
Glas, A.M., Kersten, M.J., Delahaye, L.J.M.J., Witteveen, A.T., Kibbelaar, R.E., Velds, A., Wessels, L.F.A., Joosten, P.,
Kerkhoven, R.M., Bernards, R., Krieken, J.H.J.M. van, Kluin, P.M., Veer, L.J. van 't, Jong, D. de; Gene expression profiling in
follicular lymphoma to assess clinical agressiveness and to guide the choice of treatment. Blood, The American Society of
Hematology, ISSN 0006-4971, vol. 105, no. 1, pp. 301-307.
Loog, M., Ginneken, B. van, Duin, R.P.W.; Dimensionality reduction of image features using the canonical contextual
correlation projection. Pattern Recogntion, Elsevier, ISSN 0167-8655, vol. 38, no. 12, pp. 2409-2418.
Ridder, D. de, Linden, C.E. van der, Schonewille, T., Dik, W.A., Reinders, M.J.T., Dongen, J.J.M. van, Staal, F.J.T.; Purity for
clarity: the need for purification of tumor cells in DNA microarray studies. Leukemia, Nature Publishing Group, ISSN 08876924, vol. 19, no. 4, pp. 618-627.
Roepman, P., Wessels, L.F.A., Kettelarij, N., Kemmeren, P., Miles, A.J., Lijnzaad, P., Tilanus, M.G.J., Koole, R., Hordijk, G.J., Vliet, P.C. van der, Reinders, M.J.T., Slootweg, P.J., Holstege, F.C.P.; An expression profile for diagnosis of lymph node
metastases from primary head and neck squamous cell carcinomas. Nature Genetics, ISSN 1061-4036, vol. 37, no. 2, pp.
182-186.
Vaes, B.L.T., Dechering, K.J., Someren, E.P. van, Hendriks, J.M.A., Ven, C.J.J.M. van de, Feijen, A., Mummery, C.L.,
Reinders, M.J.T., Olijve, W., Zoelen, E.J.J. van, Steegenga, W.T.; Microarray analysis reveals expression regulation of Wnt
antagonists in differentiating osteoblasts.
Bone, Elsevier, ISSN 8756-3282, vol. 36, no. 5, pp. 803-811.
Veenman, C.J., Reinders, M.J.T.; The nearest subclass classifier: a compromise between the nearest meand and nearest
neighbor classifier. IEEE Transactions on Pattern Analysis and Machine Intelligence, IEEE, ISSN 0162-8828, vol. 27, no. 9,
pp. 1417-1429.
Veld, D.C.G. de, Skurichina, M., Witjes, M.J.H., Duin, R.P.W., Sterenborg, H.J.C.M., Roodenburg, J.L.N.; Autofluorescence
and diffuse reflectance spectroscopy for oral oncology. Lasers in Surgery and Medicine, Wiley-Liss, Inc., ISSN 0196-8092,
vol. 36, no. 5, pp. 356-364.
Vliet, M.H. van, Kempen, G.M.P. van, Reinders, M.J.T., Ridder, D. de; Computational estimation of the composition of fat/oil
mixtures containing interesterification from gas and liquid chromatography data.
Journal of the American Oil Chemists' Society, American Oil Chemists' Society, ISSN 0003-021X, vol. 82, no. 10, pp. 707716.
Weigelt, B., Wessels, L.F.A., Bosma, A.J., Glas, A.M., Nuyten, D.S.A., He, Y.D., Dai, H., Peterse, J.L., Veer, L.J. van 't; No
common denominator for breast cancer lymph node metastasis. British Journal of Cancer, Nature Publishing Group, ISSN
0007-0920, vol. 93, no. 8, pp. 924-932.
Wessels, L.F.A., Reinders, M.J.T., Hart, A.A.M., Veenman, C.J., Dai, H., He, Y.D., Veer, L.J. van 't; A protocol for building
and evaluating predictors of disease state based on microarry data. Bioinformatics, Oxford University Press, ISSN 13674803, vol. 21, no. 19, pp. 3755-3762
Zelm, M.C. van, Burg, M. van der, Ridder, D. de, Barendregt, B.H., Haas, E.F.E. de, Reinders, M.J.T., Lankester, A.C.,
Révész, T., Staal, F.J.T., Dongen, J.J.M. van; Ig gene rearrangement steps are initiated in early human precursor B cell
subsets and correlate with specific transcription factor expression. The Journal of Immunology, American Association of
Immunologists, Inc., ISSN 0022-1767, vol. 175, no. 9, pp. 5912-5922.
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Contributions to international conference proceedings)
Dongen, J.J.M. van, Velden, V.H.J. van der, Ridder, D. de, Langerak, A.W., Staal, F.J.T.; Laboratory diagnosis of leukemia:
can we replace current molecular diagnostics by novel flow cytometry? The 10th Congress of the European Hematology
Association, Stockholm, 2-5 Juni 2005, Proceedings of the 10th Congress of the European Hematology Association, pp. 3640.
Duin, R.P.W., Pekalska, E.M.; Open issues in pattern recognition. The 4th International Conference on Computer Recognition
Systems, Wroclaw, 22-23 May 2005, Proceedings of the 4th International Conference on Computer Recognition Systems,
Kurzynski, M., Puchala, E., Wozniak, M., Zolnierek, A. (eds.), Springer Verlag Berlin, ISBN 3-540-25054-9, pp. 27-42.
Juszczak, P., Duin, R.P.W.; Learning from a test set. The 4th International Conference on Computer Recognition Systems,
Wroclaw, 22-23 May 2005, Proceedings of the 4th International Conference on Computer Recognition Systems, Kurzynski,
M., Puchala, E., Wozniak, M., Zolnierek, A. (eds.), Springer Verlag Berlin, ISBN 3-540-25054-9, pp. 203-210.
Landgrebe, T.C.W., Duin, R.P.W.; On Neyman-Pearson optimisation for multiclass classifiers. The Sixteenth Annual
Symposium of the Pattern Recognition Association of South Africa, Langebaan, 23-25 November 2005, Proceedings of the
Sixteenth Annual Symposium of the Pattern Recognition Association of South Africa, Nicolss, F. (ed.), IAPR, ISBN 0-79922264-X, pp. 165-170.
Landgrebe, T.C.W., Paclik, P., Tax, D.M.J., Duin, R.P.W.; Optimising two-stage recognition systems.
The 6th International Workshop Multiple Classifier Systems, Seaside, CA, USA, 13-15 June 2005, Proceedings of the 6th
International Workshop Multiple Classifier Systems / Lecture Notes in Computer Science, vol. 3541, Oza, N.C., Polikar, R.,
Kittler, J., Roli, F. (eds.), Springer Verlag, Berlin, Heidelberg, ISBN 3-540-26306-3, pp. 206-215.
Paclik, P., Duin, R.P.W.; Designing multi-modal classifiers of spectra: a study on industrial sorting application.
The 2nd International Spectral Imaging Workshop, Austria, September 2005, Proceedings of the 2nd International Spectral
Imaging Workshop, Leitner, R. (ed.), Austrian Computer Society, ISBN 3-85403-194-7, pp. 19-25.
Paclik, P., Landgrebe, T.C.W., Tax, D.M.J., Duin, R.P.W.; On deriving the second-stage training set for trainable combiners.
The 6th International Workshop Multiple Classifier Systems, Seaside, CA, USA, 13-15 June 2005, Proceedings of the 6th
International Workshop Multiple Classifier Systems / Lecture Notes in Computer Science, vol. 3541, Oza, N.C., Polikar, R.,
Kittler, J., Roli, F. (eds.), Springer Verlag, Berlin, Heidelberg, ISBN 3-540-26306-3, pp. 136-146
Paclik, P., Tax, D.M.J., Verzakov, S., Duin, R.P.W.; Simplifying the model-based classifiers for multi-modal problems in
classification of spectra. 33-38.
Paclik, P., Verzakov, S., Duin, R.P.W.; Improving the maximum-likelihood co-occurrence classifier: a study on classification
of inhomogeneous rock images. The 14th Scandinavian Conference on Image Analysis, Joensuu, Finland, 19-22 June 2006,
Proceedings of the 14th Scandinavian Conference on Image Analysis / Lecture Notes in Computer Science, vol. 3540,
Kalviainen, H., Parkinen, J., Kaarna, A. (eds.), Springer Verlag Berlin Heidelberg 2005, ISBN 3-540-26161-3, pp. 998-1008.
Pekalska, E.M, Harol, A., Lai, C., Duin, R.P.W.; Pairwise selection of features and prototypes. The 4th International
Conference on Computer Recognition Systems, Wroclaw, 22-23 May 2005, Proceedings of the 4th International Conference
on Computer Recognition Systems, Kurzynski, M., Puchala, E., Wozniak, M., Zolnierek, A. (eds.), Springer Verlag Berlin,
ISBN 3-540-25054-9, pp. 271-278.
Pekalska, E.M., Duin, R.P.W.; The use of dissimilarities for object recognition. The EOS Conference on Industrial Imaging
and Machine Vision, Munich, 13-15 June 2005, Proceedings of the EOS Conference on Industrial Imaging and Machine
Vision, SPIE, ISBN 3-00-0163161-1, pp. 50-53.
Skurichina, M., Duin, R.P.W.; Combining feature subsets in feature selection. The 6th International Workshop Multiple
Classifier Systems, Seaside, CA, USA, 13-15 June 2005, Proceedings of the 6th International Workshop Multiple Classifier
Systems / Lecture Notes in Computer Science, vol. 3541, Oza, N.C., Polikar, R., Kittler, J., Roli, F. (eds.), Springer Verlag,
Berlin, Heidelberg, ISBN 3-540-26306-3, pp. 165-175.
Tax, D.M.J., Duin, R.P.W.; Characterizing one-class datasets. The Sixteenth Annual Symposium of the Pattern Recognition
Association of South Africa, Langebaan, 23-25 November 2005, Proceedings of the Sixteenth Annual Symposium of the
Pattern Recognition Association of South Africa, Nicolss, F. (ed.), IAPR, ISBN 0-7992-2264-X, pp. 21-26.
Veenman, C.J., Tax, D.M.J.; A weighted nearest mean classifier for sparse subspaces. Proceedings of the Conference on
Computer Vision and Pattern Recognition, San Diego, CA, USA, 20-26 July 2006, Proceedings of he Conference on
61
Computer Vision and Pattern Recognition, Schmid, C., Soatto, S., Tomasi, C. (eds.), IEEE Computer Society, pp. 6.
Verzakov, S., Paclik, P., Duin, R.P.W.; The tangent kernel approach to illumination-robust texture classification.
The 14th Scandinavian Conference on Image Analysis, Joensuu, Finland, 19-22 June 2006, Proceedings of the 14th
Scandinavian Conference on Image Analysis / Lecture Notes in Computer Science, vol. 3540, Kalviainen, H., Parkinen, J.,
Kaarna, A. (eds.), Springer Verlag Berlin Heidelberg 2005, ISBN 3-540-26161-3, pp. 1009-1016.
Veenman, C.J., Reinders, M.J.T.; The nearest subclass classifier: a compromise between the nearest meand and nearest
neighbor classifier. IEEE Transactions on Pattern Analysis and Machine Intelligence, IEEE, ISSN 0162-8828, vol. 27, no. 9,
pp. 1417-1429.
Veenman, C.J., Tax, D.M.J.; A weighted nearest mean classifier for sparse subspaces. Proceedings of the Conference on
Computer Vision and Pattern Recognition, San Diego, CA, USA, 20-26 July 2006, Proceedings of he Conference on
Computer Vision and Pattern Recognition, Schmid, C., Soatto, S., Tomasi, C. (eds.), IEEE Computer Society, pp. 6.
2.3.5
Contribution of TUE-BT-bmia
Multi-scale computer vision
Analysis and exploitation of the deep (i.e. over scale) structure of images. This is biologically inspired, fundamental research
into singularities and toppoints in images, to come to a hierarchical representation. A NWO VICI grant was rewarded to dr.
Luc Florack (see highlights below). A new class of multi-scale image structure (α-scale-spaces) has been developed.
Methods have been designed to exploit the extracted toppoints for image retrieval, and to efficiently reconstruct the image
from the toppoints, using new methods based on inner products of Sobolev type. Together with Oce BV we develop a
toppoint-based document analysis system for the IOP project “Intelligent Scanners”.
Perceptual grouping and contect operators. This biologically inspired research focuses on the exploitation of the multi-scale
orientation structure of images. A new class of invertible orientation wavelets has been developed, as well as new theories
for stochastic completion fields and efficient steerable tensor voting, with applications for the detection of dim elongated
structures (contours, catheters, bloodvessels, electrodes) in images. In collaboration with Philips we improved the detection
of cardiac electro-physiology catheters at low-dose fluoroscopy.
Diffusion tensor imaging analysis and 3D visualization
3D visualization techniques for MR diffusion tensor imaging (DTI) data have been investigated in an interactive setting, in
close collaboration with the TUE Dept. of Computing Science. Clinical studies focus on neonatal brain fibre development,
muscle fibre orientations in the heart and skeletal muscle, and the extraction of grouped bundles in DTI. We started
programming on modern GPU graphics cards. A NWO VENI grant was rewarded to dr. Anna Vilanova (see highlights
below).
Methods were developed to automatically extract transfer functions from the data itself, i.e. from LH histograms (fig. 2).
Illustrative rendering techniques have been developed for medical 3D volume datasets, in the styleof drawing in
classicalanatomy books (fig. 5).
Fig. 2. CT of a tooth using a transfer function based on
the LH Histogram. The dentin-air (ochre) and enamel-air
(white) boundaries are set to be semitransparent to reveal
the inner boundaries. Note that part of the pulp-dentine
boundary (red) is identical with the ochre boundary
[Sereda et al. 2005].
http://www.bmi2.bmt.tue.nl/imageanalysis/Research/Projects/20010901Visualization/index.html
Clinical image analysis & applications
This research theme is in close collaboration with Philips Medical Systems, Best.
Automated detection of pulmonary emboli in spiral 3D CT acquisitions of the lung. A computer-aided diagnosis system is
developed, based on second order shape and intensity features. A detailed analysis was carried out on the dislocation of
highly curved surfaces such as of small bloodvessels.
62
Segmentation of short-axis cardiac MR using active contours.
Geometry determination, simulations and motion predictions of dynamic vessel wall behavior in abdominal aortic aneurysms
(fig. 3).
We collaborate with the Medical Imaging and Computer Aided Diagnosis group of the Catholic University Nijmegen on
mammographic image analysis (student exchanges).
Fig. 3: Left: Segmentation of an abdominal aortic aneurysm. Right: Calculation of the displacement (right, mm),
VonMises strain (middle), Von Mises stress (kPa, right). [De Putter et al., 2005]
Molecular Imaging of Ischemic Heart Disease
In 2004 a major BSIK grant “Molecular Imaging of Ischemic Heart Disease” was rewarded to Univ. of Maastricht, TU/e,
Philips and Organon. The BMIA group participates in the visualization of multi-spectal and tensor-based image data,
classification of atherosclerotic plaque from multispectral MRI data, and the quantitative analysis of heart motion (multi-scale
optic flow).
Neurosurgical navigation
In 2005 the Dept.of Neurosurgery at the Maastricht University Hospital acquired the first open low-field (0.15 Tesla) intraoperative MRI in the Netherlands. We collaborate with projects focused on the nonlinear warping of pre-operative MRI and
CT data onto the intra-operative data, the integrated and interactive 3D visualization of DTI, fMRI and atlas data, and the
optimization of image quality. These projects are carried out in collaboration with Medtronic Inc.
Fig. 4. So-called toppoints of an image, defined as singularity
points in the multi-scale structure, can efficiently be exploited for
image-based content retrieval, i.e. subscene retrieval from a
complex scene. The interest points (white) of a query object
(lower right) and a scene containing two rotated, scaled and
occluded versions of the object, are succesfully found. Interest
points that do not match are shown in grey. [Platel,
Balmashnova et al., 2005]
The development of a Mathematica software library for rapid symbolic and numerical prototyping, ‘MathVisionTools’
A general Import format to deal with a wide spectrum of image formats, such as DICOM 3.0, FDF MRI data, 3D US data etc.;
A symbolic and numerical generalized and speed-optimized toolbox for doing high order differential geometry on multidimensional images;
A library of advanced image analysis functions.
63
Fig. 5. Illustrative Volume Rendering: Crosshatching using a
smoothed direction field visualised with oriented "X" and "-" glyphs.
This project focuses on applying techniques from illustrative
rendering to (medical) volume datasets. In many cases, illustrative
methods can create a clearer image than photorealistic methods,
by leaving out unimportant details and emphasising important
features using simple illustration primitives like points and lines
[MSc project of Stef Busking, BME].
http://www.bmi2.bmt.tue.nl/imageanalysis/Research/Projects/20010901-Visualization/index.html
External projects
The Problem of Scale in Biomedical Image Analysis
VICI grant of 1.25 M€ rewarded to dr. Luc Florack, dossier number NWO: 016.053.605, allocated on 01-01-2005. See the
abstract in the description of the end of this report.
Deep Structure and Singularities in Computer Vision.
Starting date: 1 October 2002
Duration: 36 months
Funding: European Community, 5th framework.
Description: The group TUE-BMIA participates in an EU consortium (partners see below), whose overall objective is to
develop sophisticated representations of images and shapes by merging principles and methods from 1) scale space theory,
2) singularity theory, and 3) algorithmics, and to create effective algorithms for solving computer vision tasks on the basis of
these. URL: http://www.itu.dk/English/research/innovation/projects/DSSCV/
Budget total project: 1.5 M€. Partners:
• IT University of Copenhagen (IT-C), Image Group, Department of Innovation
• IT University of Copenhagen (IT-C), Algorithm Group, Theory Department
• Technical University of Eindhoven (TU/e), BME - Biomedical Image Analysis
• University of Liverpool (LU), Department of Mathematical Sciences
• University of Copenhagen, 3D Lab (3D Lab), School of Dentistry
Perceptual Grouping
Period: Sept 2001 – Sep 2005 Funding: STW-SNN (1 PhD student) and TUE-BMT (1 PhD student) The objective of this
project is to develop robust methods for segmenting contours in noisy images, inspired by the mechanisms recognized in
human front-end vision. The focus is in particular on the development of new methods to understand the multi-scale nature
of grouping perceptually equivalent elements, such as edge elements and textural features. Recently a new class of
steerable wavelet orientation kernels is discovered (‘invertible orientation bundle’) with interesting properties for feature
linking.
Hemodyn
Period: September 2002 – September 2006 Funding: Philips Medical Systems (1 PhD student) The prediction of the chance
of rupture for the abdominal aorta is calculated by cardiovascular flow calculations. The data are specific for each patient,
and derived from high resolution CT scans of the patient.
Advanced methods in volume visualization
Period: September 2002 – September 2006 Funding: Philips Medical Systems (2 PhD students) The high volumes of data
both from volume-CT and new MRI 3D fast scanning protocols need for fast and efficient 3D volume presentations, as an
effective form of data compression and communication with the referring physician and the surgeon. New algorithms are
designed in the PMS Easy-Vision environment, particularly focusing on being able to cope with rapid answers and flexibility
towards new questions of users.
64
Doctoral degrees
2005: Duits, R; Perceptual Organization in Image Analysis: a mathematical approach based on scale, orientation and
curvature. TU Eindhoven, Eindhoven 2005, xiii+256 pp.ISBN 90-386-2747-5. Project funded by STW, project 4496
M.A. van Almsick, R. Duits, E.M. Franken, B.M. ter Haar Romeny, From Stochastic Completion Fields to Tensor Voting ,
Lecture notes in computer science, 3753, 124-134, (2005)
M.A. van Almsick, R. Duits, E.M. Franken, B.M. ter Haar Romeny, From Stochastic Completion Fields to Tensor Voting,
E. Angelié, P.J.H. de Koning, M.G. Danilouchkine, H.C. van Assen, G. Koning, R.J. van der Geest, J.H.C. Reiber, Optimizing
the automatic segmentation of the left ventricle in magnetic resonance images, Med. Phys., 32(2), 369-375, (2005)
E. Balmachnova, L.M.J. Florack, B. Platel, F.M.W. Kanters, B.M. ter Haar Romeny, Stability of Top-Points in Scale Space,
H. Bouma, A. Vilanova, L.J. van Vliet, F.A. Gerritsen, Correction for the Dislocation of Curved Surfaces caused by the PSF in
2D and 3D CT Images, PAMI, 27(9), 1501-1507, (2005)
R. Duits, F.M.W. Kanters, L.M.J. Florack, B.M. ter Haar Romeny, A Comparison of the Deep Structure of ¨α-Scale Spaces,
R. Duits, B.J. Janssen, F.M.W. Kanters, L.M.J. Florack, Linear Image Reconstruction from a sparse set of alpha scale space
features by means of inner products of Sobolev type, Lecture notes in computer science, 3753, 96-111, (2005)
R. Duits, M.A. van Almsick, M. Duits, R. Duits, E.M. Franken, Invertible Orientation Scores as an Application of Generalized
Wavelet Theory, Lecture notes in computer science, 15(2), 101-140, (2005)
M. Felsberg, R. Duits, L.M.J. Florack, The Monogenic Scale Space on a Rectangular Domain and its Features, IJCV,
64(2/3), 187-201, (2005)
G.L.T.F. Hautvast, S. Lobregt, M. Breeuwer, A. Vilanova, F.A. Gerritsen, Automatic Contour Detection in Short-Axis Cardiac
Cine MR Data , Journal of Cardiovascular Magnetic Resonance, 7(1), 323-324, (2005)
A.M. Heemskerk, G.J. Strijkers (contact), A. Vilanova, M.R. Drost, K. Nicolay, Determination of mouse skeletal muscle
architecture using three dimensional diffusion tensor imaging, Magn Reson Med, 53(6), 1333-1340, (2005)
B.J. Janssen, F.M.W. Kanters, R. Duits, L.M.J. Florack, B.M. ter Haar Romeny, A Linear Image Reconstruction Framework
Based on Sobolev Type Inner Products, Lecture notes in computer science, 3459, 85-95, (2005)
F.M.W. Kanters, M. Lillholm, R. Duits, B.J.P. Jansen, B. Platel, L.M.J. Florack, B.M. ter Haar Romeny, On Image
Reconstruction from Multiscale Top Points, Lecture notes in computer science, 3459, 431-439, (2005)
B. Platel, M.. Fatih Demirci, A. Shokoufandeh, L.M.J. Florack, F.M.W. Kanters, B.M. ter Haar Romeny, S. Dickinson, Discrete
Representation of Top Points via Scale Space Tessellation, Lecture notes in computer science, 3459, 73-80, (2005)
B. Platel, E. Balmachnova, L.M.J. Florack, F.M.W. Kanters, B.M. ter Haar Romeny, Using Top-Points as Interest Points for
Image Matching, Lecture notes in computer science, 3753, 211-222, (2005)
S. de Putter, M. Breeuwer, U. Kose, et al., F.N. van de Vosse, F.A. Gerritsen, Automatic determination of the dynamic
geometry of abdominal aortic aneurysm from MR with application to wall stress simulations, ICS, 1281, 339-344, (2005)
H.C. van Assen, M.G. Danilouchkine, A.F. Frangi, S. Ordás, J.J.M. Westenberg, J.H.C. Reiber, B.P.F. Lelieveldt, SPASM:
Segmentation of Sparse and Arbitrarily Oriented Cardiac MRI Data using a 3D-ASM, in FIMH 2005. In: Lecture Notes in
Computer Science; Editors: A.F. Frangi, P. Radeva, A. Santos, and M. Hernandez, Barcelona, Spain, vol. 3504: 33-43,
(2005)
H.L.T. de Bliek, S. Lobregt, K. Visser, F.A. Gerritsen, Fast and Easy Whole-Heart MRA Segmentation and Visualization, in
Proceedings of the 8th Annual Scientific Meeting of the SCMR, 21-23 January 2005, San Francisco, United States, 309-311,
(2005)
65
H.L.T. de Bliek, S. Lobregt, K. Visser, F.A. Gerritsen, Fast and easy whole-heart MRA segmentation and visualization, in
Proceedings CARS 2005, International Congress Series, Berlin, Germany, 1270, (2005)
M.G. Danilouchkine, J.J.M. Westenberg, H.C. van Assen, J.H.C. Reiber, B.P.F. Lelieveldt, 3D Model-Based Approach to
Lung Registration and Prediction of Respiratory Cardiac Motion, in MICCAI 2005. In: Lecture Notes in Computer Science;
Editors: J. Duncan and G. Gerig, Palm Springs, United States, vol. 3750: 951-959, (2005)
L.M.J. Florack, Deep Structure from a Geometric Point of View, in Deep Structure, Singularities, and Computer Vision: Vol.
3753, Lecture Notes in Computer Science; Editors: O. Fogh Olsen, L. M. J. Florack and A. Kuijper, Maastricht, Netherlands,
135-145, (2005)
E.M. Franken, M.A. van Almsick, P.M.J. Rongen, L.M.J. Florack, B.M. ter Haar Romeny, Steerable Tensor Voting, in ASCI
Conference 2005; Heijen, Netherlands, 65-72, (2005)
B.M. ter Haar Romeny, Biomedical Image Analysis, in Proc. International Mathematica Symposium 2005; Editors: P. Abbott,
Perth, Australia, 45-85, (2005)
B.M. ter Haar Romeny, M.A. van Almsick, Edge Preserving Smoothing with Euclidean Shortening flow, in Proc.International
Mathematica Symposium 2005; Editors: P. Abbott, Perth, Australia, 361-368, (2005)
B.M. ter Haar Romeny, Dither Removal, in Proc. International Mathematica Symposium 2005; Editors: P.Abbott, Perth,
Australia, 285-299, (2005)
B.M. ter Haar Romeny, Biologically inspired multi-scale image analysis, in Proc. 4th Dutch Endo-Neuro-Psycho Meeting;
Editors: H. Pijl, S. van Dam, B. Ellenbroek, M. van Turenhout, Doorwerth, Netherlands, 293, (2005)
G.L.T.F. Hautvast, M. Breeuwer, S. Lobregt, A. Vilanova, F.A. Gerritsen, Automatic cardiac contour propagation in short axis
cardiac MR images, in CARS; International Conference Series - Elsevier, Berlin, Germany, 351--356, (2005)
M. Mlejnek, P. Ermes, A. Vilanova, R. van der Rijt, H. van den Bosch, F.A. Gerritsen, E. Gröller, Profile flags: A novel
metaphor for probing of T2 maps, in IEEE Visualization; Minneapolis, United States, 599-606, (2005)
B. Moberts, A. Vilanova, J.J. van Wijk, Evaluation of fiber clustering methods for diffusion tensor imaging, in IEEE
Visualization; Minneapolis, United States, 65-72, (2005)
S. Ordás, H.C. van Assen, J. Puente, B.P.F. Lelieveldt, A.F. Frangi, Parametric Optimization of a Model-Based
Segmentation Algorithm for Cardiac MR Image Analysis: a Grid-Computing Approach, in From Grid to Healthgrid,
Proceedings of Healthgrid 2005. Studies in health technology and informatics; Oxford, United Kingdom, vol 112: 146-156,
(2005)
S. Ordás, H.C. van Assen, L. Boisrobert, M. Laucelli, J. Puente, B.P.F. Lelieveldt, A.F. Frangi, Statistical Modeling and
Segmentation in Cardiac MRI using a Grid Computing Approach, in European Grid Conference 2005. In: Lecture Notes in
Computer Science; Editors: P.M.A. Sloot, A.G. Hoekstra, T. Priol, A. Reinefeld, and M. Brubak, Amsterdam, Netherlands,
vol. 3470: 6-15, (2005)
K.S.P. Steenstrup Pedersen, R. Duits, M. Nielsen, On Alpha Kernels, Levy Processes, and Natural Image Statistics, in Scale
Space and PDE Methods in Computer Vision; Editors: Kimmel, Sochen, Weickert, Hofgeismar, Germany, 468-479, (2005)
J.F. Peters, S.E. Grigorescu, R. Truyen, F.A. Gerritsen, A.H. de Vries , R.E. van Gelder, P. Rogella, Robust automasted
polyp detection for low-dose and normal-dise virtual colonoscopy, in Proceedings CARS 2005, International Congress Series
1281, Berlin, Germany, 1146-1150, (2005)
B. Platel, E. Balmachnova, L.M.J. Florack, F.M.W. Kanters, B.M. ter Haar Romeny, Using Top-Points as Interest Points For
Image Matching, in Deep Structure, Singularities, and Computer Vision; Editors: O. Fogh Olsen, L. M. J. Florack and A.
Kuijper, Maastricht, Netherlands, 211-222, (2005)
Contribution to Books
Fogh Olsen, L.M.J. Florack, A. Kuijper, Deep Structure, Singularities, and Computer Vision. First International Workshop,
DSSCV 2005, Maastricht, The Netherlands, June 9-10 2005. In: Lecture Notes in Computer Science, vol. 3753., SpringerVerlag, ISBN 3-540-29836-3 (2005)
66
B.P.F. Lelieveldt, A.F. Frangi, S.C. Mitchell, H.C. van Assen, S. Ordás, J.H.C. Reiber, M. Sonka, 3D Active Shape and
Appearance Models in Cardiac Image Analysis, in Mathematical Models in Computer Vision: The Handbook; Editors: N.
Paragios, Y. Chen, O. Faugeras, 471-485, Springer, Book Chapter, ISBN 0387263713 (2005)
A. Vilanova, S. Zhang, G. Kindlmann, D. Laidlaw, An Introduction to Visualization of Diffusion Tensor Imaging and its
Applications, in Visualization and Image Processing of Tensor Fields, 121-153, Springer Verlag, Book Chapter, ISBN 3-54025032-8 (2005)
Technical reports:
R. Duits, M.A. van Almsick, The Explicit Solutions of Linear Left Invariant 2nd order evolution equations on the 2D-Euclidean
Motion Group, 1-37, CASA-report 05-43, Internal Report ISSN 0926-4507 (2005)
E.M. Franken, Context-Enhanced Detection of Electrophysiology Catheters in Noisy Fluoroscopy Images, Internal BMIA
Report (2005)
Highlights
The highlights in 2005 were the reward of the NWO VICI grant to dr. Luc Florack, the NWO VENI grant to dr. Anna Vilanova
and the Cum Laude PhD of the first promovendus of our group, dr.ir. Remco Duits.
VENI: dr.Luc Florack
Title: The Problem of Scale in Biomedical Image Analysis.
Summary:Improving capabilities and resolving power of medical imaging devices, the sheer number of acquisitions (a
modern hospital produces tens of terabytes of image data per year), and their complex nature make a careful diagnosis by
visual inspection cumbersome or even prohibitive. Growing expectations from society for better diagnoses (one third of a
modern hospital's budget is dedicated to imaging) and the desire for elaborate precautionary screenings, e.g. for lung,
prostate, breast and colon cancer, further aggravate the problem. Biomedical image analysis may come at rescue.
Biomedical image analysis is intended to assist radiologists (CAD = Computer-Aided Diagnosis), surgeons (image guided
intervention), and scientists in interpreting complex image data. The capability of a (trained) human expert to visually
interpret the data (if suitably presented) is without parallel. Indeed, image analysis systems outperforming human visual
expertise are exceptionally rare. The dif culty in designing such systems lies in the fact that image analysis is a notoriously
hard problem, for two reasons:
1. Specifc visual interpretation tasks are hard to translate into operational terms needed for algorithmic design.
2. Local image values depend on discretization and quantization details, but relevant information does not.
The second problem is a generic one, common to all images regardless of task. It compels us to abstract from pixel details
and, a fortiori, to introduce an a priori free scale (= inverse resolution) parameter to replace the irrelevant grid constant. Timepolished methodologies that account for scale explicitly are, among others, scale space theory,
wavelet theory and mathematical morphology. In virtually all other generic paradigms scale enters in disguise, e.g. in
statistical techniques. The generic problem can thus aptly be rephrased as the problem of scale. I intend to solve the
problem of scale with a multidisciplinary team by
o unfication, extension, and application of scale paradigms, and
o biomimicking, i.e. simulating human visual expertise.
I will provide proof of concept in the form of specfic multi-scale biomedical image analysis algorithms, inspired by models of
the visual brain from neurophysiology and psychophysics.
VENI: Dr. A. (Anna) Vilanova í Bartrolí
Title: Visualization of global tensor information for diffusion tensor imaging
Summary: During random diffusion driven displacements, molecules follow tissue structure at microscopic scale. Diffusion
Tensor Imaging (DTI) is a recent magnetic resonance (MR) acquisition technique that measures water diffusion. This
technique allows to visualize structures at a scale well beyond the usual 3D medical imaging scanner resolution. Diffusion is
represented by a positive symmetric tensor of second order. Visualizing high-dimensional data is a challenging problem.
Several techniques have been presented in the last years to visualize tensor fields. However, these techniques either require
a simplification to a scalar or to a vector field; or they merely show local information (i.e.,at isolated points, but no
neighborhood interactions). The goal of this proposal is research and development of visualization techniques for secondorder tensor fields (specifically, for DTI) which reveal the complex spatial relationships of tensors (i.e., global information).
The success of this research should provide and improve visualization and image processing techniques for tensor data.
These techniques will ultimately help scientists and physicians to obtain a better understanding of the complex information of
tensor fields.
CUM LAUDE PhD defence:
Remco Duits: Perceptual Organization in Image Analysis: a mathematical approach based on scale, orientation and
curvature. TU Eindhoven, Eindhoven 2005, xiii+256 pp.
ISBN 90-386-2747-5. Project funded by STW, project 4496. September 15, 2005.
67
2.3.6
Contribution of TUD-TNW-tn-qi
Multidimensional Image Analysis
We have continued our efforts in developing novel strategies for the processing, analysis and interpretation of multidimensional images, including time-series, color images and hyper-spectral images. The work focuses on the detection and
subsequent characterization of geometric image structures rather than specific intensity patterns. This approach yields
generic tools for image description that can be applied in a wide variety of applications. The methods are largely independent
of the physical imaging technique used or the intrinsic image resolution. The theoretical component in this work has focused
on
· Interactive 3D segmentation using connected orthogonal contours
· Model based segmentation of material mixtures near boundaries using an analytical scale-invariant model for the relation
between intensity and gradient magnitude.
· Model based segmentation of three-material mixtures near generalized T-junctions.
· Level set PDE’s for modeling single-curved surfaces.
· Segmentation and size measurements of bumps.
· Improved wave-front modeling for fast marching.
· Decomposition of the structure tensor near multi-model neighborhoods.
· Quantitative evaluation of dynamic superresolution methods.
· Characterization of pore spaces and network structures in tablets.
· Motion and flow analysis of liquid flow in micro-machined nanoliter wells.
· Design of orientation selective filters for lines, planes, edges in 3D space.
· An addressable multi-resolution sampling grid for 3D orientation.
· Dynamic super-resolution in image sequences based on adaptive (scale, orientation and curvature) data fusion of
registered local image data.
· Partial volume effects estimation in 3-D CT based on density and gradient trajectories.
· Computer aided diagnosis by automatic screening for polyps in colonography.
· Inter and intra patient registration of DTI images applied to atlas building, tractography and patient studies.
· Using line segments as structuring elements for sampling-invariant measurements
· The generalized Radon transform: sampling, accuracy and memory considerations
The aforementioned developments have been applied in numerous industrial collaborations and medical applications.
· Analysis of micro-structures formed by complex networks of bio-polymers;
· Detection of channels and faults in 3D seismic images;
· Analysis of liquid flow and diffision using tracer particles;
· Analysis of perceptual image quality of printed materials using local image features, scale and color;
· Analysis, transformation, visualization and registration of diagnostic and surgical images for use in minimally invasive
surgery and placement of endoprostheses.
· Virtual endoscopy;
· Detection and progression analysis of glaucoma.
· MRI thermography.
· Diffusion Tensor MRI
· Characterizing the Three- Dimensional Organization of Telomeres
External projects
4D image processing for analyzing motion patterns of the wrist
Period: 2005-2009; Funding STW In this project we will develop image processing and analysis methods for 4D
characterization of the wrist. The extracted information will be combined with biomechanical models for diagnosis and
treatment planning.
Processing and analysis of Diffusion Tensor MRI at 3Tesla
Period: 2005-2008; Funding VL-e through AMC Amsterdam In this project we will develop image processing and analysis
methods for Diffusion Tensor MRI images.
Dynamic superresolution of small moving objects
Period: 2004-2007; Funding: TNO Investigating techniques for detection, registration and subsequent superresolution of
small moving objects
Intelligent image interpretation for automated quality grading of young tomato plants in horticulture
Period: 2003-2006; Funding: IOP beeldverwerkingOntology driven image processing and analysis for the quality grading of
young tomato plants in horticulture.
68
Detection and progression analysis of glaucoma
Period: 2002-2005; Funding: LDT (Laser Diagnostic Technologies, recently taken over by Carl Zeiss Meditec).
Early detection of glaucoma and its progression in images acquired through scanning laser polarimetry, by means of the
GDx apparatus.
Cyttron
Period: 2003-2007; Funding: Bsik
Nanophoresis
Period: 2002-2010; Funding: FOM
Superresolution in undersampled image sequences
Period: 2002-2005; Funding: IOP beeldverwerking Increasing the spatial resolution in exchange for temporal resolution
through adaptive techniques.
Automatic polyp detection in 3D CT
Period 2002-2006; Funding IOP beeldverwerking Image processing, analysis and recognition to facilitate automatic
screening for polyps in 3D CT of the colon.
Multi-dimensional measurement techniques
Period: 2002-2006; Funding: FOM Fundamental techniques for multi-dimensional image processing and analysis.
Improved techniques for virtual endoscopy
Period: 2001-2005; Funding: Philips Medical Systems;
Doctoral degrees
Pekalska, E.; (cum laude) 17 January 2005;
Dissimilarity representations in pattern recognition ,
TU Delft, Delft 2005, 322 pp., ISBN 90-9019021-X, External project (=2e geldstroom).
Vos, F.M., R.E. van Gelder, I.W.O. Serlie, J. Florie, Y.C. Nio, F.H. Post, R. Truyen, A.M. Vossepoel, and J. Stoker; Virtual
Colonoscopy (Ch.9), in: J. Dankelman, C.A. Grimbergen, H.G. Stassen (eds.), Engineering for Patient Safety: Issues in
Minimally Invasive Procedures, Lawrence Erlbaum Associates, Mahwah, NJ, 2005, 206-225.
Bouma, H., A. Vilanova, L.J. van Vliet, and F.A. Gerritsen; Correction for the dislocation of curved surfaces caused by the
PSF in 2D and 3D CT images, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 27, no. 9, 2005, 15011507.
Bruin, P.W. de, V.J. Dercksen, F.H. Post, A.M. Vossepoel, G.J. Streekstra, and F.M. Vos; Interactive 3D segmentation using
connected orthogonal contours, Computers in Biology and Medicine, vol. 35, no. 4, 2005 (@2004), 329-346.
Doel, L.R. van den, P.T. Nagy, L.J. van Vliet, and G.P. Neitzel; Regularized phase-tracker with iso-phase scanning strategy
for analysis of dynamic interferograms of nonwetting droplets under excitation, Applied Optics (Optical Society of America),
vol. 44, no. 14, 2005, 2695-2704.
Fulwyler, M., Q.S. Hanley, C. Schnetter, I.T. Young, E.A. Jares-Erijman, D.J. Arndt-Jovin, and T.M. Jovin; Selective
Photoreactions in a Programmable Array Microscope (PAM): Photoinitiated Polymerization, Photodecaging, and
Photochromic Conversion, Cytometry, vol. 67A, no. 2, 2005, 68-75.
Garini, Y., B.J. Vermolen, and I.T. Young; From micro to nano: recent advances in high-resolution microscopy, Current
Opinion in Biotechnology, vol. 16, no. 1, 2005, 3-12.
Garling, E.H., M. van Eck, T. Wedding, D.J. Veeger, E.R. Valstar, and R.G.H.H. Nelissen; Increased muscle activity to
stabilise mobile bearing knees in patients with rheumatoid arthritis, The Knee, vol. 12, no. 3, 2005, 177-182.
Garling, E.H., B.L. Kaptein, K. Geleijns, R.G.H.H. Nelissen, and E.R. Valstar; Marker Configuration Model-Based Roentgen
Fluoroscopic Analysis, Journal of Biomechanics, vol. 38, no. 4, 2005, 893-901.
69
Kaptein, B.L., E.R. Valstar, B.C. Stoel, P.M. Rozing, and J.H.C. Reiber; A new type of model-based Roentgen
stereophotogrammetric analysis for solving the occluded marker problem, Journal of Biomechanics, vol. 38, no. 11, 2005,
2330-2334.
Kutchoukov, V.G., L. Pakula, G.O.F. Parikesit, Y. Garini, L.K. Nanver, and A. Bossche; Fabrication of nanofluidic devices in
glass with polysilicon electrodes, Sensors and Actuators A, Physical, vol. 123-124 (Eurosensors XVIII 2004 - The 18th
European Conf. on Solid-State Transducers), 2005, 602-607.
Louis, S.F., B.J. Vermolen, Y. Garini, I.T. Young, A. Guffei, Z. Lichtensztejn, F. Kuttler, T.C.Y. Chuang, S. Moshir, V.
Mougey, A.Y.C. Chuang, P.D. Kerr, T. Fest, P. Boukamp, and S. Mai; c-Myc induces chromosomal rearrangements through
telomere and chromosome remodeling in the interphase nucleus, Proceedings of the National Academy of Sciences USA,
vol. 102, no. 27, 2005, July 5, 9613-9618.
Luengo Hendriks, C.L., M. van Ginkel, P.W. Verbeek, and L.J. van Vliet; The generalized Radon transform: sampling,
accuracy and memory considerations, Pattern Recognition, vol. 38, no. 12, 2005, 2494-2505.
Luengo Hendriks, C.L., and L.J. van Vliet; Using line segments as structuring elements for sampling-invariant
measurements, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 27, no. 11, 2005, 1826-1831.
Mai, S., and Y. Garini; Oncogenic Remodeling of the Three-Dimensional Organization of the Interphase Nucleus: c-Myc
Induces Telomeric Aggregates Whose Formation Precedes Chromosomal Rearrangements, Cell Cycle, vol. 4, no. 10, 2005,
1327-1331.
Melissant, C., A. Ypma, E.E.E. Frietman, and C.J. Stam; A method for detection of Alzheimers disease using ICA-enhanced
EEG measurements, Artificial Intelligence in Medicine, vol. 33, no. 3, 2005, 209-222.
Minekus, J.P.J., E.R. Valstar, P.M. Rozing, M.J. de Vos, R.L. Diercks, W.J. Willems, and J. Dankelman; Factors influencing
the surgical process during shoulder joint replacement: Time-action analysis of five different prostheses and three different
approaches, Medical Science Monitor: Clinical Research, vol. 11, no. 1, 2005, CR14-20.
Moerman, R., J. Knoll, C. Apetrei, L.R. van den Doel, and G.W.K. van Dedem; Quantitative Analysis in Nanoliter Wells by
Prefilling of Wells Using Electrospray Deposition Followed by Sample Introduction with a Coverslip Method, Analytical
Chemistry, vol. 77, no. 1, 2005, 225-231.
Parikesit, G.O.F., A.P. Markesteijn, V.G. Kutchoukov, O. Piciu, A. Bossche, J. Westerweel, Y. Garini, and I.T. Young;
Electroosmotic flow analysis of a branched U-turn nanofluidic device, Lab on a Chip, vol. 5, no. 10, 2005, 1067-1074.
Valstar, E.R., R. Gill, L. Ryd, G. Flivik, N. Borlin, and J. Karrholm; Guidelines for standardization of radiostereometry (RSA)
of implants, Acta Orthopaedica, vol. 76, no. 4, 2005, p. 563-572.
Vermeer, K.A., N.J. Reus, F.M. Vos, A.M. Vossepoel, and H.G. Lemij; Automated detection of wedge-shaped defects in
polarimetric images of the retinal nerve fiber layer, Eye, vol. 19, 2005, 1-9 (at the press).
Vermolen, B.J., Y. Garini, S. Mai, V. Mougey, T. Fest, T.C.-Y. Chuang, A.Y.-C. Chuang, L. Wark, and I.T. Young;
Characterizing the Three- Dimensional Organization of Telomeres, Cytometry, vol. 67A, no. 2, 2005, 144-150.
Wu, Y.S., H.W. Frijlink, L.J. van Vliet, L. Stokroos, and K. van der Voort Maarschalk; Localization dependent analysis of
porosity and pore direction in tablets, Pharmaceutical Research, vol. 22, no. 8, 2005, 1399-1405.
Blaas, J., C.P. Botha, B. Peters, F.M. Vos, and F.H. Post; Fast and Reproducible Fiber Bundle Selection in DTI Visualization,
IEEE Visualization 2005 (Proc. Conf. Mineapolis, MN, USA, Oct.23-25), ACM Press, 2005, p. accepted.
Dietrich, H.R.C., L.R. v.d. Doel, W. Hoyer, W. van Oel, G. Liqui Lung, Y. Garini, T. Jovin, and I.T. Young; Adaptation of
Nanoarrays for the Study of a-synuclein aggregation - preliminary results, in: D.V. Nicolau, J. Enderlein, R.C. Leif, D.L.
Farkas, R.Raghavachari (eds.), Imaging, Manipulation, and Analysis of Biomolecules and Cells: Fundamentals and
Applications III (Proc. SPIE Photonics West: Biomedical Optics (BiOS) San Jose, California, USA, Jan.22-27), Proc. SPIE,
vol. 5699, 2005, 395-402.
Dietrich, H.R.C., E. van IJsseldijk, S. de Vries, I.T. Young, and Y. Garini; Advances in the Development of a Novel Method to
be used in Proteomics using Gold Nanoparticles, Proc. Int. Conf. on Biopartitioning and Purification (SL, June 20-24), 2005,
17-18
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Dietrich, H.R.C., I.T. Young, and Y. Garini; Gold nanoparticles: A novel application of spectral imaging in proteomics preliminary results, in: G.H. Bearman, Anita Mahadevan-Jansen, Richard M. Levenson (eds.), Spectral Imaging:
Instrumentation, Applications, and Analysis III (Proc. SPIE Photonics West: Biomedical Optics (BiOS) San Jose, California,
USA, Jan.22-27), Proc SPIE, vol. 5694, 2005, 82-89.
Dijkers, J.J., C. van Wijk, F.M. Vos, J. Florie, Y.C. Nio, H.W. Venema, R. Truyen, and L.J. van Vliet; Segmentation and size
measurement of polyps in CT colonography, Medical Image Computing and Computer-Assisted Intervention - MICCAI 2005
(Proc. 8th Int. Conf., Palm Springs, CA, USA, Oct. 26-29), Lecture Notes in Computer Science, vol. 3749, Springer Verlag,
Heidelberg, 2005, 712-719.
Docter, M.W., I.T. Young, V.G. Kutchoukov, A. Bossche, P.F.A. Alkemade, and Y. Garini; A novel concept for a mid-field
microscope, in: Tuan Vo-Dinh, J.R. Lakowicz, Z.K. Gryczynski (eds.), Plasmonics in Biology and Medicine II (Proc. SPIE
Photonics West: Biomedical Optics (BiOS) San Jose, California, USA, Jan.22-27), Proc. SPIE, vol. 5703, 2005, 118-126.
Parikesit, G.O.F., V.G. Kutchoukov, A. Bossche, I.T. Young, and Y. Garini; Optical detection of electrokinetically manipulated
single molecules in a nanofluidic chip, in: I. Papautsky, I. Chartier (eds.), Proc. Conf. Microfluidics, BioMEMS, and Medical
Microsystems III, Proc. SPIE, vol. 5718, 2005, 133-141.
Pham, T.Q., M. Bezuijen, L.J. van Vliet, K. Schutte, and C.L. Luengo Hendriks; Performance of optimal registration
estimators, in: Z. Rahman, R.A. Schowengerdt, S.E. Reichenbach (eds.), Visual Information Processing XIV (Proc. SPIE
Defense and Security Symposium, Orlando, Florida, USA, Mar.29-Apr.1), Proc. SPIE, vol. 5817, 2005, 133-144.
Pham, T.Q., and L.J. van Vliet; Separable bilinear filtering for fast video preprocessing, CD Proc. IEEE Int. Conf. on
Multimedia & Expo (Amsterdam, July 6-8), 2005, 1-4.
Pham, T.Q., L.J. van Vliet, and K. Schutte; Influence of signal-to-noise ratio and point spread function on limits of superresolution, in: E.R. Dougherty, J.T. Astola, K.O. Egiazarian (eds.), Image Processing: Algorithms and Systems IV (Proc.
IS&T/SPIE's 17th Annual Symposium Electronic Imaging, San Jose, California, USA, Jan.1620), 2005, 169-180.
Pham, T.Q., and L.J. van Vliet, Blocking artifacts removal by a hybrid filter method, in: B.J.A. Krose, H.J. Bos, E.A. Hendriks,
J.W.J. Heijnsdijk (eds.), ASCI 2005; Proceedings of the eleventh annual conference of the Advanced School for Computing
and Imaging (Heijen, NL, June 8-10), ASCI, Delft, 2005, 372-377.
Rollano-Hijarrubia, E., F. van der Meer, A. van der Lugt, H. Weinans, H.A. Vrooman, A.M. Vossepoel, and R. Stokking;
Improving the imaging of calcifications in CT by histogram-based selective deblurring, in: M.J. Flynn (eds.), Physics of
Medical Imaging (Proc. Conf. San Diego, CA, USA, Feb.13-15), Proc. SPIE, vol. 5745-09, 2005, 67-78.
Suprijanto, M.W. Vogel, F.M. Vos, H.A. Vrooman, and A.M. Vossepoel; Inter-frame Motion Correction for MR Thermometry,
in: J. Duncan, G. Gerig (eds.), Medical Image Computing and Computer-Assisted Intervention - MICCAI 2005 (Proc. 8th Int.
Conf., Palm Springs, CA, USA, Oct. 26-29), Lecture Notes in Computer Science, vol. 3749, Springer Verlag, Heidelberg,
2005, 580-588.
Vermolen, B.J., I.T. Young, A. Chuang, L. Wark, T. Chuang, S. Mai, and Y. Garini; Three-dimensional analysis tool for
segmenting and measuring the structure of telomeres in mammalian nuclei, in: D.V. Nicolau, J. Enderlein, R.C. Leif, D.L.
Farkas, R.Raghavachari (eds.), Imaging, Manipulation, and Analysis of Biomolecules and Cells: Fundamentals and
Applications III (Proc. SPIE Photonics West: Biomedical Optics (BiOS) San Jose, California, USA, Jan.22-27), Proc. SPIE,
vol. 5699, 2005, 111-120.
With : TUD-EWI-mm-cgcc, TUD-EWI-mm-ict, UL-LUMC-lkeb and with EU-EMCR-bigr
HIGHLIGHT
Our publication in PNAS in 2005 (see below) represented a clear illustration of the power of applying quantitative, multidimensional image analysis tools that we developed to the study of cell replication in normal and malignant cell lines. Having
participated in the discovery of the “telomeric disc” (published in BMC Biology in 2004), we showed in this work how this
disc’s development is altered by the protein c-Myc and how this is related to chromosomal rearrangement.
Relevant publication:
Louis, S.F., B.J. Vermolen, Y. Garini, I.T. Young, A. Guffei, Z. Lichtensztejn, F. Kuttler, T.C.Y. Chuang, S. Moshir, V.
Mougey, A.Y.C. Chuang, P.D. Kerr, T. Fest, P. Boukamp, and S. Mai; c-Myc induces chromosomal rearrangements through
telomere and chromosome remodeling in the interphase nucleus, Proceedings of the National Academy of Sciences USA,
vol. 102, no. 27, 2005, July 5, 9613-9618.
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2.3.7
The Cyttron (www.cyttron.nl) consortium wants to implement a comprehensive, integrated infrastructure for bio-imaging and
modeling cells down to atomic detail. We would like to provide a generic tool for identifying the molecular causes of disease,
essential for the prevention of disease and the development of new drug and therapies, and to establish a platform for
advanced diagnosis and tuning of individualized therapy, increasing effectiveness in health care. The consortium is highly
multidisciplinary including (bio-)physicists, chemists, mathematicians, bio-informatics and image processing specialists, cell
biologists, microscopists and medical researches from various research institutes. This sub-project of Cyttron focuses on
image search algorithms and methods for bio-image data bases.
External Projects
2004-2008, Bsik, 8.8 MEuro.
N. Sebe, E.M. Bakker, I. Cohen, T. Gevers, and T. Huang, Bimodal Emotion Recognition, proceedings 5th International
Conference on Methods and Techniques in Behavioral Research, Measuring Behaviour 2005.
2.3.8
Contribution of UvA-FdNWI-ias
Perception for autonomous systems
We develop methodologies for accurate motion estimation and interpretation from image sequences. Mobile vision platforms
have their applications in traffic and driving in unstructured terrain. Applications of static platforms are in public safety and
intelligent care homes for the elderly. We cooperate with TNO Defense, Security and Safety on a number of projects, which
are related to autonomous systems, such as the RoboJeep autonomous robot vehicle.
We have continued our investigation into terrain classification. This is an important topic for off-road autonomous robot
vehicle guidance. Range based sensor systems, such as stereo vision, cannot distinguish between solid obstacles such as
rocks or soft obstacles such as tall patches of grass. Terrain classification is needed to prevent that the robot vehicle is
stopped needlessly by the obstacle detection system. It can also be used to recognize sand roads or other drivable areas.
Possible image features that can be exploited are color and texture. Using color recognition outdoors is difficult, because the
observed color of a material is heavily influenced by environment conditions such as the scene composition and illumination.
Previously, we have developed an approach that distinguished between different environment states in order to reduce the
variation in to be recognized material colors. This approach has been extended so that additional features such as texture
can be exploited. Further improvements have also eliminated the need for setting thresholds during the environment
clustering stage.
Also in cooperation with TNO D&V methodologies for public safety are developed. Many surveillance algorithms consist of
different parts, such as object detection, segmentation, tracking, and recognition. Literature focuses on algorithms for one of
these individual tasks. Integration of and communication between these tasks is often rather ad-hoc. In this project we
worked on a statistical framework for visual tracking applications. It allows easy adaptation of the tracking application by
substitution of one of the algorithms for part of the problem, without altering the remainder of the application. Furthermore,
the framework uses minimum cost classification and feedback for updating the models using knowledge available elsewhere
in the application.
A common problem for surveillance algorithms is the occurrence of shadows. A novel technique for shadow detection has
been developed. It is based on the assumption that often scenes are illuminated by several light sources, each with a
different color. This gives rise to a color shift for shadow, as not all light sources are occluded to the same amount. The
developed technique estimates this color shift and allows more accurate distinction between shadow and foreground objects.
Visual perception of humans and their activities
The ability to recognize humans and their activities by vision is key for a machine to interact intelligently and effortlessly with
a human-inhabited environment. There are numerous important applications ranging from public safety, elderly care and
intelligent vehicles to human motion capture/analysis. Two projects have started this year in the area of Looking-at-People
and public safety. In the MultimediaN – Safety Pilot project (07/05-06/09) the initial focus is on 3-D human pose estimation
from single images. We are looking into approaches that use a template hierarchy to match hundred of thousands of
possible poses in near real-time. In particular, we are investigating appropriate matching metrics for hierarchical detection
and subsequent verification stage, and ways to incorporate prior scene knowledge.
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The CASSANDRA (Context-Aware SenSing for AggressioN Detection and Risk Assessment, 09/05-08/09) project, funded by
NWO and in collaboration with the University of Groningen, aims to detect aggression in dynamic environments. Because
events associated with the build-up or enactment of aggression are difficult to detect by a single sensor modality (e.g.
shouting versus hitting someone) we investigate the fusion of video- and audio- sensing.
Learning, probabilistic, and neural computing
We develop learning methods and probabilistic reasoning methods for intelligent systems operating in a real world. In 2005
there was an increased focus on intelligent environments, which observe the persons moving in it, and have a ‘context
awareness’. We focussed on two applications areas. The first one is a surveillance application with many cameras that do
not have overlapping field of views. We developed a person tracking method that outperforms conventional (multihypothesis) tracking methods. A patent on the method is pending and there is strong interest in licenses. The STW project
ended in 2005, but a proposal for an STW ‘Valorization grant’ was honoured (BaViS: Bayesian Visual Surveillance). The
second application area is ‘cognitive robotics.’ Robots tend to move out of the factory floor into our daily lives. The IAS group
is one of the 8 partners in a 9 MEuro European Integrated Project in which a ‘robot servant’ is developed. Novel methods for
spatial cognition and space learning have been developed and are implemented.
Another line of research concerns sensor data fusion. Typical real-world data have several modalities. In the past we have
developed powerful probabilistic methods for sensor fusion in robotics or tracking. In a newly started project, funded by
MultimediaN, we develop methods for fusion of audio and video data in multimodal information streams (such as movies,
webcams, surveillance cameras) in order to create a robust tool for the detection of scene transitions and events, for
example to detect, identify and track humans, or to find scenes with a predefined situational signature such as aggressive
scenes, romantic scenes, etc.
Principles of autonomous systems
In the project on geometric algebra, we have continued the development of the conformal model as a compact language for
programming geometry. We have deepened the work on efficient implementation, and on facilities for visualization of and
experimentation with geometric algebra and geometry. This involves compiler and interpreter construction, and is a
cooperation with the Faculty of Computer Science at the Free University (VU) Amsterdam. We currently have the world's
fastest implementation of geometric algebra (by an order of magnitude). A simple ray tracer is about 20% slower than the
optimal classical implementation of the same algorithms, while having much more structured code. Considerable effort was
spent on finishing a tutorial book for the computer science audience, to help spread the distribution of the techniques to the
field.
Decision making in single- and multi-agent systems
In the context of agent decision making under uncertainty, we have developed Perseus, the world’s fastest approximate
POMDP solver. We recently extended Perseus to planning domains in which an agent has a continuous set of actions at its
disposal, and to domains involving continuous states, which is relevant for planning in robotic domains. We also explored
methods for decentralized planning under uncertainty for teams of communicating agents. Here we studied scenarios in
which the agents have the ability to communicate, but bandwidth is limited and communication has a certain cost.
Our work has also focused on algorithms for large-scale multi-agent coordination. Here we use the framework of
coordination graphs which allows for a tractable approach to the coordination problem, by decomposing the global payoff
function of the system into a sum of local terms. Recent work here involves (i) message passing techniques for approximate
decision making (similar to belief propagation in Bayesian networks), (ii) distributed cooperative reinforcement learning (Qlearning) in large agent networks by decomposing the action-value using a coordination graph, and (iii) automatically learning
the dependencies between the agents in cooperative multi-agent systems. Parts of this framework were incorporated in our
UvA Trilearn RoboCup simulation team which reached 10th place at the 2005 World Championship in Osaka, Japan. The
accompanied paper at the RoboCup Symposium describing our message passing techniques won the best scientific paper
award.
We have applied our experience to the soccer game when performed by a team of 4-Legged robots. The 4-Legged Soccer
League is an ideal challenge, because it defines a standard hardware platform, which allows benchmark algorithms to
perceive the environment, to reason about the optimal (joint) actions, and to perform those actions in a smooth way. This
year we had to concentrate our effort to the localization algorithm, to cope with a field with no boundaries. The vertical
structures on the field are two brightly colored goals and four uniquely colored flags that can be used by the robots for a
coarse localization. When making use of the white field lines on the carpet, it has been shown that the error in localization
can be pushed below six centimeters. Our group also contributed to the Variable Lighting Challenge, by using algorithm
multiple pre-calibrated color-cluster lookup tables for different lighting conditions and switched between them dynamically
(based on a brightness estimate). This approach is illustrated in the figure.
The soccer world is dynamic, but has a fixed number of agents, and small playing field. To study the influence of larger realworld models, we focused on cooperation between teams of rescue-agents in a city after a disaster. As part of this research,
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a preliminary literature study is made with respect to models and algorithms for multi-agent planning under partial
observability. The focus has been on decentralized partially observable Markov decision processes (Dec-POMDPs), but also
the more general case is studied in which agent's have their own pay-off function (Partially observable stochastic games POSGs). The benefit of both approaches is their clean way to represent a multi-agent decision problem. The down-side is
that solving them (i.e. finding the optimal joint policy) is provably intractable (NEXP-complete). Therefore, exact algorithms,
of which only few exist, are limited to extremely small problems. To tackle realistic problems, approximation models and
algorithms have to be developed.
Another research line involves Ìnteractive Hierarchical Awareness’ in a multi-agent system. Modeling and control of such a
system may benefit immensely from representing it at multiple levels of abstraction, i.e., using a hierarchy of representations.
This means that the system's state is represented at multiple resolutions (in terms of time and abstraction) simultaneously for
different levels in the hierarchy, and similarly, that actions are taken at multiple resolutions. In the Interactive Collaborative
Information Systems (ICIS) project we aim at developing scalable and theoretically sound methods for constructing and
updating hierarchical state representations for multi-agent systems. We are working on establishing criteria for hierarchical
state representations, for instance based on action utilities, the Markov property, uncertainty, etc. Our main application
domain is road traffic management.
Distributed perception and sensor fusion
Intelligent process control and decision making in complex systems require adequate situation assessment, which in turn
requires processing of large amounts of heterogeneous information originating from different, spatially dispersed sources,
such as, sensory systems, human observers, databases, etc. However, such "sensor fusion" is not trivial, since it requires
adequate mapping between very heterogeneous concepts, we are confronted with noisy information sources and, due to
large amounts of information, significant processing resources might be required (i.e. computational bottlenecks). Another
characteristic of the domains we are focusing on is that constellations of information sources can change frequently and,
prior to the operation, we never know which information sources will be available. In addition, such fusion systems often
provide results which have a critical impact on the decision making process and, consequently, further course of events.
Therefore, high quality of fusion results and prevention of misleading results is indispensable.
In order to be able to deal with the mentioned challenges, we have introduced Distributed Perception Networks (DPN), multiagent systems which support fusion based on distributed Bayesian Networks (BN). This work was carried out within the
project Combined Systems at the Decis research institute. In this context, our research is focused primarily on the following
problems: (i) Task driven self-configuration of DPN agents at runtime, which allows adaptation to dynamic information source
constellations and supports reuse of partial fusion results. (ii) Efficient and robust information fusion with distributed BNs,
which provide adequate mapping between observable events and beliefs in hypotheses about hidden events. (iii) Resource
allocation in distributed fusion systems based on information theoretic criteria. (iv) Approaches to improved fusion accuracy,
such as fail-safe design of fusion systems as well as localization of faulty model components and information sources.
We find applications of our research in the field of crisis management. Decentralized information sources can fuse
information and extract the relevant events in the environment. Such a set-up is depicted in the figure.
External Projects
Geometric Algebra: a New Foundation for Geometric Programming
2000-2006, 637kf This projects makes geometric algebra into a practical tool for geometric programming applications within
computer science, notably robotics, vision and computer graphics. New techniques for specification of geometric programs
are being developed, and a freely available fast implementation constructed. This is an NWO-sponsored project.
Probabilistic models for distributed surveillance
2001-2005, STW, 545kf This project studies how probabilistic models like belief networks can be used in distributed
surveillance system, where moving objects have to be tracked by a system of cameras with non-overlapping views.The
information from the different camera systems will have to be combined. A number of fundamental problems has to be
solved such as the identification problem (ìs the object which is observed by one camera the same as the object observed
by some other camera some time ago?') and the representation problem (`how can probabilistic information be integrated in
a distributed system?').
Distributed User Modeling for Personalized Exploring Recommender Systems (DUMPERS)
2002-2006, NWO(ToKen2000), 225kE In the project DUMPERS we will develop methods for adding adaptive navigation
support for users of web sites. Goal of this project is to extend existing methods with extra components like exploration of the
effect of recommendation by using techniques from the field of reinforcement learning. We will use locally stored user models
to provide the information about the individual users needed for personal recommendation without violating the privacy of the
users.
74
COMBINED systems
2002-2006, 800kE In this project we study innovative methods for disaster management. In particular aspects concerning
distributed observation systems are investigated. An important property of distributed observation systems is that they
autonomously extract information from the monitored area. This information is shared with other services in the disaster
management platform. The project is conducted in cooperation with TUDelft, Thales en TNO within the DECIS laboratory.
Environment Representation for Autonomous Vehicles
2001-2005, 200kf In this project we develop a "RoboJeep" robotic vehicle. This vehicle must be able to navigate and perform
useful observations autonomously in an unstructured environment. Different sensors such as stereovision cameras, ultrasonic sensors, odometers, and a laser range scanner are applied for this goal. The objective of this research is to develop
techniques for acquiring reliable representations of the environment from these sensors. Collaboration with TNO.
A structure for maintaining a shared world model in a dynamic environment between differentiated embedded
systems and their interaction with human supervisors
2001-2006, 490 kf We study embedded autonomous systems in distributed environments, for applications in public safety;
monitoring and control of traffic and environmental conditions; assistance and clean-up work in disaster areas. Collaboration
between systems requires a collective world model, and we develop methods for its consistency maintenance, in time-critical
situations. We use robot soccer (RoboCup) as a case study. This project is a collaboration with the VU and is sponsored by
Progress.
COGNIRON: Cognitive Robot Companion
2004-2008, 600kE In this 6th framework project within IST we develop a cognitive robot which interacts with humans and has
conceptual representations. Our group works on human activity analysis and on cognitive representations of objects and
space.
Interactive Collaborative Information Systems
004-2009, 736 k€ The ICIS project is an attempt to bridge the gap between traditional information capture, transmission and
transaction processing to full-blown intelligent information systems techniques. This is a road starting with traditional
information management techniques such as better structuring and managing of information (including data mining and data
warehousing) and the development of self-generating software through to artificial intelligence and agent based systems and
complete integration of technologies with human and social systems.
W. Zajdel, N. Vlassis, and B. J. A Kröse. Bayesian methods for tracking and localization. In E. Aarts, J. Korts, and W.
Verhaegh, editors, Intelligent Algorithms, pages 243-258. Kluwer Academic Publishers, 2005.
B. Bakker.The concept of circular causality should be discarded. Commentary on Marc D. Lewis: Bridging emotion theory
and neurobiology through dynamic system modeling. Behavioral and Brain Sciences, 28:195-196, 2005.
O. Booij and H. T. Nguyen.A gradient descent rule for spiking neurons emitting multiple spikes. Information Processing
Letters, 95(6):552-558, September 2005.
L. Dorst Error propagation of the Procrustes method for 3-D attitude estimation. IEEE Transactions on Pattern Analysis and
Machine Intelligence, 27(2):221-229, February 2005.
Jelle R. Kok, Matthijs T. J. Spaan, and Nikos Vlassis.Non-communicative multi-robot coordination in dynamic environments.
Robotics and Autonomous Systems, 50(2-3):99-114, February 2005.
J.M. Porta and E. Celaya. Reinforcement learning for agents with many sensors and actuators acting in categorizable
environments.Journal of Artificial Intelligence Research, 23:79-122, 2005.
J.M. Porta and B. J. A Kröse. Appearance-based concurrent map building and localization. Robotics and Autonomous
Systems, 54(2):159-164, 2005.
J.M. Porta, J.J. Verbeek, and B.J.A. Kröse. Active appearance-based robot localization using stereo vision. Autonomous
Robots, 18(1):59-80, 2005.
Matthijs T. J. Spaan and Nikos Vlassis. Perseus: Randomized point-based value iteration for POMDPs. Journal of Artificial
Intelligence Research, 24:195-220, 2005.
J. J. Verbeek, N. Vlassis, and B. J. A. Kröse. Self-organizing mixture models. Neurocomputing, 63:99-123, 2005.
75
W. Zajdel and B. J. A. Kröse. A sequential Bayesian algorithm for surveillance with non-overlapping cameras.
Int. Journal of Pattern Recognition and Artificial Intelligence, 19(8):977-996, 2005.
B. Bakker, M. Steingrover, R. Schouten, E. Nijhuis, and L. Kester. Cooperative multi-agent reinforcement learning of traffic
lights. In Proc. of the Workshop on Cooperative Multi-Agent Learning, European Conference on Machine Learning, pages
24-36, 2005.
B. Bakker, Z. Zivkovic, and B.J.A. Kröse. Hierarchical dynamic programming for robot path planning.
In Proc. IEEE/RSJ International Conference on Intelligent Robots and Systems, pages 3720-3725, 2005.
O. Booij, Z. Zivkovic, and B. Kröse. Pruning the image set for appearance based robot localization.
In Proceedings of the Annual Conference of the Advanced School for Computing and Imaging, pages 57-64, June 2005.
A. T. Cemgil, W. Zajdel, and B. Kröse. A hybrid graphical model for robust feature extraction from video.
In C. Schmid, S. Soatto, and C. Tomasi, editors, IEEE Computer Vision and Pattern Recognition (CVPR), pages 1158-1165,
San Diego, June 2005.
P. de Oude, J. Nunnink, and G. Pavlin. Distributed bayesian networks in highly dynamic agent organizations.
In Proc. Belgian Dutch AI Conf., pages 104-111, Brussels, Belgium, 2005.
P. Jansen, W. van der Mark, J.C. van der Heuvel, and F.C.A. Groen. Colour based off-road environment and terrain type
classification. In Proc. IEEE ITSC 8th Int. Conf. on Intelligent Transport Systems, pages 61-66, Vienna, Austria, September
2005.
G. Klaassen, W. Zajdel, and B.J.A. Kröse. Speech-based localization of multiple persons for an interface robot.
In Proc. of IEEE Int. Conference on Computational Intelligence in Robotics and Automation (CIRA2005), pages 47-52, 2005.
Jelle R. Kok, Pieter Jan 't Hoen, Bram Bakker, and Nikos Vlassis. Utile coordination: Learning interdependencies among
cooperative agents. In Proc. of the IEEE Symposium on Computational Intelligence and Games (CIG'05), pages 29-36,
Colchester, United Kingdom, April 2005.
Jelle R. Kok and Nikos Vlassis. Using the max-plus algorithm for multiagent decision making in coordination graphs. In
RoboCup 2005: Robot Soccer World Cup IX, Osaka, Japan, July 2005. Best Scientific Paper Award.
Jelle R. Kok and Nikos Vlassis. Using the max-plus algorithm for multiagent decision making in coordination graphs:
Extended abstract. In K. Verbeeck, K. Tuyls, A. Now'e, B. Manderick, and B. Kuijpers, editors, Proc. of the 17th BelgianDutch Conference on Artifical Intelligence, pages 359-360, October 2005.
W. Kowalczyk and N. Vlassis. Newscast EM. In L. K. Saul, Y. Weiss, and L. Bottou, editors, Advances in Neural Information
Processing Systems 17, pages 713-720. MIT Press, Cambridge, MA, 2005.
J. Nunnink and G. Pavlin. Accuracy of sequential bayesian information fusion. In Proc. IASTED Int. Conf. on Artificial
Intelligence and Applications, pages 545-550, Innsbruck, Austria, 2005.
J. Nunnink and G. Pavlin. A probabilistic approach to resource allocation in distributed fusion systems. In Proc. Int. Conf. on
Autonomous Agents and Multi-Agent Systems, pages 846-852, Utrecht, The Netherlands, 2005.
Frans Oliehoek, Matthijs T. J. Spaan, and Nikos Vlassis. Best-response play in partially observable card games. In
Benelearn 2005: Proceedings of the 14th Annual Machine Learning Conference of Belgium and the Netherlands, pages 4550, February 2005.
Frans Oliehoek, Nikos Vlassis, and Edwin de Jong. Coevolutionary Nash in poker games. In Proceedings of the 17th
Belgian-Dutch Conference on Artifical Intelligence, pages 188-193, Brussels, Belgium, October 2005.
G. Pavlin, P. de Oude, and J. Nunnink. A MAS approach to fusion of heterogeneous information. In Proc. Int. Conf. on Web
Intelligence, pages 802-804, 2005.
P.J.Withagen, F.C.A.Groen, and K.Schutte. Ccd characterization for a range of color camera's. In Proceedings
Instrumentation and Measurement Conference, IMTC 2005, pages 2232-2235, Ottawa, Ontario, Canada, May 2005.
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Josep M. Porta, Matthijs T. J. Spaan, and Nikos Vlassis. Robot planning in partially observable continuous domains. In K.
Verbeeck, K. Tuyls, A. Now'e, B. Manderick, and B. Kuijpers, editors, Proc. of the 17th Belgian-Dutch Conference on Artifical
Intelligence, pages 375-376, Brussels, Belgium, October 2005.
Josep M. Porta, Matthijs T. J. Spaan, and Nikos Vlassis. Robot planning in partially observable continuous domains. In Proc.
Robotics: Science and Systems, pages 217-224. MIT Press, 2005.
B. Slamet and A. Visser. Purposeful perception by attention-steered robots. In Proc. 17th Dutch-Belgian Artificial Intelligence
Conference, BNAIC'05, pages 209-215, Brussels, October 2005.
Matthijs T. J. Spaan and Nikos Vlassis. Planning with continuous actions in partially observable environments. In
Proceedings of the IEEE International Conference on Robotics and Automation, pages 3469-3474, Barcelona, Spain, April
2005.
M. Steingrover, R. Schouten, S. Peelen, E. Nijhuis, and B. Bakker. Reinforcement learning of traffic light controllers adapting
to traffic congestion. In Proc. of the Belgium-Netherlands Artificial Intelligence Conference, BNAIC'05, pages 216-223, 2005.
M. van Someren and S. ten Hagen. Machine learning and reinforcement learning. In Bogdan Gabrys, Kauko Leiviska, and
Jens Strackeljan, editors, Do Smart Adaptive Systems Exist?, volume 173 of Studies in Fuzziness and Soft Computing,
pages 81-104. Springer-Verlag, January 2005.
N. Vlassis, Y. Sfakianakis, and W. Kowalczyk. Gossip-based greedy Gaussian mixture learning. In Lecture Notes in
Computer Science, volume 3746, pages 349-359. Springer-Verlag, 2005.
W. Zajdel, Z. Zivkovic, and B.J.A. Kröse. Keeping track of humans: have I seen this person before? In Proc. Int. Conference
on Robotics and Automation (ICRA), pages 2093-2098, 2005.
Z. Zivkovic, B. Bakker, and B.J.A. Kröse. Hierarchical map building using visual landmarks and geometric constraints. In
Proc. IEEE/RSJ International Conference on Intelligent Robots and Systems, pages 7-12, 2005.
Z. Zivkovic and B.J.A. Kröse. On matching interest regions using local descriptors - can an information theoretic approach
help? In Proc. British Machine Vision Conference, pages 50-58, 2005.
The Dutch AIBO Team - Osaka 2005 Source Code, C++, 2005
http://www.dutchaiboteam.nl/robocup/robocup2005/DT2005-diff-GT2004.zip
Source code for the Dutch robot dog team participating in the world championships.
Patent
W. Zajdel, A.T. Cemgil, B.J.A. Kröse A hybrid graphical model for on-line multicamera tracking,
Europese octrooiaanvrage 04077917.5
RoboCup/Progress: with TUD -TN en VU, also UU (Siks) and TUD- ET (DISC).
2.3.9
Contribution of EUR-RMI-bigr
Cardiovascular Image Analysis
Vascular imaging has gone beyond the traditional depiction of vascular luminal morphology. State-of-the art imaging
techniques have the potential to provide detailed information on the vessel wall, such as plaque composition, elastic wall
properties, and even biochemical processes that take place in the plaque. In addition, dynamic and perfusion imaging can
provide functional information, e.g. for determining the perfusion or motion of the heart, or to study tumor activity. Owing to
the growing complexity and sheer size of cardiovascular data, in combination with the large increase in the number of studies
in clinical practice and biomedical research, there is a strong and increasing interest in robust, automated processing tools to
aid in the analysis of these data. This research line aims to develop and evaluate novel image processing techniques for
visualization, quantification and integrated analysis of multimodal anatomical and functional cardiovascular imaging data.
The research in 2005 has focused on:
Vessel enhancement filtering (CTA/MRA).
Automated central vessel axis extraction in CTA data.
Deblurring for improved visualization and calcification quantification in CTA.
77
Quantitative analysis of microvasculature in cancer tissue.
Cellular and Molecular Image Analysis
Advances in fluorescent probing and microscopic imaging have revolutionized biology in the past decade and have opened
up the door to studying the structure and function of even single molecules. In addition, in vivo molecular imaging is expected
to have a large impact in clinical practice, as it will be able to study disease processes at the molecular and cellular level, can
be used for therapy, and therapy monitoring. Generally, these imaging studies require the processing and analysis of huge
amounts of (3D and 4D) image data, which is at present still done mainly by hand. Manual image analysis is very time
consuming (thus costly) and also potentially inaccurate and poorly reproducible. As a result, many biologically and clinically
interesting questions are either left unaddressed, or answered with great uncertainty. In an attempt to alleviate this problem,
this research line aims to develop automated image analysis technology with specific emphasis on accurate and
reproducible analysis of cellular and molecular image sequences.
Tracking and analysis of biological molecular dynamics in living cells.
Pharmacokinetic modeling of contrast uptake in tumors for anticancer treatment.
Neuro Image Analysis
MR brain imaging is widely used in basic scientific research and in clinical practice, as it is a technique that non-invasively
provides both anatomical and functional information. In order to study brain morphometry and function, and its relation to e.g.
disease processes or patient characteristics, often large imaging databases are collected. In this research line, advanced
techniques for the automated processing and analysis of such databases are developed.
Automated MR brain tissue classification
Automated quantification of brain structures
Intersubject MR brain registration
External projects:
“3D Multimodal vascular image analysis for improved diagnosis and therapy”
NWO STW VICI grant, 1,25 MEuro: 2006-2010 In this project, methods for the integrated analysis of vascular imaging data
obtained with various imaging techniques will be developed and evaluated. The focus is on the analysis of the diseased
vessel wall, so as to improve diagnosis of cardiovascular diseases, and to monitor and guide their treatment.
Collaboration with Applied Physics, Delft
“Aneurist: Integrated Biomedical Informatics for the Management of Cerebral Aneurysms”
European grant IST call 4, 420 kEuro: 2006-2009 In this multi-center project, the vertical integration of information related to
cerebral aneurysms, from the genetic to the epidemiological level is pursued. Our group is involved in the analysis of the
morphodynamics of brain aneurysms.
“Quantification of tumor vessel morphology: a tool to monitor treatment”.
NWO Mozaiek Grant, 180 kEuro: 2005-2009 In this project techniques will be developed and evaluated for the quantitative
analysis of multi-sequence MRI data, in order to better monitor the effects of treatment.
“ADVAnCE: Automatic Diagnostic Vascular Analysis of CTA Examinations”.
Senter grant, 600 kEuro: 2005-2009. In this project, computer aided diagnosis techniques will be developed to support the
analysis of CTA data in clinical practice, to improve the workflow of cardiovascular diagnosis.
Collaboration with LKEB-Leiden
“MOSAIC: Multiscale Object Segmentation by Analyzing Image Content”,
NWO EW, 455 kEuro: 2005-2009. In this project, a hierarchical, model-based approach toward multiple-object segmentation
is developed, with an application to automated MR brain segmentation.
“Model-driven spatiotemporal tracking for quantitative analysis of subcellular dynamics”
NWO EW VIDI grant, 600 kEuro: 2005-2009 In this project, automated image analysis techniques for the accurate and
reproducible quantification of the motion of subcellular structures from time-lapse fluorescence microscopy image data are
developed and evaluated. Collaboration with Applied Physics, Delft
Vos, F.M., R.E. van Gelder, I.W.O. Serlie, J. Florie, Y.C. Nio, F.H. Post, R. Truyen, A.M. Vossepoel, and J. Stoker; Virtual
Colonoscopy (Ch.9), in: J. Dankelman, C.A. Grimbergen, H.G. Stassen (eds.), Engineering for Patient Safety: Issues in
Minimally Invasive Procedures, Lawrence Erlbaum Associates, Mahwah, NJ, 2005, 206-225.
78
De Bruin PW, Dercksen VJ, Post FH, Vossepoel AM, Streekstra, GJ, Vos FM. Interactive 3D segmentation using connected
orthogonal contours. Comp in Biol and Med 2005; 34(4):329-346.
Letteboer, MM, Willems PW, Viergever MA, Niessen WJ. Brain shift estimation in image-guided neurosurgery using 3-D
ultrasound. IEEE Trans Biomed Eng 2005;52(2):268-76.
Murphy RF, Meijering E, Danuser G. Special Issue on Molecular and Cellular Bioimaging. IEEE Trans Image Processing
2005;14(9):1233-6.
Olabarriaga SD, Rouet JM, Fradkin M, Breeuwer M, Niessen WJ. Segmentation of thrombus in abdominal aortic aneurysms
from CTA with nonparametric statistical grey level appearance modeling. IEEE Trans Med Imaging 2005;24(4):477-85.
Van de Kraats EB, Carelsen B, Fokkens WJ, Boon SN, Noordhoek N, Niessen WJ, et al. Direct navigation on 3D rotational
x-ray data acquired with a mobile propeller C-arm: accuracy and application in functional endoscopic sinus surgery. Phys
Med Biol 2005;50(24):5769-81.
Van de Kraats EB, Penney GP, Tomazevic D, van Walsum T, Niessen WJ. Standardized evaluation methodology for 2-D-3D registration. IEEE Trans Med Imaging 2005;24(9):1177-89.
Van Dijk EJ, Prins ND, Vermeer SE, Vrooman HA, Hofman A, Koudstaal PJ, et al. C-reactive protein and cerebral smallvessel disease: the Rotterdam Scan Study. Circulation 2005;112(6):900-5.
Van Vliet M, van Dijke CF, Wielopolski PA, ten Hagen TL, Veenland JF, Preda A, et al. MR angiography of tumor-related
vasculature: from the clinic to the micro-environment. Radiographics 2005;25 Suppl 1:S85-97; discussion S97-8.
Ver laan JJ, van de Kraats EB, Oner FC, van Walsum T, Niessen WJ, Dhert WJ. The reduction of endplate fractures during
balloon vertebroplasty: a detailed radiological analysis of the treatment of burst fractures using pedicle screws, balloon
vertebroplasty, and calcium phosphate cement. Spine 2005;30(16):1840-5.
Verlaan JJ, van de Kraats EB, Oner FC, van Walsum T, Niessen WJ, Dhert WJ. Bone displacement and the role of
longitudinal ligaments during balloon vertebroplasty in traumatic thoracolumbar fractures. Spine 2005;30(16):1832-9.
Verlaan JJ, van de Kraats EB, van Walsum T, Dhert WJ, Oner FC, Niessen WJ. Three-dimensional rotational X-ray imaging
for spine surgery: a quantitative validation study comparing reconstructed images with corresponding anatomical sections.
Spine 2005;30(5):556-61.
Van Walsum Th, Baert, SA, Niessen, WJ. Guide wire reconstruction and visualization in 3DRA using monoplane fluoroscopic
imaging. IEEE Transactions on Medical Imaging, 24(5):612-623.
Rollano-Hijarrubia, E., F. van der Meer, A. van der Lugt, H. Weinans, H.A. Vrooman, A.M. Vossepoel, and R. Stokking;
Improving the imaging of calcifications in CT by histogram-based selective deblurring, in: M.J. Flynn (eds.), Physics of
Medical Imaging (Proc. Conf. San Diego, CA, USA, Feb.13-15), Proc. SPIE, vol. 5745-09, 2005, 67-78.
Suprijanto, M.W. Vogel, F.M. Vos, H.A. Vrooman, and A.M. Vossepoel; Inter-frame Motion Correction for MR Thermometry,
in: J. Duncan, G. Gerig (eds.), Medical Image Computing and Computer-Assisted Intervention - MICCAI 2005 (Proc. 8th Int.
Conf., Palm Springs, CA, USA, Oct. 26-29), Lecture Notes in Computer Science, vol. 3749, Springer Verlag, Heidelberg,
2005, 580-588. Collaboration Applied Physics, TU Delft.
van de Kraats EB, Penney GP, van Walsum Th, Niessen WJ. Multispectral MR to X-Ray Registration of Vertebral Bodies by
Generating CT-Like Data. In: Medical Image Computing and Computer-Assisted Intervention - MICCAI 2005. Duncan J,
Gerig G (eds.), vol. 3750 of Lecture Notes in Computer Science, Springer-Verlag, Berlin, October 2005, pp. 911-918.
Manniesing R, Niessen WJ. Multiscale Vessel Enhancing Diffusion in CT Angiography Noise Filtering. In: Information
Processing in Medical Imaging - IPMI 2005. Christensen GE, Sonka M (eds.), vol. 3565 of Lecture Notes in Computer
Science, Springer-Verlag, Berlin, July 2005, pp. 138-149.
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2.3.10 Contribution of UU-WI-ics
Geometry, Imaging and Virtual Environments
The advances in information and communication technology have led to an enormous amount of spatial and image data.
There are many application domains where one needs to analyze, process, or visualize such data. Examples include
computer-aided training and simulation, multimedia, medical imaging, molecular modeling, automated cartography, 3D web
design, virtual reality, and computer games. The research program is concerned with the design, analysis, and
implementation of algorithms and data structures for spatial data, and their application in the above mentioned domains. The
type of research ranges from theoretical algorithms research leading to the design and analysis of fundamental geometric
algorithms and data structures, to application-oriented research leading to new systems applying algorithmic results in
domains like geographic information systems, automated cartography, navigation and manipulation for robots and virtual
characters, and content-based image retrieval and multimedia. The program has three main lines of research:
Computational geometry The field of computational geometry studies fundamental algorithmic techniques and data
structures for geometric problems. The main goal is to design correct and provably efficient algorithms and data structures
for generic algorithmic questions dealing with collections of points, lines, polygons, and more complicated geometric
primitives in the plane and in higher-dimensional space. The robust implementation of such algorithms has become another
key research question in this line of research. We also study geometric algorithmic questions that are derived from particular
application domains, in particular from geographic information systems (dealing with terrain data), automated cartography
(for example map labeling), robotics, and manufacturing.
Imaging and multimedia In this line of research we study algorithmic questions related to the interpretation of images, 3D
models, music, and video. The topics we work on include segmentation, feature extraction, matching of objects and
organization of media in index structures, with a focus on shape-based multimedia, and music retrieval. The research is
concerned with the algorithmic aspects of shape analysis, in particular the representation, decomposition, approximation,
and deformation of shapes, the transformation of one shape into another, measures for similarity of shapes, and the
organization of shapes in search structures for efficient content-based retrieval. Here shape can be derived from images but
also from 3D models and music.
Virtual environments Navigation (or motion) and interaction (often in the form of manipulation) are key issues in virtual
environments. The research concentrates on algorithms for planning and simulation of motion and manipulation in complex
environments, such as models of industrial installations and computer games. Path planning and collision detection are
crucial underlying algorithmic techniques for this. Motion is often not a goal in itself but a means of reaching a target area
where a manipulation task is to be performed, such as the assembly of a spare part in a virtual factory or the removal of a
tissue sample in virtual minimal-invasive surgery. For realistic simulation of these tasks we apply knowledge of techniques
from robotics such as kinematics and the mechanics of manipulation, in combination with sophisticated models of physical
behavior.
In all three lines of research we aim both for new fundamental algorithms and data structures, and for techniques that have
been verified on practical problem instances and can be used in the different application domains.
External Projects
MOCCAM
1999-2005, NWO, 250 KEuro. This project aims at developing new algorithms for motion planning in complex environment.
On one hand we concentrate on efficient data structures for storing such environments, and on the other hand, we study
probabilistic planners to better understand their behavior, improve them, and extend them to new domains.
MOVE-ME
2002-2007, NWO, 150 KEuro. This project studies motion planning for large groups of entities in huge virtual environments.
We will try to combine flocking techniques with motion planning techniques to let groups move together in realistic ways.
MOVIE
2003-2005, EU Fifth Framework, Utrecht part: 300 Keuro. This project aims at applying motion planning technology to
efficiently create natural looking motion for individual entities and groups of entities in complex virtual environment, for
example in computer games. The project is a combination of algorithms research to obtain new motion planning techniques
and more development work to integrate it in virtual environment applications.
Clamp
2003-2007, NWO, 280 KEuro This project studies manipulation problems from an algorithmic perspective. The goal is to
devise new algorithms to fixtures 2- and 3-dimensional objects and to reorient those using passive devices.
80
BRICKS
2004-2008, subproject Modelling, Simulation and Visualization, 320 KEuro Our subproject concentrates on interaction with
virtual environments. In particular we work on navigation through virtual environments and manipulation of objects in virtual
environments. ASCI groups in Delft and CWI are involved in this project as well.
AIM@SHAPE
2004-2007, EU Sixth Framework, Utrecht part: 450 Keuro. This project aims to develop techniques for advanced modeling
and analysis of shapes. Within the network we work on merging of scans, hole filling, 3D face recognition, and 3D shape
matching and retrieval.
SHAME
2000-2005, STW, 450Keuro The goal of this project is to create a SHApe Matchign Environment consisting of a software
library of efficient shape matching algorithms based on shape. To achieve this we implement, test, and improve existing
shape matching algorithms, and develop new ones.
C-Minor
2005-2008, subproject of bsik project MultimediaN, 200 KEuro The objectives of this project is to perform music retrieval on
the basis of perceptual and cognitive relevant features, to match these feature efficiently, and to model user feedback.
Profi
2005-2007, EU Sixth Framework, 300 KEuro In this collaborative project we aim to invent and develop new techniques for
the retrieval of figurative images (such as clip art, logos, signs) from large databases. Our techniques will be based on the
extraction and matching of perceptually relevant shape features.
GOGO
2005-2009, NWO, 350 KEuro This project is about geometric computation for cartography, realistic terrain modeling, and
delineating of imprecise geographic regions, where several geometric criteria must be met simultaneously.
Doctoral Degrees
Tanase, M.; February 16 2005; Shape decomposition and retrieval, Utrecht University, Utrecht, 169 pp.,Project: MindShade,
2e geldstroom.
Giannopoulos, P.; September 21 2005; Geometric matching of weighted point sets, Utrecht University, Utrecht, 129 pp.,
Project: SHAME, 2e geldstroom.
Books
Erdman, M., Hsu, D., Overmars, M.H., & Stappen, A.F. van der (Eds.). (2005). Algorithmic Foundations of Robotics VI
(Springer Tracts in Advanced Robotics, 17). Berlin-Heidelberg: Springer-Verlag.
Merabti, M., Lee, N., Overmars, M.H., & El Rhalibi, A. (Eds.). (2005). Proceedings Third International Game Design and
Technology Workshop and Conference. Liverpool: Liverpool John Moores University.
Contribution to Books
Stappen, A.F. van der (2005). Immobilization: analysis, existence, and output-sensitive synthesis. In R. Janardan, M. Smid,
& D. Dutta (Eds.), Computer-Aided Design and Manufacturing (AMS-DIMACS Volumes Series, 67) (pp. 165-187). American
Mathematical Society.
Berg, J.P. van den, & Overmars, M.H. (2005). Roadmap-based motion planning in dynamic environments. IEEE transactions
on robotics and automation, 21, 885-897.
Berg, J.P. van den, & Overmars, M.H. (2005). Using workspace information as a guide to non-uniform sampling in
probabilistic roadmap planners. The international journal of robotics research, 24, 1055-1071.
Berg, M.T. de, Gudmundsson, J. G., Katz, M.J., Levcopoulos, C., Overmars, M.H., & Stappen, A.F. van der (2005). The TSP
with neighborhoods of varying size. Journal of Algorithms, 57, 22-36.
Bose, P., & Kreveld, M.J. van (2005). Generalizing monotonicity: on recognizing special classes of polygons and polyhedra.
Int. J. Comp. Geom. & Appl., 15, 591-608.
Cabello, S., Berg, M.T. de, & Kreveld, M.J. van (2005). Schematization of networks. Comput. Geom. Theory & Appl., 30,
223-238.
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Demaine, E.D., Erickson, J., Hurtado, F., Iacono, J., Langerman, S., Meijer, H., Overmars, M.H., & Whitesides, S. (2005).
Separating point sets in polygonal environments. International journal of computational geometry & applications, 403-419.
Gudmundsson, J., Haverkort, H.J., & Kreveld, M.J. van (2005). Constrained higher order Delaunay triangulations. Comput.
Geom. Theory & Appl., 30, 271-277.
Kreveld, M.J. van, Reinbacher, I., Arampatzis, A., & Zwol, R. van (2005). Multi-dimensional scattered ranking methods for
geographic information retrieval. GeoInformatica, 9, 61-84.
Kuijper, A., Groep, P. van der, Wall, E. van der, & Diest, P.J. van (2005). Expression of HIF-1alpha and its downstream
targets in fibroepithelial tumors of the breast. Breast, 7, 808-818.
Veltkamp, R.C. (2005). Multimedia Algorithmics. Multimedia Tools and Applications, 27, 187-193.
Berg, J.P. van den, Nieuwenhuisen, D., Jaillet, J., & Overmars, M.H. (2005). Creating robust roadmaps for motion planning in
changing environments. In IEEE/RSJ International Conference on Intelligent Robots and Systems (pp. 2415-2421).
Berg, J.P. van den, & Overmars, M.H. (2005). Prioritized motion planning for multiple robots. In IEEE/RSJ International
Conference on Intelligent Robots and Systems (pp. 2217-2222).
Berg, M.T. de, Goaoc, X., & Stappen, A.F. van der (2005). A polynomial-time algorithm to design push plans for sensorless
parts sorting. In Proceedings of Robotics: Science and Systems (pp. 89-95).
Cheong, J.S., & Stappen, A.F. van der (2005). Output-sensitive computation of all form-closure grasps of a semi-algebraic
set. In Proceedings of the IEEE International Conference on Robotics and Automation (pp. 784-790).
Demaine, E., Erickson, J., Krizanc, D., Meijer, H., Morin, P., Overmars, M.H., & Whitesides, S. (2005). Realizing partitions
respecting full and partial order information. In J. Ryan, P. Manyem, K. Sugeng, & M. Miller (Eds.), Proceedings of the 16th
Australasian Workshop on Combinatorial Algorithms (pp. 105-113).
Florisson, S., Kreveld, M.J. van, & Speckmann, B. (2005). Rectangular cartograms: construction and animation. In Proc. 21st
Annu. ACM Sympos. Comput. Geom. (pp. 372-373).
Geraerts, R.J., & Overmars, M.H. (2005). Creating small roadmaps for solving motion planning problems. In Proc. 11th IEEE
International Conference on Methods and Models in Automation (pp. 531-536).
Geraerts, R.J., & Overmars, M.H. (2005). On improving the clearance for robots in high-dimensional configuration spaces. In
IEEE/RSJ International Conference on Intelligent Robots and Systems (pp. 4075-4079).
Geraerts, R.J., & Overmars, M.H. (2005). On the Analysis and Success of Sampling Based Motion Planning. In Conference
of the Advanced School for Computing and Imaging (pp. 313-319).
Geraerts, R.J., & Overmars, M.H. (2005). Reachability analysis of sampling based planners. In Proceedings of the IEEE
International Conference on Robotics and Automation (pp. 406-412).
Goemans, O.C., Levandowski, A., Goldberg, K., & Stappen, A.F. van der (2005). On the design of guillotine traps for
vibratory bowl feeders. In Proceedings of the eleventh annual conference of the Advanced School for Imaging and
Computing (pp. 320-327).
Goemans, O.C., Levandowski, A., Goldberg, K., & Stappen, A.F. van der (2005). On the design of guillotine traps for
vibratory bowl feeders. In Proceedings of the IEEE Conference on Automation Science (pp. 79-86).
Gulik, R. van, & Vignoli, F. (2005). Visual playlist generation on the artist map. In Proceedings of the Sixth International
Conference on Music Information Retrieval (ISMIR) 2005 . London, UK.
Haar, F.B. ter, Cignoni, P., Min, P., & Veltkamp, R.C. (2005). A Comparison of Systems and Tools for 3D Scanning. In 3D
Digital Imaging and Modeling: Applications of Heritage, Industry, Medicine and Land .
Kamphuis, A., Pettre, J., Overmars, M.H., & Laumond, J.P. (2005). Path finding for the animation of walking characters. In
Poster Proceedings Eurographics/ACM Symposium on Computer Animation (pp. 8-9). New York: The Association for
Computing Machinery, Inc..
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Kamphuis, A., Rook, M., & Overmars, M.H. (2005). Tactical Path Finding in Urban Environments. In Proceedings First
International Workshop on Crowd Simulation (pp. 51-60). Lausanne: VRLab, EPFL.
Klein, O., & Veltkamp, R.C. (2005). Approximation Algorithms for Computing the Earth Movers Distance Under
Transformations. In Proceedings 16th Annual Symposium on Algorithms and Computation (ISAAC) (pp. 1019-1028).
Springer LNCS 3827.
Klein, O., & Veltkamp, R.C. (2005). Approximation Algorithms for the Earth Movers Distance Under Transformations Using
Reference Points. In Proceedings 21th European Workshop on Computational Geometry (EWCG) (pp. 53-56).
Kok, T. de, Kreveld, M.J. van, & Löffler, M. (2005). Generating realistic terrains with higher-order Delaunay triangulations. In
Proc. 13th Europ. Symp. on Algorithms (pp. 343-354). Berlin: Springer.
Kok, T. de, Kreveld, M.J. van, & Löffler, M. (2005). Minimizing local minima in terrains with higher-order Delaunay
triangulations. In Abstracts of the 21th Europ. Workshop on Comput. Geom. (pp. 115-118).
Kreveld, M.J. van, & Schlechter, T. (2005). Automated label placement for groups of islands. In Proc. 22th Int. Cart. Conf. .
Kreveld, M.J. van, & Speckmann, B. (2005). Rectangular cartogram computation with sea regions. In Proc. 22st Int.
Cartographic Conference .
Niemeijer, M., Ginneken, B. van, Haar, F.B. ter, & Abramoff, M.D. (2005). Automatic detection of the optic disc, fovea and
vascular arch in digital color photographs of the retina. In W.F. Clocksin, A.W. Fitzgibbon, & P.H.S. Torr (Eds.), Proceedings
of the British Machine Vision Conference (pp. 109-118).
Nieuwenhuisen, D., Kamphuis, A., Mooijekind, M., & Overmars, M.H. (2005). Automatic Construction of Roadmaps for Path
Planning in Games. In Proceedings Advanced School for Computing and Imaging Conference (pp. 153-163). Delft: ASCI.
Nieuwenhuisen, D., Stappen, A.F. van der, & Overmars, M.H. (2005). Path planning for pushing a disk using compliance. In
IEEE/RSJ International Conference on Intelligent Robots and Systems (pp. 4061-4067).
Overmars, M.H. (2005). Path planning for games. In Proceedings Third International Game Design and Technology
Workshop and Conference (pp. 29-33). Liverpool: Liverpool John Moores University.
Reinbacher, I., Benkert, M., Kreveld, M.J. van, Mitchell, J.S.B., & Wolff, A. (2005). Delineating boundaries for imprecise
regions. In Proc. 13th Europ. Symp. on Algorithms (pp. 143-154). Berlin: Springer.
Rook, M., & Kamphuis, A. (2005). Path Finding using Tactical Information. In Poster Proc. Eurographics/ACM SIGGRAPH
Symposium on Computer Animation (pp. 18-19). New York: The Association for Computing Machinery, Inc..
Ruifrok, A., Scheenstra, A., & Veltkamp, R.C. (2005). A Survey of 3D Face Recognition Methods. In Audio- and Video-based
Biometric Person Authentication (AVBPA) (pp. 891-899). Springer.
Ruifrok, A., Scheenstra, A., Bijhold, J., & Veltkamp, R.C. (2005). Facial Image Comparison Using 3D Techniques. In
Proceedings 2nd International Conference on Reconstruction of Soft Facial Parts (RSFP) . Luchterhand Publishers.
Tanase, M., Veltkamp, R.C., & Haverkort, H.J. (2005). Multiple Polyline to Polygon Matching. In Proceedings 16th Annual
Symposium on Algorithms and Computation (ISAAC) (pp. 60-70). Springer LNCS 3827.
Tanase, M., & Veltkamp, R.C. (2005). Part-based Shape Retrieval. In Proceedings ACM Multimedia (pp. 543-546).
Tanase, M., & Veltkamp, R.C. (2005). Part-based Shape Retrieval with Relevance Feedback. In Proceedings International
Conference on Multimedia and Expo (ICME) .
Typke, R., Hoed, M. den, Nooijer, J. de, Wiering, F., & Veltkamp, R.C. (2005). A Ground Truth For Half A Million Musical
Incipits. In Proceedings of the Fifth Dutch-Belgian Information Retrieval Workshop Proceedings of the Fifth Dutch-Belgian
Information Retrieval Workshop (pp. 63-70).
Typke, R., Hoed, M. den, Nooijer, J. de, Wiering, F., & Veltkamp, R.C. (2005). A Ground Truth For Half A Million Musical
Incipits. In Journal of Digital Information Management (pp. 34-39).
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Typke, R., Wiering, F., & Veltkamp, R.C. (2005). A Survey of Music Information Retrieval Systems. In Joshua.D. Reiss &
Geraint.A. Wiggins (Eds.), Proc. 6th International Conference on Music Information Retrieval (pp. 153-160). London: Queen
Mary, University of London.
Geraerts, R.; SAMPLE, System for Advanced Motion Planning Experiments.
2002-2005, C++, Windows.
This is software to experimentally compare various motion planning techniques on different scenes. The software is still
developed further.
Nieuwenhuisen, D.; CALISTO.
2002-2005, C++, Windows.
This is a library for visualization and collision checking in 3-dimensional scenes. The software is still developed further.
Grigore, O.; SHAME – Shape Matching Environment
2000-2005, C++, Windows.
This is a collection of modules for approximation, optimization, and matching of shapes.
2.3.11 Contribution of TUD-LR-frs
Reconstruction of building models from aerial photographs and 2D GIS databases
The research on the interpretation of the aerial images focuses on knowledge-based 3D reconstruction of buildings. Threedimensional building models are increasingly required for urban planning, tourism, telecommunication, etc. Since manual 3D
processing of aerial images is very time consuming, speeding up the reconstruction by automatic procedures has become a
necessity.
Our approach relies on combining pairs of stereo images with 2D GIS (Geographic Information System) data and domain
knowledge. The domain knowledge includes a building library describing primitive building models (flat roof, gable roof, and
hip roof building) since most buildings can be described as an aggregation of these building primitives.
In 2002, the performance of the building reconstruction system was evaluated. About 75% of buildings in a suburban
environment were successfully reconstructed. This result implies that a significant cost reduction is possible in the production
of 3D city models that are currently based on manual measurements. The results were documented in a PhD thesis that was
approved by the supervisor in December 2002.
Reconstruction of industrial sites from terrestrial laser scanner data and photographs
We present a method for 3D reconstruction of industrial sites using a combination of images and point clouds with a
motivation of achieving higher levels of automation, precision, and reliability. Recent advances in 3D scanning technologies
have made possible rapid and cost-effective acquisition of dense point clouds for 3D reconstructions. As the point clouds
provide explicit 3D information they have a much higher potential for the automation of reconstruction.
The modelling pipeline in our algorithm starts from point clouds as the main data source for automation. First of all we
segment the point cloud using surface smoothness and detect simple objects like planes and cylinders using Hough
Transform. This is followed by fitting of CSG objects to a combination of segments. The fitted CAD models are used as
registration targets for adding more scans to the project. Additionally, by fitting the projected edges to image gradients we
register images to point clouds. (STAR project)
Reconstruction of natural sites from terrestrial laser scanner data and photographs
The purpose of the research is 3D modelling and reconstruction of (real world) trees on the basis of terrestrial laser scans.
To identify the structure of a tree in terms of stem and branches, an algorithm has been designed in 3D voxel space, based
on a selection of basic and advanced 2D raster (image) processing algorithms, transferred into the 3D domain. The selection
includes filtering, mathematical morphology, skeletonization, connected component labelling and shortest route computation.
(Natscan project)
Traffic monitoring and modelling using helicopter video sequences
Traffic congestion is an important problem in modern society. Better understanding of its causes is needed to be able to
more effectively reduce its effects. Congestion appears under a variety of circumstances. Beside the size and amount of
roads and the number of vehicles on those roads, the occurrence of traffic congestion is highly dependent upon the
behaviour of the individual vehicle drivers. Important factors are reaction speeds, the gap-acceptance and the lane-changing
behaviour of the drivers. Due to the lack of detailed data on driver behaviour, contemporary traffic flow theories and models
cannot be rigorously calibrated and validated, although there are very strong indications that these models are not able to
correctly capture complex driving dynamics during congested or near-congested traffic flow.
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External Projects
Tracing Congestion Dynamics
STW/CITG, Dec. 2004 – Dec. 2008, k€ 178,4 The goal of the proposed research project is to develop a traffic data collection
system based on image sequences taken from a helicopter as well as to use this traffic data to calibrate and improve driver
behaviour models.
Abbass Malian, Ali Azizi, Frank A. van den Heuvel, Mahmoud Zolfaghari Development of a robust photogrammetric
metrology system for monitoring the healing of bedsores Photogrammetric Record 20 (111) september 2005, pp. 241-273
George Vosselman, Patrice Kessels, Ben Gorte. The utilisation of airborne laser scanning for mapping International Journal
of Applied Earth Observation and Geoinformation 6 (2005) pp. 177-186
Marco Baars, Peter van Oosterom, Edward Verbree, Ben Gorte Structuring, indexing, querying and visualizing moving
objects in a DBMS 7th AIGLE Conference on Geographic Information Science “29 April – 1 May 2004, Heraklion, Greece
Parallel Session 3.3 “Database Technology” pp. 251- 260
T. Rabbani, Frank van den Heuvel Efficient hough transform for automatic detection of cylinders in point clouds, ASCI 2005
conference, Het Heijderbos, Heijen, June 8 -10, 2005
T. Rabbani, Frank van den Heuvel Efficient hough transform for automatic detection of cylinders in point clouds, ISPRS
Workshop Laser scanning 2005, Enschede, September 12-14, 2005 pp. 60-65, ISSN 1682-1750
T. Rabbani, Frank van den Heuvel Automatic point cloud registration using constrained search for corresponding objects 7th
Conference on Optical 3-D Measurement Techniques, October 3-5, 2005, Vienna, Austria
Part 1, pp. 177-186 ISBN 3-9501492-2-8
B.G.H. Gorte, F. Karimi Nejadasl, Serge P. Hoogendoorn Outline extraction of a motorway from helicopter image sequence
ISPRS, DAGM Vienna Workshop CMRT 05 August 29-30, 2005 pp. 179-184, ISSN 1682-1750
B.G.H. Gorte, N.Pfeifer, S. Oude Elberink Height texture of low vegetation in airborne laser scanner data and its potential for
DTM correction IAPRS Vol XXXVI, 3/W3, Proceedings of Laserscanning 2005, Enschede, The Netherlands, 2005
pp.174-179, ISSN 1682-1750
R. Lindenbergh, N.Pfeifer, T. Rabbani Accuracy analysis of the Leica HDS3000 and feasibility of tunnel deformation
monitoring IAPRS Vol XXXVI, 3/W3, Proceedings of Laserscanning 2005, Enschede, The Netherlands, 2005 pp. 24-29,
ISSN 1682-1750
G. Sithole, G. Vosselman Filtering of airborne laser scanner data based on segmented point clouds IAPRS Vol XXXVI, 3/W3,
Proceedings of Laserscanning 2005, Enschede, The Netherlands, 2005 pp.66-71, ISSN 1682-1750
2.3.12 Contribution of TUD-EWI-mm-cgcc
Geometric modeling
Research on geometric modeling is directed towards feature modeling, which allows modeling of 3D objects with features,
i.e. parametric shapes with a functional meaning. The most important research issues are feature validity maintenance,
constraint solving, multiple-view feature modeling and conversion, freeform features, mesh generation, and collaborative
design.
Scientific visualisation
Research on visualisation is focused on the development of algorithms and data structures for extracting information from
large scientific and engineering data sets, and visualizing this information with computer graphics and virtual reality
techniques. Main application areas are flow visualization and medical visualization.
Virtual reality
Interaction techniques for exploring and manipulating data in 3D virtual environments, and techniques for collaborative
visualization. Important applications are in atmospheric research and molecular biophysics.
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External projects
Direct Numerical Simulation of Oil/Water Mixtures Using Front Capturing Techniques
NWO-EW Computationjal Science program, 2001-2005, 1 OIO, Ir. B. Vrolijk Joint project with the Fluid Dynamics group
(Mechanical Engineering), and the Numerical Mathematics group (EWI). Goal of the project is the development of
visualization techniques for very large 3D time-dependent flow datasets; extension of feature extraction and time tracking
techniques to visualize the shape of phase fronts in a multi-phase flow, and its development in time.
Semantics of families of objects
NWO-EW, 2003-2007, 1 OIO, ir. R. van der Meijden Techniques for defining and classifying objects as member of a family of
parametric objects. These methods will be based on semantic feature modelling, in which shapes with well-defined
semantics and constraints are used to model objects. Of particular interest are techniques to compute the ranges of
parameters that correspond to members of a family.
Visualization of Cumulus Clouds in Virtual Reality
NWO-EW, 2004-2009, 1 OIO, E.J. Griffith MSc. Joint project with the Physics Department on visualiszation of Large-Eddy
Simulations (LES) for atmospheric research to help resolve important research questions on cloud dynamics, cloud mixing
phenomena, and precipitation. Our contribution is data handling and interactive visualization for very large time-varying data
sets from cloud simulations.
Architectures for scientific and medical visualization, Bsik VL-e (Virtual Laboratory for e-science)
2004 - 2007, postdoc, dr. C.P. Botha. The aim of this project is to extend the DeVIDE visualization architecture with more
general facilities for grid-based computing (resource and data management) and intelligent techniques for semi-automatic
network configuration and prototyping for component development. Cooperation with LUMC (Reiber, Lelieveldt) and UvA
(Belleman, Olabarriaga).
Techniques for Collaborative Visualization in Virtual Environments, Bsik VL-e
2004-2007, post-doc, dr. M. Koutek. Techniques for distributed and collaborative visualization in virtual environments, and
3D interaction; design of software architectures for multi-platform collaborative VR support.Cooperation with CWI (van Liere),
VU (Bal) and TUD-PGS (Epema).
Interaction techniques for virtual environments, Bsik BRICKS-MSV2, 2004-2008
1 OIO, ir. G. de Haan. Research on generic Virtual Reality software architecture and interaction techniques for navigation,
object manipulation, and exploration, to make 3D interaction more comfortable, fast, and effective. Interaction metaphors
such as pseudo-haptic visual force feedback are investigated.Cooperation with CWI (van Liere) and UU (van der Stappen).
Surface and volume geometry processing for lesion detection and segmentation in virtual colonoscopy
Philips Medical Systems, 2004-2008, 1 AIO, Lingxiao Zhao MSc.Research on the determination and use of geometric
properties of the inner surface of the human colon for automatic pre-detection of colonic polyps. Invertigation of higher-order
geometric properties (curvature) for claculation of distinctive features for polyp detection. Cooperation with TUD-TNW-QI
(van Vliet)
Integration of design and analysis
NWO-EW, 2005-2009, 1 OIO, drs. M. Sypkens Smit.The goal of this project is to develop efficient meshing methods for finite
element analysis. For 3D meshes, a method will be developed to only locally update the mesh where the design model has
actually been modified. For cases in which it is unfeasible to analyse a full 3D model, methods will be developed to generate
meshes for idealised (simplified) models, and to automatically propagate changes in such a model to the design model.
Multifield Medical Visualization
NWO-VIEW, 2005-2010, 2 OIO, ir. J. Blaas and S. Busking, MSc. An increasing number of medical acquisition and
processing techniques are generating large amounts of multi-field data, such as data from different imaging modalities. Many
of these datasets are also time-varying, for example in heart motion studies. In this project, we want to transfer knowledge
and techniques from closely related fields such as vector and tensor field visualization in scientific visualization, to medical
visualization applications.Joint project with TUE-BME (ter Haar-Romeny, Vilanova).
Doctoral Degrees
Botha, CP (2005, september 12). Techniques and software architectures for medical visualisation and image processing.
TUD Technische Universiteit Delft, 180 pag., ISBN 90-8559-094-9. Internal project.
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Vos, FM, Gelder, RE van, Serlie, IWO, Florie, J, Nio, CY, Post, FH, Truyen, R, Vossepoel, AM, & Stoker, J (2005). Virtual
colonoscopy (Ch. 9). In J Dankelman, CA Grimbergen, & HG Stassen (Eds.), Engineering for patient safety: issues in
minimally invasive procedures (pp. 206-227). Mahwah (NJ), USA: Lawrence Erlbaum Associates (ISBN 0-8058-4905-X).
Bidarra, AR, Madeira, J, Neels, WJ, & Bronsvoort, WF (2005). Efficiency of boundary evaluation for a cellular model.
Computer-aided design, (ISSN 0010-4485), 37(12), 1266-1284.
Botha, CP, & Post, FH (2005). Improved perspective visibility ordering for object-order volume rendering. The Visual
Computer, (ISSN 0178-2789), 21(11), 887-896.
Bruin, PW de, Dercksen, V.J., Post, FH, Vossepoel, AM, Streekstra, G.J., & Vos, FM (2005). Interactive 3D segmentation
using connected orthogonal contours. Computers in biology and medicine, (ISSN 0010-4825), 35(4), 329-346.
Meiden, HA van der, & Bronsvoort, WF (2005). An efficient method to determine the intended solution for a system of
geometric constraints. International journal of computational geometry & applications, (ISSN 0218-1959), 15(3), 279-298.
Song, Y, Vergeest, JSM, & Bronsvoort, WF (2005). Fitting and manipulating freeform shapes using templates. Journal of
Computing and Information Science in Engineering, (ISSN 1530-9827), 5(2), 86-94.
Bidarra, AR, Nyirenda, PJ, & Bronsvoort, WF (2005). A feature-based solution to the persistent naming problem. In LA Piegl
(Ed.), Computer-aided design and applications, CAD'05 Vol. 2. Computer-aided design and applications, (ISSN 1686-4360)
(pp. 517-526). Bangkok, Thailand: CAD Solutions Company Ltd..
Blaas, J, Botha, CP, Peters, B, Vos, FM, & Post, FH (2005). Fast and reproducible fiber bundle selection in DTI visualization.
In CT Silva, E Gröller, & H Rushmeier (Eds.), Proceedings IEEE Visualization 2005 (pp. 59-64). Piscataway (NJ), USA:
IEEE (ISBN 0-7803-9462-3).
Botha, CP, Graaf, T de, Root, R, Wielopolski, P, Schutte, S, Post, FH, Helm, FCT van der, Simonsz, H, & Simonsz, H
(2005). Time-varying three-dimensional vector field visualisation for the analysis of retrobulbar fat mobility during eye motion.
In BJA Kröse, HJ Bos, EA Hendriks, & JWJ Heijnsdijk (Eds.), ASCI 2005 - Proceedings of the 11th annual conference of the
Advanced School for Computing and Imaging (pp. 271-275). Delft, The Netherlands: Advanced School for Computing and
Imaging (ISBN 90-803086-0-9).
Carpentier, GJP, & Bidarra, AR (2005). Behavioral assumption-based prediction for high-latency hiding in mobile games. In
Q Mehdi & N Gough (Eds.), Proceedings of CGAMES'2005 (pp. 83-88). Wolverhampton, UK: University of Wolverhampton
(ISBN 0-9549016-2-6).
Griffith, EJ, Post, FH, Koutek, M, Heus, T, & Jonker, HJJ (2005). Feature tracking in VR for cumulus cloud life-cycle studies.
In R Blach & E Kjems (Eds.), Virtual Environments 2005, Eurographics/ ACM SIGGRAPH Symposium Proceedings (pp. 5964). Aire-la-Ville, Switzerland: Eurographics Association (ISBN 3-905673-21-5).
Haan, G de, Koutek, M, & Post, FH (2005). IntenSelect: using dynamic object rating for assisting 3D object selection. In R
Blach & E Kjems (Eds.), Virtual Enviroments 2005, Eurographics/ ACM SIGGRAPH Symposium Proceedings (pp. 201-209).
Aire-la-Ville, Switzerland: Eurographics Association (ISBN 3-905673-21-5).
Meiden, HA van der, & Bronsvoort, WF (2005). A constructive approach to calculate parameter ranges for systems of
geometric constraints. In L Kobbelt & V Shapiro (Eds.), Proceedings of SPM 2005, ACM symposium on Solid and Physical
Modeling (pp. 135-142). New York, USA: ACM Press (ISBN 1-59593-015-9).
Nyirenda, PJ, Bronsvoort, WF, Langerak, TR, Song, Y, & Vergeest, JSM (2005). A generic taxonomy for defining free-form
feature classes. In LA Piegl (Ed.), Computer-aided design and applications, CAD'05 Vol. 2. Computer-aided design and
applications, (ISSN 1686-4360) (pp. 497-506). Bangkok, Thailand: CAD Solutions Company Ltd..
Vergeest, JSM, Langerak, TR, Song, Y, Wang, C, Bronsvoort, WF, & Nyirenda, PJ (2005). Towards reverse design of
freeform shapes. In V Skala (Ed.), WSCG'2005 Short papers proceedings (pp. 165-168). Plzen, Czech Republic: University
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of West Bohemia (ISBN 80-903100-9-5).
Vrolijk, B, & Post, FH (2005). Fast out-of-core isosurface extraction and rendering of time-varying data sets. In BJA Kröse,
HJ Bos, EA Hendriks, & JWJ Heijnsdijk (Eds.), ASCI 2005 - Proceedings of the 11th annual conference of the Advanced
School for Computing and Imaging (pp. 120-129). Delft, The Netherlands: Advanced School for Computing and Imaging
(ASCI) (ISBN 90-803086-0-9).
C.P. Botha, DeVIDE = Delft Visualisation and Image Processing Development Environment
Developed from 2002-present, language: Python / C++, OS: Linux, Windows
DeVIDE is a generic software platform created in order to prototype, test and deploy new visualization and image processing
algorithms and ideas, mainly intended for medical applications, but also usable for other applications. It provides a highly
interactive and flexible development and test environment, and it features integrated functionality of the VTK and ITK toolkits
for visualisation and image processing.
Highlight
G. de Haan, E.J. Griffith, M Koutek and F.H. Post
Supportive Interaction and Hybrid Interfaces in Virtual Environments
Hybrid user interfaces integrate well-known 2D user interface elements in a 3D virtual environment, and provide a familiar
and portable interface across a variety of Virtual Reality systems. We employ Virtual Reality as a means for enhancing
interactive scientific visualization and data exploration. We focus on the visualization and control of simulations of physical
processes. The Cloud Explorer, illustrated here, is one of our main applications of interest. The goal of this application is to
facilitate cumulus cloud life-cycle studies. Large data sets are generated by atmospheric simulations, from which various
information modalities and features are extracted in an offline preprocessing phase. The resulting data can be interactively
explored in a virtual environment, such as the Virtual Workbench, equipped with tracked stereo glasses, a stylus and a
transparent acrylic hand-held panel called the PlexiPad.
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2.3.13 Contribution of UvA- FdNWI-isis
The main research themes are
In the area of computer vision our efforts concentrate on semantic access to images by providing a description of objects
regardless the accidental effects that illumination and viewpoint have on the appearance of the objects. As a next type we do
similar research in the description of object classes regardless the accidental recording conditions. Specifically, we employ
color as an important source of information, as well as texture and local shape.
Content-based access of visual data has been a topic of study for some time now. Based on the invariant colour, texture,
and shape features, described above, successful methods have been designed to achieve image description at a semantic
level. Recently, we have included the recognition of emotion, motion patterns, scenes, and individuals, in addition to objects
and object types as important means to access visual data.
Computer vision
Colour is an important cue in image analysis. Image processing of color images requires special attention as well as new
possibilities to see detail where grey value methods cannot.
In previous years, local color, geometric and spatial frequency invariants were developed at ISIS. These local features aim at
the robust measurement of the color, shape and texture of an object, under the most common accidental viewing conditions.
These accidental conditions can be largely characterized by direction of view, the incident light, the color of the light and the
other accidents such as the presence of foreground or background cluttering. An invariant representation of the object
implies that the various conditions under which the same view of the object may be perceived do not have to be learned. To
test the discriminative power of color, geometric and spatial frequency invariants, the ALOI collection was recorded,
containing color images of 1000 real-world objects recorded under various illumination directions, and different illumination
colors.
Another important topic is feature detection by color saliency boosting. There exists a broad agreement that local features
(such as depicted in Figure 2) are an efficient tool for object recognition due to their robustness with respect to occlusion and
geometrical transformations. The success of local features is greatly dependent on the information content of the selected
features. From information theory it is known that the information content of a feature is related to its frequency of
occurrence. Features with high information content, so called salient features, are characterized by a low frequency of
occurrence. They represent rare events in the world.
Another important research result is on color invariance. We proposed invariants which increase discriminative power for
object recognition when compared to the visual measurements of which the invariants were composed. More specifically, the
illumination intensity invariant W and the color constant shadow and shading invariant N proof to be discriminative when
recognizing objects from a data set containing much photometric variation. However, the invariants are shown to be only
marginally color constant. The invariant sets outperform SIFT-features extracted from distinctive key points when the object
is recorded under various illumination directions or when the object is rotated in 3 dimensions. Combining local invariant
features and the incorporation of color are known to be nontrivial problems in computer vision, for which we have provided
solutions.
From the general theory, methods are derived for industrial colour vision, analysis of colour in documents, colour in
microscopy, general images as appearing on the worldwide web. The topic on colour has led a Ph.D. thesis by J. van de
Weijer entitled "Color Features and Local Structure in Images" and many publications in journals (International Journal on
Computer Vision and IEEE Trans. on Pattern Analysis and Machine Intelligence). IEEE Trans. on PAMI is the most
prominent journal in the area of pattern recognition and is among the top three journals in computer science in the world. We
aim at expanding the analysis to take on the same invariant representation of texture next, learning to fuse various color
invariant models as well as the semantic meaning of colour.
Another important aspect in computer vision is Segmentation and Learning and Tracking. Image segmentation is the task of
delineating the image of an object from the real world in the digital data array. It is one of the fundamental difficulties of
computer vision, easily surpassed by man's superior capabilities. The difficulty resides in the fact that even man cannot
rarely give a formal pictorial description why a boundary is positioned at a certain location and that is what a computer needs
to perform the job. We contribute a variety of solutions.
First, we found proper solutions to combine derivatives of the different color channels to compute locale image structures
such as edges, corners, circles etc. Further, learning methods have been used to select and weight color (invariant) models
for discriminatory and robust image feature detection. Finally, we proposed a classification scheme to classify the physical
nature of image structures such as shadow, highlight and material edges/corners.
Content-based access of visual data
Color plays an indispensable role in the attribution of saliency. Postboxes are painted red to facilitate locating them, flowers
take on bright colors to attract birds, and traffic signs use highly saturated colors to attract attention of traffic participants. An
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evaluation of existing features detectors, including both color and luminance-based methods reveals that these methods fail
to detect salient features. We have developed powerful methods to improve the saliency, and thereby the information
content, of existing feature detectors.
To assess the information content of color features, we investigated their frequency of occurrence. To this end, the
probability distribution of color-derivatives, which are the most commonly used building blocks for feature detectors, is
computed on a dataset of 40.000 images (the Corel dataset). The distribution is given in Figure 2. The axes are in the
opponent color space, where the xy-plane indicates the variation in color values, and the z-axis the variation in intensity.
Here an interesting phenomena is revealed, which clarifies the failure of classical feature detectors. Variations in the real
world are dominated by luminance changes. Classical feature detectors which equally value changes in the color and in the
luminance direction are therefore dominated by luminance variations.
To improve the saliency of the detected features, we developed a proper method to correct the inhomogeneous distribution
of color derivatives. The function which attains this result, called the color saliency boosting function, regulates the
amplification of the color variations. The amount of amplification is derived from information theory applied to the distribution
of color derivatives. Results of saliency boosting are depicted in Figure 2. After saliency boosting the detectors focus on the
regions with higher information content: the commercial panes in the shopping street, and the yellow-jersey and the
American flag in the sport picture.
Figure 2. a) Distribution of color derivatives in opponent color space. The ellipsoid-like surfaces indicate derivatives with
equal probability. Variations in the luminance direction (z-axis) occur more frequent than in the variations in the color-plane
(xy-plane). b) Kalverstraat-image, with in red a Harris detector and in yellow the Harris detector with color saliency boosting.
c) Lance-image, with in yellow the affine invariant features Harris-Laplace detector, and in red the same detector after color
boosting.
In the context of object recognition, proper methods to recognize object classes have been proposed. The first solution is to
formulate the recognition task as a graph problem searching for the characteristic geographical arrangements of (possibly
missing) parts. The objective function is Bayesian maximum a posteriori estimation, integrating the image likelihood as a
posteriori probability of the part detectors. The variability in the arrangement of object parts is captured by a Gaussian
distribution after translation normalization. Further, a sparse representation has been proposed for coarse and fine object
recognition
The topic on learning for object recognition has led a Ph.D. thesis by Pham Viet Thang entitled "Learning Spatial Relations
for Object Recognition" and one publication will appear in IEEE Trans. on PAMIi. Further, the topic on learning and image
segmentation has lead to several papers in Conference on Computer Vision and Pattern Recognition, the most prestigious
conference on the field of compute vision.
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Figure 1. The MediaMill Semantic Video Search Engine, showing various advanced interfaces for effective video retrieval.
External Projects
D: ImIK
2002-2005, IOP, 400 Keuro, Uva-Science-ISIS and VU. The project considers the interactive exploration of multimedia
information and knowledge.
A computational theory for visual cognition (NWO Veni)
2003-2007, NWO, Uva-Science-ISIS, 200 KEuro. The project aims at developing a computational theory of vision based on
invariant representations.
MultimediaN
2004-2008, BSIK, 32 MEuro, UvA-Science-ISIS, UU-CS, UT-CS, TUD-CS, CTIT-CS, VU-CS, TNO, NFI, Telematica Inst.,
V2, Philips, Ilse, LogicaCMG, Waag Society, DBNL, eMAXX, NOS*NSF, Thales, SPSS, Compano, Paradiso, Verenigd
Digitaal Erfgoed. The project aims at various forms of multi-media access including e-documents and video.
Image retrieval
2001-2005, IOP, Markgraaf, UvA-Science-ISIS. The project aims at analyzing logos, signs to classify them on perceptual
similarity.
Tracking Sport Video
2002-2005, IOP, Philips CFT, UvA-Science-ISIS. The project aims at tracking of objects in sport video.
AMIS
NWO, UvA-Science-ISIS, UU-CS, UT-CS, TUD-CS. The project studies multi-media information analysis.
Parallel library tools for image processing
NWO, TUD-CS, TUD-PH, UvA-ISIS. The project aims at analyzing parallel processes, processing for image processing.
MuNCH
a NWO-CATCH project for the semantic access to video archives, with Guus Schreiber, VU and Maarten de Rijke, ISLAILPS, Beeld&Geluid.
91
Jade
a NWO-Glance project for parallel processing of multimedia data with Henri Bal, VU, and CWI.
TODS
A project with NFI, the forensic lab and ISIS, for forensic data processing, among others on surveillance and crime scene
reconstruction.
CIOS, ISIS
participates in the TNO-center. The Intelligent Sensory Information Systems group was supported by: bsik, IOP-BV, IOPMMI, EU, NWO, STW, Netherlands Forensic Institute, TNO, Philips, Beeld en Geluid.
Doctoral Degrees
T.V. Pham, “Learning Spatial Relations for Object Recognition”, PhD. Thesis, University of Amsterdam, 1 February 2005.
C.G.M. Snoek, The Authoring Metaphor to Machine Understanding of Multimedia, Ph.D. Thesis, University of Amsterdam, 26
October 2005.
J. van de Weijer, “Color Features and Local Structure in Images”, Ph.D. Thesis, University of Amsterdam, 3 March 2005.
Books
Ip, H., Smeaton, A., Smith, J., Smeulders A. (eds); Proceedings of the International Conference on Multimedia and Expo
2005. IEEE Press, 2005.
Sebe, N., Cohen, I., Garg, A., Huang, T.S.; Machine Learning in Computer Vision, Springer Verlag, ISBN 1-4020-3274-9,
2005.
Sebe, N., Lew, M.S., Huang, T.S. (ed); Computer Vision in Human-Computer Interaction, HCI/ICCV 2005, Lecture Notes in
Computer Science, Volume 3766, Springer-Verlag, ISBN 3-540-29620-4, October 2005.
Geusebroek, J.M.; Early cognitive computer vision. In: Zelkowitz, M.V (ed), Advances in Computers. Elsevier Science, 2005.
Sebe, N., Cohen, I., Huang, T.S.; Multimodal Emotion Recognition. In: Handbook of Pattern Recognition and Computer
Vision, World Scientific, ISBN 981-256-105-6, 2005.
Sebe, N., Tian, Q.; Ranking Metrics and Evaluation Measures. In: Advances in Imaging and Electron Physics, Elsevier,
2005.
Cohen, I., Sebe, N., Cozman, F.G., Gevers, Th., Huang, T.S.; Learning Probabilistic Classifiers for Human-Computer
Interaction Applications. ACM Multimedia Systems Journal, volume 10 (6), 2005, pp 484-498.
Hoang, M.A., Geusebroek, J.M., Smeulders, A.W.M.; Color texture measurement and segmentation. Signal Processing,
Volume 85(2), 2005, pp 265-275.
Pham, T.V., Smeulders, A.W.M.; Object recognition with uncertain geometry and uncertain part detection. Computer Vision
Image Understanding, volume 99 (2), 2005, pp 241 – 258.
Sebe, N., Cohen, I., Cozman, F.G, Huang, T.S.; Learning Probabilistic Classifiers for Human-Computer Interaction
Applications. ACM Multimedia Systems, Journal, Volume 10 (6), 2005, pp 484-498.
Weijer, J. van de, Gevers, Th., Geusebroek, J.M.; Color edge and corner detection by photometric quasi-invariants. IEEE
Trans. Pattern Anal. Machine Intell. Volume 27 (4), 2005, pp.625-630.
Wessels, L.F.A., Reinders, M.J.T., Hart, A.A.M., Veenman, C.J., Dai, H., He, T., Veer, L.J. van ‘t; A protocol for building and
evaluating predictors of disease state based on microarray data. Bioinformatics, Volume 21 (19), 2005, pp. 3755-3762.
Aldershoff, F., Gevers, TH., Prins, P.; Model-assisted object tracking. SPIE, Internet Imaging, San Jose 2005.
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Amores, J., Sebe, N., Radeva, P.; Fast Spatial Pattern Discovery Integrating Boosting with Constellations of Contextual
Descriptors. IEEE Conference on Computer Vision and Pattern Recognition (CVPR’05), San Diego, USA, June 2005.
Blok, M., Danilouchkine, M.G., Veenman, C.J., Admiraal-Behloul, F., Hendriks, E.A., Reiber, J.H.C.,
Lelieveldt, B.P.F.; Long-Axis Cardiac MRI Contour Detection with Adaptive Virtual Exploring Robot. Functional Imaging and
Modeling of the Heart, Barcelona 2005, Lecture Notes in Computer Science 3504 Springer 2005, ISBN 3-540-26161-3.
Damen, R., Putten, M.J.A.M. van, Veenman, C.J.; Feature and classifier selection for computer assisted EEG interpretation
in Book of Abstracts of the 12th European Congress of Clinical Neurophysiology (ECCN), Stockholm 2005.
Geusebroek, J.M.; The stochastic structure of images. In :R. Kimmel, N. Sochen, and J. Weickert, (ed), Proc. 5th Int. Conf.
Scale Space and PDE Methods in Comput. Vision (Scale Space 2005), pages 327-338. Springer Verlag (LNCS), 2005.
Gemert, J.C. van, Burghouts, G.J., Seinstra, F.J., Geusebroek, J.M.; Color invariant object recognition using entropic graphs.
In: Wijk, J.J. van (ed), ASCI’05, Proceedings of the 11th annual conference of the Advanced School for Computing and
Imaging, pp. 192-199.
Gevers, Th. and Aldershoff, F.; Color Feature Detection and Classification by Learning. IEEE International Conference on
Image Processing (ICIP), Genova 2005.
Jaimes, A., Nagamine, T., Liu, J., Omura, K., Sebe, N.; Affective Meeting Video Analysis. IEEE International Conference on
Multimedia and Expo (ICME’05), Amsterdam, The Netherlands, 2005.
Jaimes, A., Sebe, N.; Multimodal Human Computer Interaction: A Survey. IEEE International Workshop on Human-computer
Interaction, Beijing, China, 2005.
Lehmann, A.S., Pont, S.C., Geusebroek, J.M.; Tree textures: Modern techniques in art-historical context. In: Chantler, M.
(ed) Proc. 4th Int. Workshop on Texture Anal. and Synthesis (Texture 2005), Heriot-Watt University, 2005, pp. 43-48
Nguyen, G.P., Worring, M.; Scenario optimization for interactive category search. 7th ACM SIGMM International Workshop
on Multimedia Information Retrieval, Singapore 2005.
Viet Pham, T., Smeulders, A.W.M., Ruis, S.; Adaboost learning of shape and colour features for object recognition. ICML
2005 Workshop on Machine Learning Techniques for Processing Multimedia Content, 2005.
Sebe, N., Cohen, I., Gevers, Th., Huang, T.S.; Multimodal Approaches for Emotion Recognition: A Survey. Internet Imaging
VI, SPIE’05, San Jose 2005.
Sebe, N., Cohen, I., Huang, T.S., Gevers, Th.; Semi-supervised Face Detection. IEEE Workshop on Learning in Computer
Vision and Pattern Recognition, San Diego, USA, June 2005.
Sebe, N., Cohen, I., Huang, T.S., Gevers, Th.; Human-Computer Interaction: A Bayesian Network Approach. IEEE
International Symposium on Signals, Circuits and Systems, Iasi, Romania, 2005.
Sebe, N., Bakker, E., Cohen, I., Gevers, Th., Huang, T.S.; Bimodal Emotion Recognition. 5th International Conference on
Methods and Techniques in Behavioral Research, Wageningen 2005, The Netherlands.
Pantic, M., Sebe, N., Cohen, J., Huang, T.S.; Affective Multimodal Human-Computer Interaction. ACM Multimedia,
Singapore 2005.
Putten, M.J.A.M. van, Vliegen, H.R., Veenman, C.J.; Detecting seizure activity from scalp EEG recordings: a comparison of
different features and classifiers. Book of Abstracts of the 12th European Congress of Clinical Neurophysiology (ECCN),
Stockholm, Sweden, May, 2005.
Putten, M.J.A.M. van, Vliegen, H.R., Veenman, C.J.; Feature and classifier selection for computer assisted EEG
interpretation. 3rd European Medical and Biological Engineering Conference; IFMBE European Conference on Biomedical
Engineering, Prague, Czech Republic, 2005.
Seinstra, F.J., Snoek, C.G.M., Koelma, D.C., Geusebroek, J.M., Worring, M.; User Transparent Parallel Processing of the
2004 NIST TRECVID Data Set. 19th International Parallel and Distributed Processing Symposium, Denver 2005 USA.
Snoek, C.G.M, Gemert, J.C. van, Geusebroek, J.M., Huurnink, B., Koelma, D.C., Nguyen, G.P., Rooij, O de,
93
Stokman, H.G.M., Gevers, Th.; Selection and Fusion of Color Models for Feature Detection. International Conference on
Computer Vision and Pattern Recognition (CVPR05), San Diego 2005.
Stokman, H.M.G., Gevers, Th.; Optimal weighting of color channels for discriminative edge detection. SPIE, Internet
Imaging, San Jose 2005.
Su, K., Tian, Q., Xue, Q., Sebe, N., Ma, J.; Neighborhood Issue in Single-frame Image Super-resolution. IEEE International
Conference on Multimedia and Expo (ICME’05), Amsterdam 2005, The Netherlands.
Tax, D.M.J., Veenman, C.J.; Tuning the hyperparameter of an AUCoptimized classifier. 17th Belgium-Netherlands
Conference on Artificial Intelligence 2005, pp 224-231.
Veenman, C.J., Tax, D.M.J.; A Weighted Nearest Mean Classifier for Sparse Subspaces. IEEE Computer Society
Conference on Computer Vision and Pattern Recognition, San Diego 2005, USA.
Weijer, J. van de, Gevers, Th.; Boosting Saliency in Color Image Features. International Conference on Computer Vision and
Pattern Recognition (CVPR05), San Diego 2005.
Weijer, J. van de, Gevers, Th.; Color Constancy based on the Grey-Edge Hypothesis. IEEE International Conference on
Image Processing (ICIP), Genova 2005.
Zhang, L., Tian, Q., Sebe, N., Ma, J.; Video Object Boundary Reconstruction by 2-pass voting. IEEE International
Conference on Multimedia and Expo (ICME’05), Amsterdam 2005, The Netherlands.
Geusebroek, J.M., Burghouts, G., Smeulders, A.W.M.; The Amsterdam Library of Object Images. ALOI is a color image
collection of one-thousand small objects. In order to capture the sensory variation in object recordings, we systematically
varied viewing angle, illumination angle, and illumination color for each object, and additionally captured wide-baseline stereo
images. We recorded over a hundred images of each object, yielding a total of 110,250 images for the collection.
http://www.science.uva.nl/~aloi/
Geusebroek, J.M.; Fast Anisotropic Gauss Filtering software, performs two-dimensional anisotropic Gaussian smoothing and
differentiation by recursive filtering techniques. http://www.science.uva.nl/~mark/downloads/
Koelma, D., Poll, E.; Horus: a vision library based on patterns. http://www.science.uva.nl/~koelma/isis/projects/horus.html
van Liempt, M., Smeulders, A.W.M, Nguyen, H.T.; Template Tracking Using Color Invariant Pixel Features. Tracking objects
robust to photometric variations, such as shadow, shading, and specularities. Handselected objects are followed real-time
from either mpg or webcam video stream. http://staff.science.uva.nl/~mliempt/isis/downloads.html
Nguyen, G.P., Worring, M.; A demo on similarity based visualization of large image collections.
Seinstra, F.J., Koelma, D.; Parallel Horus - 'Proof-of-concept' implementation (partial version) of user transparent parallel
image processing functionality as provided in Horus. http://staff.science.uva.nl/~fjseins/ParHorusCode/
Snoek, C.G.M., Worring, M.; Goalgle: A Soccer Video Search Engine, Goalgle is a prototype search engine for soccer video.
A fully automatic soccer video analysis system has been developed which analyses soccer broadcasts and makes them
accessible by names of players, teams, and highlight events. http://www.goalgle.com
Snoek, C.G.M., Worring, M., Geusebroek, J.M., Koelma, D.C., Seinstra, F.J.; Mediamill demo: Semantic Video Search
Engine. This system allows for interactive retrieval based on a lexicon of 32 automatically derived semantic concepts. The
demo searches a broadcast news archive of 184 hours. http://staff.science.uva.nl/~cgmsnoek/tv/
Snoek, C.G.M., Worring, M.; VIPER: Video Personalizer. VIPER is a prototype search engine for personalized video retrieval
over the Internet. The demo searches a broadcast news archive of 184 hours. http://staff.science.uva.nl/~cgmsnoek/viper/
Todoran, L., Worring, M.; Document Ground Truthing and evaluation tool. A tool has been built for assisting users in ground
truthing scanned color documents based on layout and logical information. It has been used to create the UvA color
document dataset. Tools for evaluating algorithms with respect to the ground truth have been developed as well. Documents
and tools will be made available to the research community.
94
Highlight
We applied our real-time facial expression recognition system on still images, notably on many famous paintings. Our result
on Mona Lisa was fist mentioned in one of the December issues of the New Scientist and was cited in the media worldwide,
see Figure 3. The innovative part was to adapt the system to accommodate static images. Since the original system uses
motion displacements from neutral positions of key facial features to classify the facial expression into one of the emotional
classes, in the case of images we needed to create a prototypical neutral face. This was obtained as a statistical average of
many Caucasian female faces and was adapted to fit Mona Lisa’s face. The obtained results were surprising in the sense
that they were not only credible but also showed a blended facial expression on Mona Lisa’s face, see Figure 3.
Figure 3. Facial expression recognition for Mona Lisa: on the right the wireframe model overlayed on the face; on the left the
recognized facial expression.
2.3.14 Contribution of UL-LUMC-lkeb
Processing, Interpretation and Visualization of Medical Images
Contribution of LUMC-lkeb
The main goal of the Division of Image Processing is the research, implementation and validation of image processing
approaches, which allow the objective and reproducible assessment of objects in medical images. LKEB activities belong to
one of the seven main research fields of the LUMC under the headings “Vascular Medicine” and “Neuro-science”. Part of the
research involves computer vision research and algorithm development, whereas clinical applications also play an important
role. Applications focus on Neuro-imaging, Pulmonology, Orthopaedics, Cardiology and molecular and cellular imaging. In
2005, important research directions were:
Statistical shape modeling
Statistical shape models are widely used to integrate a-priori knowledge about shape and image appearance into
segmentation algorithms. Research at LKEB is directed towards dimensional extension of statistical shape models. A 3D
Active Shape Model has been developed, along with 3D and multi-view Active Appearance Models; these models have been
applied to segmentation of cardiac MR, CT, echo and X-angiographic data. Apart from segmentation, we are developing
statistical shape models for computer-aided diagnosis to detect cardiac shape- and motion abnormalities in MR images for
patients with a cardiac infarction, and for quantifying local shape changes caused by brain diseases. We recently
investigated shape differences of the brain ventricles in the aging population and Alzheimer disease. Because of the
challenging shape of the ventricles, we developed a new method based on growing neural networks to fully automatically
model complexly shaped objects.
Multi-agent image processing
The major objective of this research is to develop a general and adaptive learning multi-agent image interpretation system,
which automatically learns how to interpret (medical) images from examples and user-interactions. The system should be
flexible and easy to adapt to changes in patient context, expert preferences, or imaging devices, by the use of both low-level
training / optimization and high-level rules.
The system will be applied to very difficult segmentation problems in images that cannot be solved with only traditional
and/or model-based segmentation methods alone. To this end we are investigating how probabilistic models, reinforcement
learning techniques, evolutionary algorithms, high-level (explicit) knowledge and low-level image processing may be
integrated into our current multi-agent image interpretation system. The system will first be used for the interpretation of
IntraVascular UltraSound (IVUS) and Computed Tomography Angiography (CTA) images.
95
Development of a virtual mobile exploration robot
In this project, we address the problem of virtual central navigation in 3D tubular structures. A virtual mobile robot, equipped
with a neuro-fuzzy controller, is trained to navigate inside image datasets of tubular structures, keeping a central position;
virtual range sensors are used to sense the surrounding walls and to provide input to the controller. Aim of this research is:
first the identification of smooth and continuous central paths which are useful in several medical applications: virtual
endoscopy, virtual colonoscopy, virtual angioscopy, virtual bronchoscopy, etc. We fully validated the algorithm on synthetic
datasets, and performed successful experiments on a colon dataset. Second to train the virtual robot to detect novelties
(pathologies) along the path, just like a security agent would do. It will highlight any significant deviation from the normal
environment (training using images acquired from healthy subjects),
Clinical Image Analysis Applications
Much of the research at LKEB is driven by questions from clinical partners. To this end, we are developing algorithms and
software for:
• Detection and quantification of pulmonary emphysema in CT Images
• Early detection of micro motion of prosthetic implants in bi-plane X-ray images
• Fusion of molecular, functional and structural imaging
• Automatic analysis of coronary vessels in CT and intravascular ultrasound images
• Automatic analysis of coronary and left-ventricular angiograms
• Automatic analysis of cardiac funtion in MR and CT patient studies
• Automatic analysis of changes in brain structure with ageing and disease
• Automatic analysis of vascular MR data
• Automatic white matter lesion detection in MR images of the brain
• Automatic analysis of quantitative MR images of the brain
External projects
CYTTRON
2004-2008 BSIK, with UL-WI-I and TUD-TNW-tn-qi: Development of a comprehensive, integrated infrastructure for bioimaging and modeling cells down to atomic detail.
SAVAGE
2004-2008, NWO-E, with UL-WI-I: Development of self-learning image processing agents in a multi-agent framework for
medical image interpretation.
LAISA
2004-2008, STW: Application of multi-agent image processing platform in IVUS and CTA image data.
Automated evaluation of vascular MR image data
2004-2007 STW
Autonomous virtual robots for medical image exploration
2003-2007 SNN
Automatic analysis of 3D echocardiographic data acquired with a fast rotating ultrasound probe
2003-2007, SENTER IOP BV
Software Development for the Detection and Assessment of Small Airways Disease in COPD with Multi Slice
Computed Tomography,
2003-2007 Netherlands Asthma Foundation
Data fusion of different components of MR patient studies
2002-2006 STW
Computer-aided diagnosis for cardiac MR data
2002-2007, NWO VIDI
Model-based röntgen-stereofotogrammetric analysis of orthopedic implants
2002-2005 STW
96
Contributions to books
A.F. Frangi, W.J. Niessen, M.A. Viergever, B.P.F. Lelieveldt, “A survey of three-dimensional modelling techniques for
quantitative functional analysis of cardiac images”, in “Advanced Image Processing in Magnetic Resonance Imaging” (eds.
Landini, Positano, Santarelli), pp 267-341, Taylor & Francis, ISBN 0-8247-2542-5, 2005.
B.P.F. Lelieveldt, A.F. Frangi, S.C. Mitchell, H.C. van Assen, S. Ordas, J.H.C. Reiber, M. Sonka, “3D active shape and
appearance models in cardiac image analysis”, in “Mathematical Models of Computer Vision: The Handbook” (eds N.
Paragios, O. Faugeras), pp 471-484, Springer Verlag, ISBN 0387263713, 2005,
Formatted: Bullets and Numbering
M.Sonka, D.R. Thedens, B.P.F. Lelieveldt, S.C. Mitchell, R.J. van der Geest, J.H.C. Reiber, “Cardiovascular MR image
analysis”, in “Computer vision beyond the visible spectrum”, (Eds B.Bir, I.Pavlidis), pp 193-240, Springer Verlag, Berlin,
ISBN: 1-85233-604-8, 2005.
F.Admiraal-Behloul, J.H.C Reiber, “Neural Network System Technology and Fuzzy-Rule Extraction in High Dimensional Data
sets” .Invited Book Chapter in Cornelius T. Leondes (ed): Intelligent Knowledge-Based Systems: Business and Technology
in the New Millennium , Kluwer Academic Press International, ISBN: 1-4020-7829-3, 2005.
Papers in international Journals
Admiraal-Behloul, F., Heuvel, D. v. d., Olofsen, H., van Osch, M. J. P., van der Grond, J., and van Buchem, M. A. R. J. H. C.,
"Fully automatic segmentation of white matter hyperintensities in MR images of the elderly," Neuroimage, vol. 28, no. 3, pp.
607-617, Nov.2005.
Bakker, ME, Stolk J, Putter H, Shaker SB, Parr DG, Piitulainen E, Russi EW, Dirksen A, Stockley RA, Reiber JH, and Stoel
BC. 2005. Variability in Densitometric Assessment of Pulmonary Emphysema with Computed Tomography. Invest Radiol.
40:777-783.
J.G. Bosch, F. Nijland, S.C. Mitchell, B.P.F. Lelieveldt, O.Kamp, M.Sonka, J.H.C. Reiber, Computer-Aided Diagnosis via
Model-Based Shape Analysis: Automated Classification of Wall Motion Abnormalities in Echocardiograms, Academic
Radiology vol. 12(3):358-67, 2005.
Box FMA, Geest RJ van der, Rutten MCM, Reiber JHC. The influence of flow, vessel diameter, and non-Newtonion blood
viscosity on the wall shear stress in a carotid bifurcation model for unsteady flow. Invest Radiol 2005; 40: 277-94.
Danilouchkine MG, Westenberg JJM, Roos A de, Reiber JHC, Lelieveldt BPF. Operator induced variability in cardiovascular
MR: left ventricular measurements and their reproducibility. J Cardiovasc Magnetic Resonance 2005; 7: 447-57.
Danilouchkine MG, Westenberg JJM, Reiber JHC, Lelieveldt BPF. Accuracy of short-axis cardiac MRI automatically derived
from scout acquisitions in free-breathing and breath-holding modes. MAGMA 2005; 18: 7-18.
M.G. Danilouchkine, R.J. van der Geest, J.J.M. Westenberg, B.P.F. Lelieveldt, J.H.C. Reiber, “Impact of Inaccurate
Positioning and Tilting of Automatically Planned Short-Axis Stack on Quantification of Left Ventricular Dimensions and
Function with Cardiovascular Magnetic Resonance” Journal of Magnetic Resonance Imaging, vol 22(6), pp 754-764, 2005.
M.S.Dirksen, J.W. Jukema, J.J. Bax, H.J. Lamb, E. Boersma, J.C. Tuinenburg, J. Geleijns, E.E. van der Wal, A. de Roos.
Cardiac Multidetector-Row Computed Tomography in Patients with Unstable Angina. Am. J. Cardiol 2005 Feb 15; 95(4):45761.
van Es, A. C., van der Flier, W. M., Admiraal-Behloul, F., Olofsen, H., Bollen, E. L., Middelkoop, H. A., WeverlingRijnsburger, A. W., Westendorp, R. G., and van Buchem, M. A., "Magnetization transfer imaging of gray and white matter in
mild cognitive impairment and Alzheimer's disease," Neurobiol.Aging, Nov.2005.
van der Flier, W. M., Middelkoop, H. A., Weverling-Rijnsburger, A. W., Admiraal-Behloul, F., Bollen, E. L., Westendorp, R.
G., and van Buchem, M. A., "Neuropsychological correlates of MRI measures in the continuum of cognitive decline at old
age," Dement.Geriatr.Cogn Disord., vol. 20, no. 2-3, pp. 82-88, 2005.
van der Flier, W. M., van der Vlies, A. E., Weverling-Rijnsburger, A. W., de Boer, N. L., Admiraal-Behloul, F., Bollen, E. L.,
Westendorp, R. G., van Buchem, M. A., and Middelkoop, H. A., "MRI measures and progression of cognitive decline in
nondemented elderly attending a memory clinic," Int.J.Geriatr.Psychiatry, vol. 20, no. 11, pp. 1060-1066, Nov.2005.
Janssen JP, Koning G, Koning PJH de, Bosch JG, Tuinenburg JC, Reiber JHC. A new approach to contour detection in Xray arteriograms. The Wavecontour. Invest Radiol 2005; 40 (8): 514-20.
97
Kaptein BL, Valstar ER, Stoel BC, Rozing PM, Reiber JHC. A new type of model-based Roentgen stereo-photogrammetic
analysis for solving the occluded marker problem. J Biomechanics 2005; 38: 2330-4.
Marquering HA, Dijkstra J, Koning PJH de, Stoel BC, Reiber JHC. Towards quantitative analysis of coronary CTA. Int J
Cardiovasc Imaging 2005; 21: 73-84.
Meijler FL, Billette J, Jalife J, Kik MJL, Reiber JHC, Stokhof AA, Westenberg JJM, Wassenaar C, Strackee J. Atrioventricular
conduction in mammalian species: Hemodynamic and electrical scaling. Heart Rhythm 2005; 2: 188-96.
S.C. Ordas, H.C. van Assen, J. Puentes, B.P.F. Lelieveldt, A.F. Frangi, “Parametric Optimization of a Model Based
Segmentation Algorithm for Cardiac MR Image Analysis: A Grid-Computing Approach”, Studies in Health Technology and
Informatics, vol 112 / 2005, pp 146-156, 2005.
Paelinck BP, de Roos A, Bax JJ, Bosmans JM, van der Geest RJ, Dhondt D, Parizel PM, Vrints CJ, Lamb HJ. Feasibility of
tissue magnetic resonance imaging: a pilot study in comparison with tissue Doppler imaging and invasive measurement. J
Am Coll Cardiol. 2005;45 (7):1109-1116
van de Sande, MA, Stoel BC, Obermann WR, Lieng JG, and Rozing PM. Quantitative assessment of fatty degeneration in
rotator cuff muscles determined with computed tomography. Invest Radiol 2005; 40:313-319.
Steens, S. C., Steup-Beekman, G. M., Bosma, G. P., Admiraal-Behloul, F., Olofsen, H., Doornbos, J., Huizinga, T. W., and
van Buchem, M. A., "The effect of corticosteroid medication on quantitative MR parameters of the brain," AJNR
Am.J.Neuroradiol., vol. 26, no. 10, pp. 2475-2480, Nov.2005.
Stralen M van, Bosch JG, Voormolen MM, Burken G van, Krenning BJ, Geuns R-JM, Lancée CT, Jong N de, Reiber JHC.
Left ventricular volume estimation in cardiac three-dimensional ultrasound : a semiautomatic border detection approach.
Acad Radiol 2005; 12: 1241-9.
Üzümcü M, Geest RJ van der, Sonka M, Lamb HJ, Reiber JHC, Lelieveldt BPF. Multiview Active Appearance Models for
simultaneous segmentation of cardiac 2- and 4-chamber long-axis magnetic resonance images. Invest Radiol 2005; 40(4):
195-203.
de Vries M, de Koning PJ, de Haan MW, Kessels AG, Nelemans PJ, Nijenhuis RJ, Planken RN, Vasbinder GBC, van
Engelshoven JMA, van der Geest RJ, Leiner T. Accuracy of Semiautomated Analysis of 3D Contrast-Enhanced Magnetic
Resonance Angiography for detection and quantification of aortoiliac stenoses. Invest Radiol 2005;40:495-503.
Wesselius, T., Heersema, D. J., Mostert, J. P., Heerings, M., Admiraal-Behloul, F., Talebian, A., van Buchem, M. A., and De
Keyser, J., "A randomized crossover study of bee sting therapy for multiple sclerosis," Neurology, vol. 65, no. 11, pp. 17641768, Dec.2005.
Westenberg JJM, Doornbos J, Versteegh MIM, Bax JJ, Geest RJ van der, Roos A de, Dion RAE, Reiber JHC. Accurate
quantitation of regurgitant volume with MRI in patients selected for mitral valve repair. Eur J Cardio-thoracic Surgery 2005;
27: 462-7.
Westenberg JJM, Geest RJ van der, Lamb HJ, Versteegh MIM, Braun J, Doornbos J, Roos A de, Wall EE van der, Dion
RAE, Reiber JHC, Bax JJ. MRI to evaluate left atrial and ventricular reverse remodeling after restrictive mitral annuloplasty in
dilated cardiomyopathy. Circulation 2005; 112 (Suppl I): I-437-42.
van Wijk JPH, Castro Cabezas M, de Koning EJP, Rabelink TJ, van der Geest RJ, Hoepelman IM. In vivo evidence of
impaired peripheral fatty acid trapping in patients with human immunodeficiency virus-associated lipodystrophy J of Clin
Endocrinology Metab. 2005;90:3575-3582.
van den Dool SW, Wasser MN, de Fijter JW, Hoekstra J, van der Geest RJ. Functional renal volume: Quantitative analysis at
gadolinium-enhanced MR angiography – Feasibility study in healthy potential kidney donors. Radiology 2005;236:189-195.
ten Dam VH , Box FMA, de Craen AJM, van den Heuvel DMJ, Bollen ELEM, Murray HM, van Buchem MA, Westendorp
RGJ, Blauw GJ. Lack of Effect of Pravastatin on Cerebral Blood Flow or Parenchymal Volume Loss in Elderly at Risk for
Vascular Disease. Stroke. 2005;36:1633.
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Abrahamyan L, Schaap JA, Hoekstra AG, Shamonin D, Box FMA, Geest RJ van der, Reiber JHC, Sloot PMA. A problem
solving environment for image-based computational hemodynamics. In: Lecture Notes in Computer Science. VS Sunderam,
GD van Albada, PMA Sloot et al. (Eds.). Springer-Verlag Berlin Heidelberg 2005; 287-94.
H.C. van Assen, M.G. Danilouchkine, A.F. Frangi, S. Ordas, J.J.M. Westenberg, J.H.C. Reiber, B.P.F. Lelieveldt, “SPASM:
Segmentation of Sparse and Arbitrarily Oriented Cardiac MRI data using a 3D ASM”, proc. FIMH 2005, Lecture Notes in
Computer Science, vol 3504, pp 33-43, 2005.
M. Blok, M.G. Danilouchkine, C.J. Veenman, F. Admiraal-Behloul, E.A. Hendriks, J.H.C. Reiber, B.P.F. Lelieveldt, “Long-Axis
Cardiac MRI Contour Detection with Adaptive Virtual Robot”, proc. FIMH 2005, Lecture Notes in Computer Science, vol
3504, pp 54-64, 2005.
M.G. Danilouchkine, R.J. van der Geest, F. Admiraal-Behloul, B.P.F. Lelieveldt, J.H.C. Reiber, “Automated Quantification of
Cardiac Short-Axis Multi-Slice CT Images for Assessment of Left Ventricular Global Function”, proc SPIE medical imaging
2005, pp 463-474.
M.G. Danilouchkine, J.J.M. Westenberg, H.C. van Assen, Johan H.C. Reiber, B.P.F. Lelieveldt, “3D Model-Based Approach
to Lung Registration and Prediction of Cardiac Motion due to Respiration”, proc. MICCAI, Lecture Notes in Computer
Science, vol 3750, pp 751-759, 2005.
Ferrarini L, Olofsen H, Reiber JHC, Admiraal-Behloul F. Exploration of 3D medical images of tubular structures: a neurofuzzy
controller for virtual centered navigation. Proceedings 11th Annual Conference ASCI, Heijen: 297-304.
Ferrarini L, Olofsen H, Buchem MA van, Reiber JHC, Admiraal-Behloul F. Fully automatic shape modelling using growing
cell Neural Networks. In: Medical Image Computing and Computer Assisted Intervention - MICCAI 2005: J. Duncan, G. Gerig
(Eds.). Springer-Verlag Berlin, 2005: 451-8.
Ferrarini L, Olofsen H, Reiber JHC, Admiraal-Behloul F. A neurofuzzy controller for 3D virtual centered navigation in medical
images of tubular structures. In: Artificial Neural Networks: Formal models and their Applications – ICANN 2005. W. Duch, J.
Kacprzyk, E. Oja, S. Zadrozny (Eds.). Springer-Verlag Berlin 2005: 371-6
C.R. Oost, G. Koning, M. Sonka, J.H.C. Reiber, B.P.F. Lelieveldt, “Automated Segmentation of X-Ray Left Ventricular
Angiograms using Multi-View Active Appearance Models”, proc. FIMH 2005, Lecture Notes in Computer Science, vol 3504,
pp 23-32, 2005.
S. Ordas, H.C. van Assen, L. Boisrobert, M. Laucelli, J. Puente, B.P.F. Lelieveldt and A.F. Frangi, “Statistical Modeling and
Segmentation in Cardiac MRI using a Grid Computing Approach”, Lecture Notes in Computer Science, vol 3470, pp 6-15,
2005
Sanderse M, Marquering HA, Hendriks EA, Lugt A van der, Reiber JHC. Automatic initialization algorithm for carotid artery
segmentation in CTA images. In: Medical Image Computing and Computer Assisted Intervention - MICCAI 2005: J. Duncan,
G. Gerig (Eds.). Lecture Notes in Computer Science, vol 3750, pp 846-53, 2005
Stralen M van, Bosch JG, Voormolen MM, Burken G van, Krenning BJ, Geuns RJM van, Angelié E, Geest RJ van der,
Lancée CT, Jong N de, Reiber JHC. Semi-automatic border detection method for left ventricular volume estimation in 4D
ultrasound data. Proceedings 11th Annual Conference ASCI, Heijen: 200-7.
Suinesiaputra, A.F. Frangi, H.J. Lamb, J.H.C. Reiber, B.P.F. Lelieveldt, “Automatic Prediction of Myocardial Contractility
Improvement in Stress MRI using Shape Morphometrics with Independent Component Analysis”, proc. IPMI 2005, Lecture
Notes in Computer Science, vol. 3565, pp 321-332, 2005.
Vessel wall MASS: segmentation and analysis of vessel wall MR images
Segmentation component for QLV-CMS: AAM-based segmentation of left ventricular X-ray angiograms
Segmentation component for MRA-CMS: segmentation and analysis of MRA datasets
SNIPER: quantification and segmentation software for brain MR studies
Reiber JHC, Koning G, Tuinenburg JC, Lansky A, Goedhart B. Quantitative Coronary Arteriography. In: Coronary Radiology.
M. Oudkerk (Ed.) Springer-Verlag Berlin 2004: 41-58.
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Adame IM, Geest RJ van der, Wasserman BA, Mohamed MA, Reiber JHC, Lelieveldt BPF. Automatic segmentation and
plaque characterization in atherosclerotic carotid artery MR images. MAGMA (Magnetic Resonance Materials in Physics,
Biology and Medicine) 2004, 16 (5): 227-34.
Adame IM, Geest RJ van der, Wasserman BA, Mohamed M, Reiber JHC, Lelieveldt BPF. Automatic plaque characterization
and vessel wall segmentation in magnetic resonance images of atherosclerotic carotic arteries. Medical Imaging 2004:
Image Processing. J.M. Fitzpatrick, M. Sonka (Eds.). Proceedings of SPIE: vol 5370: 265-73.
2.3.15 Contribution of UG-CS-IS
Biologically motivated Image processing and computer vision
Models of the visual cortex are developed and used in computer algorithms. This research is relevant for the areas of image
processing, computer vision, pattern recognition, visual perception, and computational neuroscience. Our goal is to
understand how humans see and deploy principles of natural vision in artificial vision systems. Using facts from
neuroscience and visual perception, we build models of visual neurons and use them in computer simulations to obtain
insights and derive practical
computer vision algorithms.
One example is the model of a grating cell that we developed [Petkov and Kruizinga: 1997 Biological Cybernetics 76 (2) 8396] and used in a texture operator [Kruizinga and Petkov: 1999 IEEE Transactions on Image Processing 8 (10) 1395-1407],
[Grigorescu, Petkov and Kruizinga: 2002 IEEE Trans. on Image Processing 11 (10) 1160-1167]. By means of computer
simulations we demonstrated that grating cells may play an important role in the disambiguation of edge information in early
vision (texture vs. contours). In contrast to traditional texture operators used in image processing, the texture operator
derived from a computational model of a grating cell responds
only to texture and does not respond to non-textural features, such as object contours.
Another example is our model of non-classical receptive filed inhibition, also called surround suppression, in groups of
orientation selective neurons [Petkov and Westenberg: 2003 Biological Cybernetics 88 236-246]. This biological mechanism
was simulated and applied to a large number of natural images. We demonstrated that the biological role of this inhibitory
mechanism is quick pre-attentive detection of
object contours and region boundaries in natural images that are rich in texture. We proposed various contour detection
algorithms that deploy this mechanism and showed that they are more effective in detecting object contours and region
boundaries than
traditional computer vision algorithms for edge detection [Grigorescu, Petkov, Westenberg: 2003 IEEE Trans. on Image
Processing 12 (7) 729-739], [Grigorescu, Petkov, Westenberg: 2004 Image and Vision Computing 22 609-622].
A new direction in our research that is inspired by psychological research on the human visual system is the development of
a method for the evaluation of the robustness of shape recognition algorithms to incompleteness of contours [Ghosh and
Petkov, 2005 IEEE Trans. on Pattern Analysis and Machine Intelligence 27 (11) 1793-1804].
Currently we extend our research on the use of Gabor filters to the area of motion analysis. We also develop algorithms that
mimic perceptual grouping by humans. One envisaged application is texture analysis.
Shape analysis
In shape analysis we study geometrical approaches in which a feature point is characterized by the spatial arrangement of
other feature points around it. The collection of local geometrical descriptors for the different feature points of an object is
used as a shape characteristics of that object. We study the potential of this approach for object segmentation and
classification in natural scenes in practical applications such as traffic sign recognition and image database retrieval
[Grigorescu and Petkov:
2003 IEEE Trans. on Image Processing 12 (10) 1274-1286]. We also study the robustness of shape recognition algorithms
to incomplete contour representations [Ghosh and Petkov, 2005 IEEE Trans. on Pattern Analysis and Machine Intelligence
27 (11) 1793-1804]. On the applications side, we collaborate with researchers from the University of Leon, Spain, in the area
of automatic sperm classification.
Connected filters and morphological operators
Connected filters are a comparatively new field of research within mathematical morphology. They are edge preserving
operators which have found use in noise removal, texture analysis, image compression and description, and feature
extraction. Research on connected operators in our group entails algorithm development (including parallelization),
development of new classes of filters, applications to 2-D and 3-D medical images, and the development of new connectivity
measures for these filters for
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increased robustness. One line of this research links to visual cortex modelling: developing morphological analogues of
texture operators based on models of certain visual cortical cells. It is hoped these morphological counterparts will be an
order of magnitude faster, whilst retaining the useful properties of the cortical cell models. Finally, fast visualization based on
connected attribute filters is being explored.
Segmentation is a core problem in image analysis, and methods based on both simple thresholding methods and more
advanced methods such as watersheds and deformable models are being explored. Application areas are many, but the
focus lies on biomedical imaging, both macroscopic (MRI, CT) and microscopic.
Machine learning and neural networks
Neural networks and other adaptive information processing systems can be applied in classification or regression problems.
Such systems can be trained from example data which facilitates the implementation of tasks which cannot be formulated as
a simple set of rules in a straightforward way.
Currently, prototype based learning schemes for distance based classification are in the center of our interest. We aim at a
theoretical understanding of such systems in terms of model situations. The obtained insights allow to understand and
predict phenomena which are also relevant in real world learning problems. Furthermore, they enable us to
systematically develop and improve practical training algorithms. As an important example we have investigated so-called
Learning Vector Quantization (LVQ) systems.
This heuristic approach to distance based classification is widely used in practice, but lacks through theoretical
understanding. Our framework allows for a systematic comparison of training prescriptions in terms of their typical behavior.
Applications of LVQ and similar methods, for instance in the area of medical image analysis, serve as a testing ground for
theoretical results and newly developed algorithms.
We are furthermore studying networks of so-called Integrate-and-Fire units which model the behavior of biological spiking
neurons. We aim at understanding of, for instance, masking effects in the first few layers of the visual system. Systems of
adaptive information processing, such as neural networks, can be applied in variety of classification or regression problems.
Their ability to learn from example data makes it possible to implement tasks which are not easily formulated as a simple set
of rules, but for which example data are available.
External projects
Dynamical Systems Approach to Texture Analysis
2003-2007, NWO, 110 kEuro
Generalized Connected Morphological Operators for Robust Shape Extraction
2002-2006, NWO, 150 kEuro.
A. Ghosh and N. Petkov: Robustness of shape descriptors to incomplete contour representations, IEEE Trans. on Pattern
Analysis and Machine Intelligence, 27 (11), 2005, 1793-1804.
A. Ghosh and N. Petkov: A cognitive evaluation procedure for contour based shape descriptors, Int. Journal of Hybrid
Intelligent Systems, 2 (4), 2005, 237-252.
A.C. Jalba, M.H.F. Wilkinson, J.B.T.M. Roerdink, M.M. Bayer and S. Juggins. Automatic diatom identification using contour
analysis by morphological scale spaces, Mach. Vis. Applic., 16, 2005, 217-228.
C. Bunzmann, M. Biehl, R. Urbanczik, Efficient training of multi-layer perceptrons by Principal Component Analysis, Physical
Review E 72, 026117 (2005)
T. Volkmann, F. Much, M. Biehl, and M. Kotrla, Interplay of strain relaxation and chemically induced diffusion barriers:
nanostructure formation in 2D alloys, Surface Science 586: 157-173 (2005)
K. De Raedt, H. De Raedt, and K. Michielsen, Deterministic event-based simulation of quantum interference, Comp. Phys.
Comm. 171, 19-39 (2005)
K. Michielsen, K. De Raedt, and H. De Raedt, Simulation of Quantum Computation: A deterministic event-based approach,
J. Comp. Theor. Nanoscience 2, 227 - 239 (2005)
H. De Raedt, K. De Raedt, and K. Michielsen, New method to simulate quantum interference using deterministic processes
and application to event-based simulation of quantum computation, J. Phys. Soc. Jpn. Suppl. 76, 16 - 25 (2005)
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H. De Raedt, K. De Raedt, and K. Michielsen, Event-based simulation of single-photon beam splitters and Mach-Zehnder
interferometers, Europhys. Lett. 69, 861 - 867 (2005)
A. Ghosh, M. Biehl, and B. Hammer, Dynamical analysis of LVQ-type algorithms, in: M. Cottrell (ed.), Proc. of the 5th
Workshop on Self-organizing Maps WSOM 2005, Univ. Paris I, 597-594 (2005)
M. Biehl, A. Ghosh, and B. Hammer, The dynamics of Learning Vector Quantization, in: M. Verleysen (ed.), Proc. of the
European Symposium on Artificial Neural Networks 2005, d-side publishing, 13-18 (2005)
M. Biehl, Lattice gas models and Kinetic Monte Carlo simulations of epitaxial growth, in: A. Voigt (ed.), Multiscale Modeling in
Epitaxial Growth, International Series of Numerical Mathematics, Birkhaeuser, 149:1-18 (2005)
M. Biehl, F. Much, and C. Vey, Off-lattice Kinetic Monte Carlo simulations of heteroepitaxial growth, in: A. Voigt (ed.),
Multiscale Modeling in Epitaxial Growth, International Series of Numerical Mathematics Vol. 149, Birkhaeuser, 41-57 (2005)
M. Biehl and F. Much, Off-lattice Kinetic Monte Carlo simulations of Stranski-Krastanov-like growth, in: B. Joyce, P. Kelires,
A. Naumovets and D.D. Vvedensky (eds.), Quantum Dots: Fundamentals, Applications, and Frontiers, NATO Science Series
II: Mathematics, Physics, and Chemistry Vol. 190, Springer (2005)
L. Sanchez, N. Petkov and E. Alegre: Classification of boar spermatozoid head images using a model intracellular density
distribution, in M. Lazo and A. Sanfeliu (Eds.), Progress in Pattern Recognition, Image Analysis and Applications: Proc. 10th
Iberoamerican Congress on Pattern Recognition, CIARP 2005, Lecture Notes in Computer Science, Vol. 3773, (SpringerVerlag Berlin Heidelberg, 2005) pp.154-160.
G. Papari and N. Petkov, Algorithm that mimics human perceptual grouping of dot patterns, in M. De Gregorio et al. (Eds.),
Proc. First Int. Symp. on Brain, Vision and Artificial Intelligence BVAI 2005, Naples, October 19-21, 2005, Lecture Notes in
Computer Science, Vol. 3704 (Springer-Verlag Berlin Heidelberg, 2005) pp.497-506.
A. Ghosh and N. Petkov: Incomplete contour representations and shape descriptors: ICR test studies, in M. De Gregorio et
al. (Eds.), Proc. First Int. Symp. on Brain, Vision and Artificial Intelligence BVAI 2005, Naples, October 19-21, 2005, Lecture
Notes in Computer Science, Vol. 3704 (Springer-Verlag Berlin Heidelberg, 2005) pp.416-425.
L. Sanchez, N. Petkov and E. Alegre: Statistical approach to boar semen head classification based on intracellular intensity
distribution, in A. Gagalowicz and W. Philips (Eds.), Proc. Int. Conf. on Computer Analysis of Images and Patterns, CAIP
2005, Lecture Notes in Computer Science, Vol. 3691, (Berlin, Heidelberg: Springer-Verlag, 2005) pp.88-95.
G.K. Ouzounis and M.H.F. Wilkinson. Countering Oversegmentation in Partitioning-Based Connectivities. Int. Conf. Image
Proc. 2005, September 11-14, Genova, Italy, Vol III, pp. 844-847.
G.K. Ouzounis and M.H.F. Wilkinson. Second-Order Connected Attribute Filters Using Max-Trees. In: Mathematical
Morphology: 40 years on, Proc. Int. Symp. Math. Morph. (ISMM) 2005, pp. 65-74.
E.R. Urbach, N.J. Boersma, and M.H.F. Wilkinson. Vector-Attribute Filters. In: Mathematical Morphology: 40 years on, Proc.
Int. Symp. Math. Morph. (ISMM) 2005, pp. 95-104.
M.H.F. Wilkinson. Attribute-Space Connected Filters. In: Mathematical Morphology: 40 years on, Proc. Int. Symp. Math.
Morph. (ISMM) 2005, pp. 85-94.
Web-enabled software
N. Petkov and M.B. Wieling. Gabor filter for image processing and computer vision, internet enabled implementation,
http://mathlabserver.cs.rug.nl
N. Petkov and M.B. Wieling. Canny filter for image processing and computer vision, internet enabled implementation,
http://mathlabserver.cs.rug.nl
N. Petkov and W. T. Visser. Center-surround and dot-pattern selective operators,
internet enabled implementation, http://mathlabserver.cs.rug.nl
N. M. Hol, F. Kalsbeek and N. Petkov. Grating cell operator, internet enabled implementation, http://mathlabserver.cs.rug.nl
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2.4
2.4.1
D: Multimedia Information Systems
Contribution of TUD-mm-ict
Image and Video Processing
The research on image and video processing in the ICT Group encompasses four topics:
Video compression. Compression techniques are essential in variety of Internet applications, television broadcasting, digital
cameras, music distribution and consumer digital video applications, such as DVD's and DV-cam cording. Research
concentrates on novel compression techniques for applications where the communication medium is error-prone and cases
where the device on which the compression algorithm runs is complexity constrained.
Computer vision. Focus is on 3D reconstruction of objects from multiple cameras or moving camera(s) for e.g. face
recognition, remote handling, 3D editing for 3D teleconferencing. Recent research also considers the problem of gesture
recognition.
Cultural heritage informatics. Research concerns the application and development of image processing, pattern recognition
and artificial intelligence techniques for the benefit of our cultural heritage. The focus is on virtual restoration of paintings as
well as on the dating and authenticity of painting and etchings.
Restoration. In the area of post-processing the emphasis is on the quality improvement of degraded digital image
sequences. An important application is the restoration of historically important (analogue) film and video recordings.
Multimedia Retrieval
The research efforts in the ICT Group in the field of multimedia content management address the following challenges:
- Automating multimedia content indexing and retrieval processes;
- Enabling quick, easy and personalized access to multimedia content.
We combine our expertise in multimedia signal processing and machine intelligence with state-of-the-art achievements in the
fields of "traditional" information retrieval and human perception and aim at bridging the gap between the measurable
properties (features) of one hand, by optimizing the way multimedia content is stored, organized, abstracted and represented
and, on the other hand, by developing methods for reliably learning user preferences and for filtering, pruning, adapting and
delivering multimedia content accordingly.
External Projects
Non Obtrusive Gesture Recognition
2003-2007, Delft Research Center ICT, 180 k€. In this gesture recognition project we will focus on problems involved in
tracking and interpretation of hand movements (gestures) with cameras without using additional obtrusive sensors or
markers and how this can be used optimally in different applications. Gestures that can be indicated as conventionalized
symbols are predominantly studied in an application where a sign language recognition system will be developed and
integrated in an e-learning system to assist the learning process for deaf and hearing-impaired children of Dutch sign
language vocabulary. The focus is on detection and tracking of the hand/arm movements and the extraction of relevant
features for recognition.
DIWAMETRIC (Digital image Watermarks resistant to geoMETRIC attacks)
2001-2004, STW, 270 k€. This project aims at the development of watermarking techniques that are robust against
geometric attacks. The secret information embedded in image or video data should survive most common accidental and
malicious processing operations such as filtering, compression, D/A and A/D conversion.
Cactus
2002-2005, EZ/Freeband K.I., 1.350 M€, TUD-EWI-mm-cgcc, TUD-EWI-st-pds. In this project we concentrate on the
interaction between a user and his mobile device and between the mobile device and the network. Specific research
questions concern the discovery of available foreign "resources" and the willingness of users and devices to share their own
resources.
Authenticiity
2004-2007, NWO/TOKEN2000, 300 k€. Authenticity determination and dating of works of art play an important role in the
field of art history. In the AUTHENTIC-project it is investigated how existing and new techniques from digital image
processing and knowledge discovery (data mining) can be developed and applied in order to support the process of
determination of authenticity, dating and the assessment of other characteristics of both graphic art and paintings.
Rembrandt PROJECT
2004-2007, NTWO/TOKEN2000, 300 k€. In this project methods for automatic extraction of watermarks and features
concerning the paper structure are developed. On the basis of these features, etchings printed on similar papers can be
recognized by means of automatic matching procedures. With this questions concerning authenticity and dating can be
answered. Since the aim is to construct a database of all the papers used by Dutch artists, specific attention is paid to how to
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make this database self-organizing and self-learning. This requires the application of advanced techniques from
computational intelligence.
I-SHARE
2004-2008, EZ BSIK/Freeband, 8 M€, TUD-EWI-st-pds. Sharing resources in virtual communities for storage,
communications and processing of multimedia data. The FREEBAND I-SHARE-project investigates the sharing resources in
virtual communities, which are (dynamic) groups of nodes that are willing to collaborate for the better of the whole. In
particular, I-SHARE considers the sharing of resources for processing, transmitting and storing multimedia streams:
- Funtionality sharing. Specific capabilities of terminals embodied in algorithms or, more abstractly, in services are shared to
support applications and to form new ones.
- Content sharing. This pertains to particular assets related to local hardware. We think of processing power and storage to
start with, but specific processing hardware (co-processors) and special purpose hardware are possible as well.
Video-at-your-Fingertips
2004-2008, EZ/OC&W BSIK/Multimedian, 2,5 M€. The goal of this project is video content extraction technology suited for
practical use in selectec application contexts. The basis of this technology consists of video content analysis algorithms,
which include the modeling of the semantic content in terms of signal processing and analysis routines, and the methods of
implementing the content models in software or hardware. In particular, Video-at-your-fingertips considers the following
research topics:
1. Robust, unconstrained face detection and recognition with applications in security (smart camera's) and media (consumer
home video).
2. Human body motion analysis with applications in surveillance (suspicious behavior and aggression detection) and
personal health care (revalidation at home).
3. Video content management: The parsing, pruning, abstracting, summarization and classification of video content with a
Video Concert Browser as media application.
Lagendijk, R.L., Biemond, J.; Basis methods for image restoration and identification. Bovik, A. (ed.); Handbook of Image &
Video Processing, 2nd ed. US/UK, 2005, 1371 pp., Elsevier Academic Press, ISBN 0-12-119792-1, pp. 167-181
Lagendijk, R.L., Roosmalen, P.M.B., Biemond, J., Rares, A., Reinders, M.J.T.: Video enhancement and restoration. Bovik, A.
(ed.); Handbook of Image & Video Processing, 2nd ed. US/UK, 2005, 1371 pp., Elsevier Academic Press, ISBN 0-12-1197921, pp. 275-295
Rajashekar, U., Bovik, A.C., Sage, D., Unser, M., Karam, L.J., Lagendijk, R.L.; Image Processing Education.
Bovik, A. (ed.); Handbook of Image & Video Processing, 2nd ed. US/UK, 2005, 1371 pp., Elsevier Academic Press, ISBN 012-119792-1, pp. 73-95.
Chen, M., He, Y., Lagendijk, R.L.; A fragile watermark error detection scheme for wireless video communications. IEEE
Transactions on Multimedia, IEEE, ISSN 1520-9210, vol. 7, no. 2, pp. 201-211.
Eroglu-Erdem, C., Ernst, F., Redert, A., Hendriks, E.A.; Temporal stabilization of video object segmentation for 3D-TV
applications. Signal Processing: Image Communication, Elsevier, ISSN 0923-5965, vol. 20, no. 2, pp. 151-167.
Hanjalic, A., Xu, L.Q.; Affective video content representation and modeling. IEEE Transactions on Multimedia, IEEE, ISSN
1520-9210, vol. 7, no. 1, pp. 143-154.
Hanjalic, A.; Adaptive Extraction of Highlights from a Sport Video Based on Excitement Modeling. IEEE Transactions on
Multimedia, IEEE, ISSN 1520-9210, vol. 7, no. 6, pp. 1114-1122.
Haratcherev, I., Taal, J.R., Langendoen, K., Lagendijk, R.L., Sips, H.J.; Automatic IEEE 801.11 rate control for streaming
applications. Wireless Communications and Mobile Computing, John Wiley & Sons Ltd., ISSN 1530-8669, vol. 5, no. 4, pp.
421-437.
Lin, E.T., Eskicioglu, A.M., Lagendijk, R.L., Delp, E.J.; Advances in digital video content protection. Proceedings of the IEEE
(Special issue on: Advances in video coding and delivery), IEEE, ISSN 0018-9219, vol. 93, no. 1, pp. 171-183.
Rares, A., Reinders, M.J.T., Biemond, J.; Constrained texture restoration. EURASIP Journal on Applied Signal Processing,
Hindawi Publishing Corporation, ISSN 1110-8657. vol. 2005, no. 17, pp. 2758-2771.
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Rares, A., Reinders, M.J.T., Biemond, J.; Edge-based image restoration. IEEE Transactions on Image Processing, IEEE,
ISSN 1057-7149, vol. 14, no. 10, pp. 1454-1468.
Yan, W.-Q., Wang, J., Kankanhalli, S.; Analogies based video editing. Multimedia Systems, Springer-Verlag GmbH, ISSN
0942-4962, vol. 11, no. 1, pp. 3-18.
Yan, W.-Q., Wang, J., Kankanhalli, S.: Automatic video logo detection and removal. Multimedia Systems, Springer-Verlag
GmbH, ISSN 0942-4962, vol. 10, no. 5, pp. 379-391.
Blok, M., Danilouchkine, M.G., Veenman, C.J., Admiraal-Behloul, R., Hendriks, E.A., Reiber, J.H.C., Lelieveldt, B.P.F.; Long
axis cardiac MRI contour detection with adaptive virtual exploring robot.The 3rd International Conference on Functional
Imaging and Modeling of the Heart, Barcelona, 2-4 June 2005, Proceedings of the 3rd International Conference on Functional
Imaging and Modeling of the Heart / Lecture Notes in Computer Science, vol. 3504, Frangi, A., Radeva, P., Santos, P.
Hernandez, M. (eds.), Berlin 2005, ISBN 3-540-26161-3 / ISSN 0302-9743, Springer Verlag, pp. 54-64.
Cai, R., Lu, L., Hanjalic, A.; Unsupervised content discovery in composite audio. The ACM Multimedia Workshops,
Singapore, 6-11 November 2005, Proceedings of the ACM Multimedia Workshops, ACM Press, ISBN 1-59593-273-9, pp.
628-637.
Doets, P.J.O., Lagendijk, R.L.; Extracting quality parameters for compressed audio from fingerprints. The Sixth International
Conference Music Information Retrieval, London, UK, 11-15 September 2005, Proceedings of the Sixth International
Conference Music Information Retrieval, Reiss, J.D., Wiggins, G.A. (eds.), London, Queen Mary University, ISBN 09551179-0-9, pp. 6.
Hanjalic, A., Nesvadba, J., Benois-Pineau, J.; Moving away from narrow-scope solutions in multimedia content analysis. The
2nd European workshop on the integration of knowledge, semantics and digital media technology, London, UK, 29 November
– 1 December 2005, Proceedings of the 2nd European workshop on the integration of knowledge, semantics and digital
media technology, IEE, ISBN 0-86341-595-4, ISSN 0537-9989, pp. 6.
Haratcherev, I., Langendoen, K.G., Lagendijk, R.L., Sips, H.J.; Link adaptation and cross-layer signaling for wireless videostreaming in a shared medium. The 2005 International Conference on Wireless Networks Communications and Mobile
Computing, Maui, Hawaii, USA, 13-16 June 2005, Proceedings of the 2005 International Conference on Wireless Networks
Communications and Mobile Computing, Baqai, S.M., Uzmi, Z.A. (eds.), IEEE Communications Society, ISBN 0-7803-93066, pp. 5.
Haratcherev, I., Taal, J.R., Langendoen, K.G., Lagendijk, R.L., Sips, H.J.; Fast 802.11 link adaptation for real-teim video
streaming by cross-layer signaling. The IEEE International Symposium on Circuits and Systems, Kobe, Japan, 23-26 May
2005, Proceedings of the IEEE International Symposium on Circuits and Systems, IEEE, ISBN 0-7803-8835-6, pp. 35233526.
Hollander, R.J.M. den, Hanjalic, A.; Outlier identification in stereo correspondences using quadrics. The British Machine
Vision Conference, Oxford, UK, 5-8 September 2005, Proceedings of the British Machine Vision Conference, Clocksin, W.,
Fitzgibbon, A., Torr, P. (eds.), ISBN 1-901725-29-4, pp. 1-10.
Lichtenauer, J.F., Hendriks, E.A., Reinders, M.J.T.; Isophote properties as features for object detection.
Proceedings of the Conference on Computer Vision and Pattern Recognition, San Diego, CA, USA, 20-26 July 2006,
Proceedings of he Conference on Computer Vision and Pattern Recognition, Schmid, C., Soatto, S., Tomasi, C. (eds.), IEEE
Computer Society, pp. 6.
Meyer, P.F.A., Westerlaken, R.P., Klein Gunnewiek, R., Lagendijk, R.L.; Distributed source coding of video with nonstationary side-information. The SPIE-conference Visual Communications and Image Processing, Beijing, China, 12-15 July
2005, Proceedings of the SPIE-conference Visual Communications and Image Processing, Li, S., Pereira, F., Shum, H.-Y.,
Tscher, A.G. (eds.), vol. 5960, SPIE, pp. 857-866.
Naci, U., Hanjalic, A.; A unified framework for fast and effective shot transition detection based on analysis of spatiotemporal
video data blocks. The 4th International Workshop on Content-Based Multimedia Indexing, Riga, Latvia, 21-23 June 2005,
Proceedings of the 4th International Workshop on Content-Based Multimedia Indexing, ISBN 90-74821-707, pp. 1-8.
Nesvadba, J., Fonseca, P., Sinitsyn, A., Lange, F. de, Thijssen, M., Kaam, P. van, Liu, H., Leeuwen, R. van, Lukkien, J.,
Korostelev, A., Ypma, J., Kroon, B., Celik, H., Hanjalic, A., Naci, U., Benois-Pineau, J., With, P. de, Han, J.; Real-time and
distributed AV content analysis system for consumer electronics networks. The IEEE International Conference on Multimedia
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& Expo, Amsterdam, 6-8 July 2006, Proceedings of the IEEE International Conference on Multimedia & Expo, EEE, ISBN 07803-9332-5, pp. 1-4.
Nesvadba, J., Hanjalic, A., Fonseca, P.M., Hanjalic, A., Kroon, B., Celik, H., Hendriks, E.A.; Towards a real-time and
distributed system for face detection, pose estimation and face-related features. The 5th International Conference on
Methods and Techniques in Behavioral Research, Wageningen, The Netherlands, 30 August – 2 September 2005,
Proceedings of the 5th International Conference on Methods and Techniques in Behavioral Research, Noldus, L.P.J.J.,
Grieco, F., Loijens, L.W.S., Zimmerman, P.H. (eds.), Wageningen, Noldus Information Technology B.V., ISBN 90-74821707, pp. 1-4.
Pouwelse, J., Slobbe, M. van, Wang, J., Reinders, M.J.T., Sips, H.J.; P2P-based PVR recommendation using friends, taste
buddies and superpeers. The Workshop Beyond Personalization 2005, held in conjunction with the 2005 International
Conference on Intelligent User Interfaces, San Diego, USA, 9 January 2005, Proceedings of the Workshop Beyond
Personalization, Setten, M. van, McNee, S., Konstan, J. (eds.), pp. 66-71.
Sanderse, M., Marquering, H.A., Hendriks, E.A., Lugt, A. van der, Reiber, J.C.; Automatic initialization algorithm for carotid
artery segmentation in CTA images. The Medical Image Computing and Computer-assisted Intervention-MICCAI 2005: 8th
International Conference, Palm Springs, CA, USA, 26-29 October 2005, Proceedings of the Medical Image Computing and
Computer-assisted Intervention-MICCAI 2005: 8th International Conference, Part II / Lecture Notes in Computer Science, vol.
3750, Duncan, J.S., Gerig, G. (eds.), Springer-Verlag, ISBN 3-540-29326-4, ISSN 0302-9743, pp. 846-853.
Shterev, I.D., Lagendijk, R.L.; Maximum likelihood amplitude scale estimation for quantization-based watermarking in the
presence of dither. SPIE-IS&T Electronic Imaging 2005, San Jose, USA, 17-20 January 2005, Proceedings of SPIE-IS&T
Electronic Imaging 2005, vol. 5681, Security, Steganography and Watermarking of Multimedia Contents VIII, Delp III, E.J.,
Wong, P.W. (eds.), SPIE/IS&R, ISBN 0-8194-5654-3, ISSN 0277-786X, pp. 516-527.
Shterev, I.D., Lagendijk, R.L.; Maximum likelihood amplitude scale estimation for quantization-based watermarking. The 26th
Symposium on Information Theory in the Benelux, Brussels, 19-20 May 2005, Proceedings of the 26th Symposium on
Information Theory in the Benelux, Werkgemeenschap Informatie- en Communicatietheorie (WIC), ISBN 90-71048-21-7, pp.
292-300.
Taal, J.R., Lagendijk, R.L.; Fair rate allocation of scalable multiple description video for many clients. The SPIE-conference
Visual Communications and Image Processing, Beijing, China, 12-15 July 2005, Proceedings of the SPIE-conference Visual
Communications and Image Processing, Li, S., Pereira, F., Shum, H.-Y., Tscher, A.G. (eds.), vol. 5960, SPIE, pp. 21732183.
Taal, J.R., Lagendijk, R.L.; Scalable multiple description video for many clients. The 26th Symposium on Information Theory
in the Benelux, Brussels, 19-20 May 2005, Proceedings of the 26th Symposium on Information Theory in the Benelux,
Werkgemeenschap Informatie- en Communicatietheorie (WIC), ISBN 90-71048-21-7, pp. 129-136.
Wang, J., Reinders, M.J.T., Lagendijk, R.L., Pouwelse, J.; Self-organizing distributed collaborative filtering.
The 28th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval, Salvador,
Brazil, 15-19 August 2005, Proceedings of the 28th Annual International ACM SIGIR Conference on Research and
Development in Information Retrieval, Marchionini, G., Moffat, A., Tait, J., Baeza-Yates, R., Ziviani, N. (eds.), The
Association for Computing Machinery, SIBN 1-59593-034-5, pp. 659-660.
Wang, J., Reinders, M.J.T., Pouwelse, J., Lagendijk, R.L.; Wi-Fi walkman: A wireless handhold that shares and recommends
music on peer-to-peer networks. SPIE-IS&T Electronic Imaging 2005, San Jose, USA, Proceedings of the SPIE-IS&T
Electronic Imaging, Multimedia and Communications II, Sudharsanan, S., Bove Jr., V.M., Panchanathan, S. (eds.), vol. 5863,
SPIE/IS&T, pp. 155-163.
Wang, J., Shterev, I.D., Lagendijk, R.L.; Two-band amplitude scale estimation for quantization-based watermarking. The
2005 International Symposium on Intelligent Signal Processing and Communication Systems, Hong Kong, 13-16 December
2005, Proceedings of the 2005 International Symposium on Intelligent Signal Processing and Communication Systems,
IEEE, ISBN 0-7803-9266-3, pp. 137-140.
Westerlaken, R.P., Klein Gunnewiek, R., Lagendijk, R.L.; The role of the virtual channel in distributed source coding of video.
The International Conference on Image Processing, Genova, Italy, 11-14 September 2005, Proceedings of the International
Conference on Image Processing , IEEE, ISBN 0-7803-9135-7, pp. I-581-584.
Westerlaken, R.P., Klein Gunnewiek, R., Lagendijk, R.L.; Turbo-code based wyner-zic video compression.
The 26th Symposium on Information Theory in the Benelux, Brussels, 19-20 May 2005, Proceedings of the 26th Symposium
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on Information Theory in the Benelux, Werkgemeenschap Informatie- en Communicatietheorie (WIC), ISBN 90-71048-21-7,
pp. 113-120.
Blok, M., Danilouchkine, M.G., Veenman, C.J., Admiraal-Behloul, R., Hendriks, E.A., Reiber, J.H.C., Lelieveldt, B.P.F.; Long
axis cardiac MRI contour detection with adaptive virtual exploring robot. The 3rd International Conference on Functional
Imaging and Modeling of the Heart, Barcelona, 2-4 June 2005, Proceedings of the 3rd International Conference on Functional
Imaging and Modeling of the Heart / Lecture Notes in Computer Science, vol. 3504, Frangi, A., Radeva, P., Santos, P.
Hernandez, M. (eds.), Berlin 2005, ISBN 3-540-26161-3 / ISSN 0302-9743, Springer Verlag, pp. 54-64.
Haratcherev, I., Taal, J.R., Langendoen, K., Lagendijk, R.L., Sips, H.J.; Automatic IEEE 801.11 rate control for streaming
applications.Wireless Communications and Mobile Computing, John Wiley & Sons Ltd., ISSN 1530-8669, vol. 5, no. 4, pp.
421-437.
Haratcherev, I., Langendoen, K.G., Lagendijk, R.L., Sips, H.J.; Link adaptation and cross-layer signaling for wireless videostreaming in a shared medium. The 2005 International Conference on Wireless Networks Communications and Mobile
Computing, Maui, Hawaii, USA, 13-16 June 2005, Proceedings of the 2005 International Conference on Wireless Networks
Communications and Mobile Computing, Baqai, S.M., Uzmi, Z.A. (eds.), IEEE Communications Society, ISBN 0-7803-93066, pp. 5.
Haratcherev, I., Taal, J.R., Langendoen, K.G., Lagendijk, R.L., Sips, H.J.; Fast 802.11 link adaptation for real-teim video
streaming by cross-layer signaling. The IEEE International Symposium on Circuits and Systems, Kobe, Japan, 23-26 May
2005, Proceedings of the IEEE International Symposium on Circuits and Systems, IEEE, ISBN 0-7803-8835-6, pp. 35233526.
Pouwelse, J., Slobbe, M. van, Wang, J., Reinders, M.J.T., Sips, H.J.; P2P-based PVR recommendation using friends, taste
buddies and superpeers. The Workshop Beyond Personalization 2005, held in conjunction with the 2005 International
Conference on Intelligent User Interfaces, San Diego, USA, 9 January 2005, Proceedings of the Workshop Beyond
Personalization, Setten, M. van, McNee, S., Konstan, J. (eds.), pp. 66-71.
Sanderse, M., Marquering, H.A., Hendriks, E.A., Lugt, A. van der, Reiber, J.C.; Automatic initialization algorithm for carotid
artery segmentation in CTA images. The Medical Image Computing and Computer-assisted Intervention-MICCAI 2005: 8th
International Conference, Palm Springs, CA, USA, 26-29 October 2005, Proceedings of the Medical Image Computing and
Computer-assisted Intervention-MICCAI 2005: 8th International Conference, Part II / Lecture Notes in Computer Science, vol.
3750, Duncan, J.S., Gerig, G. (eds.), Springer-Verlag, ISBN 3-540-29326-4, ISSN 0302-9743, pp. 846-853.
2.4.2
Contribution of UVA-FdNWI-isis
Systems for retrieval of video
In the theme systems for retrieval of video, we aim to make multimedia archives accessible. To that end, our research
efforts concentrate on automatic semantic indexing and interactive retrieval of multimedia sources. To value the merit of our
efforts on high international standards, all research is and will be evaluated within the TRECVID benchmark for multimedia
retrieval. To this end, we have developed the MediaMill semantic video search engine which uses a lexicon of detectable
concepts in combination with several advanced user interfaces, see Figure 1. The MediaMill system obtained the highest
score for the interactive video retrieval task of TRECVID 2005.
The topic on retrieval of video has led a Ph.D. thesis by C. Snoek entitled "The Authoring Metaphor to Machine
Understanding of Multimedia" and many publications in journals (e.g. IEEE Trans. on Multimedia). We will continue this line
of research with a further integration of multi-media sources, a further understanding of the structure of video documents and
interactive access to the semantic content of large collections of multi-media information using advanced interfaces.
The year 2005 has been a period of change for software engineering from the large complex and abstract Horus system
which is now completed to smaller targets systems solving one computer vision task at the time but completely.
The Monet database kernel and its modules for image and geo-spatial reasoning are realized in close co-operation with the
CWI-database group. In the area of database kernels, an innovative experimental analysis uncovered the lack of
performance improvement in database technology over the last decade. The underlying reason is the relative progress in
CPU- and RAM-technology, which shows an increasing performance bottleneck. As a result, traditional database solutions
use less then a few percent of the available resources. This observation has led to novel techniques to measure the resource
waste and new database algorithms to avoid resource stales.
A separate topic is the study of parallelism in multimedia processing tasks. The purpose of the research is to anticipate on
future generation computer systems while constructing a parallel processing library compatible with Horus. The developed
parallel software has been applied in the 2005 TRECVID competition.
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2006 and beyond
With first priority we will increase the effectiveness of our solutions in image retrieval and image search engines by
expanding on our experience with learning from image databases.
Computational efficiency of image search engines will be increased by the joint development with spatial and extensible
databases. This is important as it will open up domains of hundreds of thousands of images, a significant step towards datamining the content.
At the same time, we aim to expand to create full access to multimedia documents. The integration of information from text
and pictures is a very interesting topic both scientifically, as it reveals a lot about the nature of information, as well as
practically as multimedia documents will be ubiquitous as is the need for their access. The MultimediaN project provides the
opportunity to reach this goal with the intended delivery of a large-scale experimentation platform for multimedia information
analysis.
Concerning color research, we aim at the extraction of invariants from interesting regions of the image. Regions improve on
the robustness when compared to strictly local interest point based object recognition. For instance, from color distributions
we may derive appearance properties. Further, we aim at exploiting distributions of color edges to derive texture properties.
We will concentrate on regions that are interesting from an information theoretical point of view. To increase the specifity of
regions, we will incorporate the statistics of regions throughout the ALOI collection. We consider this collection to be a
natural starting point for visual cognition.
Over the years we have invested in a new, object-oriented software platform for vision. By the end of the year we hope to
deliver a first complete system for internal use with an expected life time of 10 years.
Further, the available parallel functionality to heterogeneous wide-area Grid systems is projected to be extended in 2005.
The main focus is on the development of an efficient and easy-to-use execution model based on so-called Multimedia Grid
Services, i.e. high-performance multimedia functionality that can be invoked from within sequential applications running on a
standard desktop machine. A key example is our Aibo robot dog, whose video data is being processed at multiple cluster
systems all over the globe. This research direction is prioritized with the arrival of the new Distributed ASCI Supercomputer 3
(DAS-3), which is co-financed by the MultimediaN consortium.
Geusebroek, J.M., Burghouts, G.J., Gemert, J.C. van, Smeulders, A.W.M.; Invariant representations to prepare for content
based image retrieval from first principles. In: Veltkamp, R. (ed), Trends and Advances in Content-Based Image and Video
Retrieval. Springer Verlag, Berlin, 2005.
Huijsman, D.P., Sebe, N.; Performance Evaluation in Probabilistic Information Retrieval with Noisy Indexes: The Role of
Generality. In: Trends and Advances in Content-Based Image and Video Retrieval, Springer.
Schmidt, A.R., Manegold, S., Kersten, M.L.; Storing XML Documents in Databases. In: Rivero, L.C., Doorn, J.H., Ferraggine,
V.E.;Encyclopedia of Database Technologies and Applications, Idea Group Publishing, 2005
Windhouwer, M.A., Kersten, M.L.; Digital Media Warehouses. In: Rivero, L.C., Doorn, J.H., Ferraggine, V.E.;Encyclopedia of
Database Technologies and Applications, Idea Group Publishing, 2005.
Abiteboul, S., Kersten, M.L., Zdonik S.B.; The Lowell database research selfassessment. Communications ACM, volume 5,
2005, pp111-118.
Djeraba, C., Sebe, N., Lew, M.S.; Systems and Architectures for Multimedia Information Retrieval. ACM Multimedia Systems
Journal, Volume 10 (6), 2005, pp 457-463.
Geusebroek, J.M., Burghouts, G.J., Smeulders, A.W.M.; The Amsterdam library of object images. International Journal
Computer Vision, volume 61(1), 2005, pp 103-112.
Hollink, L., Nguyen, G., Koelma, D.C., Schreiber, A., Worring, M.; Assessing user behavior in news video retrieval. IEE
proceedings on Vision, Image and Signal Processing, Volume 152 (6) 2005, pp. 911-918.
Huijsmans, D.P., Sebe, N.; How to Complete Performance Graphs in Content-Based Image Retrieval: Add Generality and
Normalize Scope. IEEE Transactions on Pattern Analysis and Machine Intelligence, Volume 27 (2), 2005, pp. 245-251.
Nguyen, G.P., Worring, M.; Relevance feedback based saliency adaptation in CBIR. Multimedia Systems, Volume 10 (6),
2005, pp 499-512.
Snoek, C.G.M., Worring, M.; Multimodal Video Indexing: A Review of the State-of-the-art. Multimedia Tools and Applications,
Volume 25 (1), 2005, pp. 5-35.
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Snoek, C.M.G., Worring, M.; Multimedia Event-Based Video Indexing using Time Intervals. IEEE Transactions on
Multimedia, Volume 7 (4), 2005, pp.638-647.
Amores, J., Sebe, N., Radeva, P.; Efficient Object-class Recognition by Boosting Contextual Information. Iberian
Conference on Pattern Recognition and ImageAnalysis, Estoril, Portugal, June 2005.
Ballegooij, R. van, Cornacchia, R., Vries, A.P. de, Kersten, M.L.; Distribution Rules for Array Database Queries. International
Workshop on Database and Expert Systems Application, Copenhagen 2005, pp 55-64.
Hollink, L., Worring, M., Schreiber, A.; Building a Visual Ontology for Video Retrieval. ACM MultiMedia, Singapore 2005.
Kersten, M.L., Manegold, S.; Cracking the Database Store. Biennial Conference on Innovative Data Systems Research
(CIDR), Asilomar, CA, USA, January 2005.
Nguyen, G.P., Worring, M.; Similarity based visualization of image collections. Seventh International Workshop of the EU
Network of Excellence DELOS on Audio-visual Content and Information Visualization in Digital Librarires (AVIVDiLib’05),
Cortona, Italy, 2005.
Sebe, N., Huijsmans, D.P., Tian, Q., Gevers, Th.; Toward Complete Performance Characterization in Content-based
Retrieval. Internet Imaging VI, SPIE’05, San Jose 2005.
Snoek, C.G.M., Worring, M., Geusebroek, J.M., Koelma, D.C., Seinstra, F.J. On the Surplus Value of Semantic Video
Analysis Beyond the Key Frame. IEEE International Conference on Multimedia & Expo (ICME), Amsterdam, The
Netherlands, July 2005.
Snoek, C.G.M., Koelma D.C., Rest, J. van, N. Schipper, F. J. Seinstra, A. Thean, and M. Worring; MediaMill: Searching
Multimedia Archives based on Learned Semantics. IEEE International Conference on Multimedia & Expo (ICME),
Amsterdam, The Netherlands, July 2005.
Seinstra, F.J., Smeulders, A.W.M., Veenman, C.J., Worring, M.; The MediaMill TRECVID 2005 Semantic Video Search
Engine. 3rd TRECVID Workshop, Gaithersburg, USA, November 2005.
Snoek, C.G.M., Worring, M., Smeulders, A.W.M. Early versus Late Fusion in Semantic Video Analysis. ACM Multimedia,
Singapore 2005.
Snoek, C.G.M., Worring, M., Gemert, J.C. van, Geusebroek, J.M., Koelma, D.C., Nguyen, G.P., Rooij, O. de, Seinstra, F.J.;
MediaMill: Exploring News Video Archives based on Learned Semantics. ACM Multimedia, Singapore 2005. * Awarded as
best technical demonstration at ACM Multimedia 2005.
Snoek, C.M.G., Worring, M.; Multimedia Pattern Recognition in Soccer Video using Time Intervals. In: Classification the
Ubiquitous Challenge GfKl2004. Series: Studies in Classification, Data Analysis, and Knowledge Organization, SpringerVerlag, 2005.
Gevers, Th., Smeulders, A.W.M.; ZOMAX, A General Purpose Image Processing and Retrieval System for the World Wide
Web. The system provides an interactive image processing module and an image search engine, called PicToSeek, for
searching images on the web. http://www.science.uva.nl/research/isis/zomax.html
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Chapter 3 ASCI-wide Events
3.1
Distributed ASCI Supercomputer DAS 2 and DAS 3
The DAS 2 will be succeeded by DAS 3:
2005-2009, N W O-EW, 900 KEuro, cooperation with all partners of the ASCI graduate school and SURFnet.
A Computer Science Grid with revolutionairy Optical interconnect
DAS-3 (Distributed ASCI Supercomputer) is a wide-area distributed system designed by the Advanced School for Computing
and Imaging (ASCI). As one of its distinguishing features, DAS-3 employs a very novel internal wide area interconnect based
on light paths. The DAS-3 system is used for research on parallel and distributed computing and imaging. DAS-3 consists of
272 compute nodes, spread out over five clusters, located at the four universities: Vrije Universiteit, Amsterdam (VU) Leiden
University (LU) University of Amsterdam (UvA) Delft University of Technology (TUD) The MultimediaN project (UvA-MN).
The system is currently being built by ClusterVision. Unlike its predecessor, DAS-2, DAS-3 is rather heterogeneous in
design.
“ADVAnCE: Automatic Diagnostic Vascular Analysis of CTA Examinations”.
Senter grant, 600 kEuro: 2005-2009. In this project, computer aided diagnosis techniques will be developed to support the
analysis of CTA data in clinical practice, to improve the workflow of cardiovascular diagnosis.
EUR-RMI-bigr collaboration with LKEB-Leiden
AMIS
NWO, UvA-Science-ISIS, UU-CS, UT-CS, TUD-CS. The project studies multi-media information analysis.
ARCHER (Architecture Exploration)
Period: 2000-2005, Funding: Philips, 0.5 Mfl, UL-WI-i, UvA-FdNWI-caps.
Architecture Exploration. The objective is to explore the design space of (lumped) embedded systems for multimedia
applications at a high level of abstraction.
Archer supports fast, abstract system-level and platform-based exploration and design strategies for the multimedia
application domain. Platforms consist of a number of heterogeneous computing components, and a communication,
synchronization, and storage infrastructure. The Archer strategy is implemented in software in three layers: An application
layer, an architecture layer, and a mapping layer. Applications and Platform are modeled at a high level of abstraction, and
the Mapping consists of transformations that take an application (model) representation to an architecture (model)
representation. Compaan and Laura are used to calibrate the abstract computing component models in an Archer platform.
Archer then concentrates on performance and cost exploration of the platform at the higher level of abstraction.
In 2003, Archer has shown its methodology is capable of predicting performance and cost with
a confidence level that is well within the range of requirements.
Duration: October 2000 – October 2004
Architectures for scientific and medical visualization, Bsik VL-e (Virtual Laboratory for e-science)
2004 - 2007, postdoc, dr. C.P. Botha. The aim of this project is to extend the DeVIDE visualization architecture with more
general facilities for grid-based computing (resource and data management) and intelligent techniques for semi-automatic
network configuration and prototyping for component development. TUD-EWI-cgcc cooperation with LUMC (Reiber,
Lelieveldt) and UvA (Belleman, Olabarriaga).
Artemis
STW/Progress,2005-2009, Euro 500K
is a cooperation between the University of Amsterdam, Leiden University, Delft University of Technology and Philips
Research, studies the design of Network-on-Chip (NoC) based MP-SoCs. Our role in this project constitutes of developing a
high-level modeling and simulation framework for system-level design space exploration of these NoC-based MP-SoCs.
ARTEMISIA
2004-2009, Progress/STW, 930 K Eur.
Leiden University, Delft University of Technology, University of Amsterdam, Philips Research Value: 1 Ph.D. student, 1 PostDoc Sponsor: PROGRESS, Philips Research
The project includes the following: Firstly, translate given applications input-output equivalent process networks (an
automated translator does exist for a restricted class of applications and is called Compaan. Secondly, model the platform,
the architecture templates derived from it as well as the instantiation of these to architectures. Also on a high level of
abstraction.Thirdly, provide low-level performance/cost numbers for the processing units on the architecture so that highlevel performance/cost numbers are well calibrated and, hence, sufficiently accurate (a calibration tool/platform does exist for
110
a restricted class processing units and is called Laura. A more advanced calibration tool/platform is to be
developed/designed within Artemisia.
A structure for maintaining a shared world model in a dynamic environment between differentiated Embedded
Systems and their interaction with human supervisors
2001-2006, 490 kf We study embedded autonomous systems in distributed environments, for applications in public safety;
monitoring and control of traffic and environmental conditions; assistance and clean-up work in disaster areas. Collaboration
between systems requires a collective world model, and we develop methods for its consistency maintenance, in time-critical
situations. We use robot soccer (RoboCup) as a case study. This project is a collaboration between UvA and the VU and is
sponsored by Progress.
Beyond the Ordinary: Design of Embedded Real-time Control (BODERC)
2003-2007. Senter, 2.5 M€, Océ Technologies, Philips CFT, AAS, Imtech ICT, Chess iT, Katholieke Universiteit Nijmegen,
Universiteit Twente, TU/e
The Boderc project focuses on distributed embedded real-time controllers of complex systems. An Océ printer is taken as a
case-study and acts as a driver for the project.
The target is an integral approach for a systematic architectural design, modeling, analysis, and validation methodology for
such heterogeneous systems.
BRICKS, Bsik
2004-2008, subproject Modelling, Simulation and Visualization, 320 KEuro Our subproject concentrates on interaction with
virtual environments. In particular we work on navigation through virtual environments and manipulation of objects in virtual
environments. UU and other ASCI groups in Delft and CWI are involved in this project as well.
Cactus
2002-2005, EZ/Freeband K.I., 1.350 M€, TUD-EWI-ict, TUD-EWI-mm-cgcc, TUD-EWI-st-pds. In this project we concentrate
on the interaction between a user and his mobile device and between the mobile device and the network. Specific research
questions concern the discovery of available foreign "resources" and the willingness of users and devices to share their own
resources.
A computational theory for visual cognition (NWO Veni)
2003-2007, NWO, TUD-EWI- cgcc, Uva-Science-ISIS, 200 KEuro. The project aims at developing a computational theory of
vision based on invariant representations.
CoreGRID
2004-2008, EU (Network of Excellence), EURO 38.000, ASCI partners TUD, VU.
This network integrates the grid research of 42 universities in Europe.
CIM
2003-2007, Senter, 300k€. TUD-EWI, VU, CWI, Almende, This project aims at the development and specification of
distributed incident management techniques.
COMBINED systems
2002-2006, 800kE In this project innovative methods for disaster management are being studied. In particular aspects
concerning distributed observation systems are investigated. An important property of distributed observation systems is that
they autonomously extract information from the monitored area. This information is shared with other services in the disaster
management platform. The project is conducted in cooperation with UvA, TUDelft, Thales en TNO within the DECIS
laboratory.
CSI
The CSI project is a close collaboration between LIACS of Leiden University and the CE Laboratory of TU Delft. CSI Media
Architecture. The Complex Streamed Instruction Set Architecture (CSI) is a memory-to-memory vector architecture targeted
at multimedia applications. A single CSI instruction can process data streams of arbitrary length and, in addition to traditional
arithmetic and logical operations, performs data accesses, conversion between storage and computation formats (packing
and unpacking), and complex arithmetic hardwired computation. The main new features of the CSI are elimination of the
vector sectioning instructions, elimination of the packing/unpacking instructions, and introduction of new complex media
related arithmetic instructions.
CYTTRON Bio-Computing Search Project
2004-2008 BSIK, Bsik, 8.8 MEuro with UL-LUMC, UL-WI-I and TUD-TNW-tn-qi: Development of a comprehensive,
integrated infrastructure for bio-imaging and modeling cells down to atomic detail.
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D: ImIK
2002-2005, IOP, 400 Keuro, Uva-Science-ISIS and VU. The project considers the interactive exploration of multimedia
information and knowledge.
“3D Multimodal vascular image analysis for improved diagnosis and therapy”
NWO STW VICI grant, 1,25 MEuro: 2006-2010 In this project, methods for the integrated analysis of vascular imaging data
obtained with various imaging techniques will be developed and evaluated. The focus is on the analysis of the diseased
vessel wall, so as to improve diagnosis of cardiovascular diseases, and to monitor and guide their treatment.
EUR-RMI-bigr collaboration with Applied Physics, Delft
Fexible Application Mapping Environment (FAME)
2002-2006, NOW-EW, Leiden University, Delft University of Technology, TUE
The FAME project aims at developing a novel approach to program optimization, namely, iterative compilation in which the
transformation space is searched and profiling is used to measure the impact of transformations. One of the most important
goals of this project is to develop heuristics to control the complexity of the search by using analytical models and domain
specific knowledge.
Freeband/PNP2008
SIK, 500 kEuro (DACS) . Cooperation project between UT and TUDelft, Philips, KPN, WMC,and TNO, to research and
develop a Personal Network, focussing on the prototyping of a Personal Mobile Gateway.
Gigaport NG
Research on Networks, 2005-2007, BSIK, 150KE, UvA & TUD. Within this project the UT investigates self-management of
hybrid IP/ Optical networks, and the measurement of traffic flows within such networks. The project is managed by
SURFnet, and supports the introduction of SURFnet6.
Globule
2003-2007, KEURO 147,(a.o.Proactive Construction of Semantic Overlay Networks) The work on Globule and other peer-topeer related research is done a cooperation between the VU-WI-i and TUD-EWI-st-pds, TUD-ti-ki. There has been a joint
NWO proposal (granted).
I-SHARE (part of Freeband)
2004-2008, EZ BSIK/Freeband, 8 M€, TUD-EWI-st-pds. Sharing resources in virtual communities for storage,
communications and processing of multimedia data. The FREEBAND I-SHARE-project investigates the sharing resources in
virtual communities, which are (dynamic) groups of nodes that are willing to collaborate for the better of the whole. In
particular, I-SHARE considers the sharing of resources for processing, transmitting and storing multimedia streams:
- Funtionality sharing. Specific capabilities of terminals embodied in algorithms or, more abstractly, in services are shared to
support applications and to form new ones.
- Content sharing. This pertains to particular assets related to local hardware. We think of processing power and storage to
start with, but specific processing hardware (co-processors) and special purpose hardware are possible as well.
“Model-driven spatiotemporal tracking for quantitative analysis of subcellular dynamics”
NWO EW VIDI grant, 600 kEuro: 2005-2009 In this project, automated image analysis techniques for the accurate and
reproducible quantification of the motion of subcellular structures from time-lapse fluorescence microscopy image data are
developed and evaluated. EUR- RMI-bigr Collaboration with Applied Physics, Delft
Multifield Medical Visualization
NWO-VIEW, 2005-2010, 2 OIO, ir. J. Blaas and S. Busking, MSc. An increasing number of medical acquisition and
processing techniques are generating large amounts of multi-field data, such as data from different imaging modalities. Many
of these datasets are also time-varying, for example in heart motion studies. In this project, we want to transfer knowledge
and techniques from closely related fields such as vector and tensor field visualization in scientific visualization, to medical
visualization applications. Joint project TUD-ewi-cgcc with TUE-BME (ter Haar-Romeny, Vilanova).
MultimediaN
2004-2008, BSIK, 35 MEuro, UvA-Science-ISIS, CWI, TUD-Mediamatica, UT-CTIT-CS, VU-CS, UU-CS, TNO, Nederlands
Forensisch Instituut, Telematica Instituut, IBM, V2_, Philips, Ilse Media, LogicaCMG, Waag Society, DBNL, eMAXX,
112
NOC*NSF, SPSS, Compano, Beeld en Geluid, FabChannel, ZiuZ, DBNL, de Politie Amstellanden, Vereniging Digitaal
Erfgoed, Roessingh. The project aims at various forms of multi-media, multi-modal analysis, interaction, system design and
knowledge engineering for several scientific and applied science goals.
RoboCup/Progress
UvA, TUD -TN en VU, also UU (Siks) and TUD- ET (DISC).
SCALPE
2004-2008, STW, EURO 220.000, ASCI partners VU and TUD
This project deals with high-productivity methods for programming parallel systems on a chip.
SmartCam
2002-2006. STW/PROGRESS, TUE-EE-dmes, Philips Natlab, Philips CFT, TNO-FEL, In3D, HP Bristol labs, 1.4 M€, TUDTNW-tn-ph The SmartCam project investigates low-cost one-chip Smart Camera solutions, contributing to a quantitatively
guided design trajectory. In particular, we investigate the impact of current applications, and we try to define relevant
architectural parameters and to develop an architectural template. Other aims are to enhance and integrate existing
application mapping environments for SIMD and ILP processors.
Surface and volume geometry processing for lesion detection and segmentation in virtual colonoscopy
Philips Medical Systems, 2004-2008, 1 AIO, Lingxiao Zhao MSc.Research on the determination and use of geometric
properties of the inner surface of the human colon for automatic pre-detection of colonic polyps. Invertigation of higher-order
geometric properties (curvature) for claculation of distinctive features for polyp detection. TUD-EWI-cgcc Cooperation with
TUD-TNW-QI (van Vliet)
Techniques for Collaborative Visualization in Virtual Environments, Bsik VL-e
2004-2007, post-doc, dr. M. Koutek. Techniques for distributed and collaborative visualization in virtual environments, and
3D interaction; design of software architectures for multi-platform collaborative VR support. TUD-EWI-cgcc cooperation with
CWI (van Liere), VU (Bal) and TUD-PGS (Epema).
Token2000
People: A.G. Hoekstra, P.M.A. Sloot, E.V. Zudilova, M. Scarpa, L. Abrahamyan ASCI partner: LKEB/LUMC (P.I.: Reiber)
Token2000 is a nationally funded project (NWO), where we collaborate closely with the Universities of Leiden and Twente on
the development of an interactive medical application, somewhat similar to the work in CrossGrid. This application is
intended for training of surgeons. In collaboration with Leiden University Medical Centre we have created Hemosolve, a
problem-solving environment for image based computational Haemodynamics. Hemosolve includes our L-BGK solver, but
also a FEM Navier-Stokes solver. Moreover, it contains a 3D editing tool and powerful visualization modules.
Project Trader
2004-2008, ESI, 1 AIO, TUD EWI/ UL-LERC/LIACS
Modern systems such as household appliances, DVD players, PCs, medical X-ray imaging systems, printers, advanced
vehicles, and airplanes rely increasingly on software, in particular for system integration. Embedded software monitors the
whole system taking care that the system accomplishes more than its parts would. In such software intensive systems,
reliability is of prime importance.
Two-level Peer-to-Peer Systems
2003-2007, NWO, KEURO 147, ASCI partners TUD-EWI-pds, VU-group Large-Scale Distributed Systems. This project aims
at exploring the notion of superpeers in p2p systems in order to improve the performance of such systems.
The work on Globule and other peer-to-peer related research is done a cooperation between the VU-WI-I and TUD-ti-ki.
Efforts continue in the Bsik IShare project, in which the TUD and VU jointly work on the Tribler
Virtual Laboratory for e-Science (VL-e)
2004-2009, EZ (BSIK program), EURO 1.000.000 (TUD-EWI-st-pds part), ASCI partners TUD-EWI-mm-cgcc, VU-EW-cs-I,
UvA-FdNWI-caps, UvA-FdNWI-scs. Amolf, Nikhef, CWI, SARA, IBM, LigicaCMG, Philips, FEI
This projects aims at designing and implementing grid technology (schedulers, communication libraries, problem-solving and
visualization environments, etc) for virtual laboratories (e.g., for simulations in the sciences) on top of the basic grid fabric.
UvA FdNWI-scs
In the BSIK funded VL-e project we collaborate with a number of ASCI groups affiliated with VU and UvA
VL-e consortium include a number of ASCI members UvA, VU, TUD. few can consider the work developing the generic VL-e
middleware as a collaboration of ASCI members
113
In the N W O funded project DIME we collaborate with UL-LUMC-lkeb on a Problem Solving Environment for Computational
Hemodynamics, and its potential use in pre-operative planning and training.
3.2
ASCI 2005 Conference
ASCI 2005 was the eleventh annual conference organized by ASCI. Apart from keynotes, and paper and poster
presentations, the program consisted of theme presentations by senior ASCI researchers.
Keynotes
¾ James Crowley from INRIA Grenoble
¾ Richard Kleihorst from Philips Research Eindhoven
¾ Andrew Herbert from Microsoft Research Cambridge.
About the conference
Number of theme presentations 3
Number of poster presentations 23
Numer of paper presentations 32
Date: June 8 - 10, 2005
Location: Conference Het Heijderbos, Heijen
Number of participants 130
Proceedings
B.J.A. Kröse, H.J. Bos, E.A. Hendriks, Heijnsdijk J.W.J., Proceedings of the eleventh annual conference of the Advanced
School for Computing and Imaging, Het Heijderbos, Heijen, June 8-10, 2005, ISBN 90-803086-0-9, Delft, 2005.
jms/30-01-07
114

Annual Report 2005 - ASCI

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