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Translating multiscale cancer models into clinical trials: Simulating breast cancer tumor dynamics within the framework of the "Trial of Principle" clinical trial and the ACGT project

Translating multiscale cancer models into clinical trials: S...

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8th IEEE International Conference on Bioinformatics and BioEngineering, BIBE 2008

作者： Kolokotroni, Eleni A. Stamatakos, Georgios S. Dionysiou, Dimitra D. Georgiadi, Eleni Ch. Desmedt, Christine Graf, Norbert M. National Technical University of Athens Institute of Communication and Computer Systems In Silico Oncology Group Iroon Polytechniou 9 Zografos GR-157 80 Greece Foundation for Research and Technology - Hellas Institute of Computer Science Biomedical Informatics Laboratory N. Plastira 100 Vassilika Vouton GR-700 13 Heraklion Crete Greece Institut Jules Bordet - Centre des Tumeurs rue Héger Bordet 1 1000 Bruxelles Belgium University Hospital of the Saarland Paediatric Haematology and Oncology D-66421 Homburg Germany

ISBN: (纸本)9781424428458

The potential of cancer multilevel modeling has been particularly emphasized over the past years. Integration of multiscale experimental and clinical information pertaining to cancer via advanced computer models seems to considerably accelerate optimization of cancer treatment in the patient individualized context. However, a sine qua non prerequisite for such models to reach clinical practice is to be thoroughly tested through clinical trials for validation and optimization purposes. This is one of the major goals of the European Commission funded "Advancing Clinico-Genomic Trials on Cancer" (ACGT) project. This paper presents a discrete state based, four dimensional, multiscale tumor dynamics model that has been specially developed by the In Silico Oncology group in order to mimick the Trial Of Principle (TOP) clinical trial concerning breast cancer treated with epirubicin. The TOP trial constitutes one of the ACGT clinical trials. A substantial part of the model can address other tumor types as well. The actual pseudoanonymized imaging, histopathological, molecular and clinical data of the patient are exploited. Special emphasis is put on the effect of cancer stem/clonogenic, progenitor, differentiated and dead cells, the cell category transition rates and the cell category relative populations within the tumor from the treatment baseline onwards. The importance of adaptation of the cell category relative populations to the cell category transition rates for free tumor growth is revealed and the concept of a pertinent nomogram is introduced. A method which ensures adaptation of these two sets of entities at the beginning of the simulation execution is proposed and subsequently successfully applied. Convergence and code checking issues are addressed. Indicative parametric/sensitivity studies are presented along with specific numerical findings. The model's behavior substantiates its potential to serve as the basis of a treatment optimization system following an ev

关键词： Genome

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A Robust Descriptor based on Weber's Law

A Robust Descriptor based on Weber's Law

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26th IEEE Conference on computer Vision and Pattern Recognition (CVPR 2008), vol.8

作者： Jie Chen Shiguang Shan Guoying Zhao Xilin Chen Wen Gao Matti Pietikainen School of Computer Science and Technology Harbin Institute of Technology Harbin China Machine Vision Group Department of Electrical and Information Engineering University of Oulu Finland Languages Informatics Systems and Software Engineering Department Faculty of Computer Science Chinese Academy and Sciences Beijing China

Inspired by Weber's Law, this paper proposes a simple, yet very powerful and robust local descriptor, Weber Local Descriptor (WLD). It is based on the fact that human perception of a pattern depends on not only the change of a stimulus (such as sound, lighting, et al.) but also the original intensity of the stimulus. Specifically, WLD consists of two components: its differential excitation and orientation. A differential excitation is a function of the ratio between two terms: One is the relative intensity differences of its neighbors against a current pixel;the other is the intensity of the current pixel. An orientation is the gradient orientation of the current pixel. For a given image, we use the differential excitation and the orientation components to construct a concatenated WLD histogram feature. Experimental results on Brodatz textures show that WLD impressively outperforms the other classical descriptors (e.g., Gabor). Especially, experimental results on face detection show a promising performance. Although we train only one classifier based on WLD features, the classifier obtains a comparable performance to state-of-the-art methods on MIT+CMU frontal face test set, AR face dataset and CMU profile test set.

关键词： Robustness Face detection Humans Content addressable storage Testing Psychology Laboratories Machine intelligence Information processing computers

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Reports of the AAAI 2008 Spring Symposia

Reports of the AAAI 2008 Spring Symposia

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作者： Balduccini, Marcello Baral, Chitta Brodaric, Boyan Colton, Simon Fox, Peter Gutelius, David Hinkelman, Knut Horswill, Ian Huberman, Bernardo Hudlicka, Eva Lerman, Kristina Lisetti, Christine McGuinness, Deborah Maher, Mary Lou Musen, Mark A. Sahami, Mehran Sleeman, Derek Thönssen, Barbara Velasquez, Juan Ventura, Dan Eastman Kodak Company Arizona State University Tempe AZ United States Geological Survey of Canada Department of Computing Imperial College London United Kingdom National Center for Atmospheric Research Artificial Intelligence Center SRI International Menlo Park CA United States University of Applied Sciences Zurich Switzerland Department of Computer Science Northwestern University Evanston IL United States Social Computing Lab. Hewlett-Packard Laboratories Psychometric Associates USC Information Sciences Institute University of Southern California Los Angeles CA United States Computer Science Department University of Southern California Los Angeles CA United States School of Computing and Information Sciences Florida International University Miami FL United States Rensselaer Polytechnic Institute Information and Intelligent Systems Division National Science Foundation University of Sydney Sydney NSW Australia Faculty of Architecture Design and Planning University of Sydney Sydney NSW Australia Department of Medicine Biomedica Informatics Research Department Stanford University Stanford CA United States Computer Science Department Stanford University Stanford CA United States Department of Computing Science University of Aberdeen Aberdeen United Kingdom MIT CSAIL Department of Computer Science Brigham Young University Provo UT United States

The Association for the Advancement of Artificial Intelligence (AAAI) was pleased to present the AAAI 2008 Spring Symposium Series, held Wednesday through Friday, March 26-28, 2008, at Stanford University, California. The eight symposia were titled (1) AI Meets Business Rules and Process Management, (2) architectures for Intelligent Theory-Based Agents, (3) Creative Intelligent systems, (4) Emotion, Personality, and Social Behavior, (5) Semantic Scientific Knowledge Integration, (6) Social Information Processing, (7) Symbiotic Relationships between Semantic Web and Knowledge Engineering, (8) Using Al to Motivate Greater Participation in computer Science. The goal of the AI Meets Business Rules and Process Management AAAI symposium was to investigate the various approaches and standards to represent business rules, business process management, and the semantic web with respect to expressiveness and reasoning capabilities. The focus of the architectures ror Intelligent Theory-Based Agents AAAI symposium was the definition or architectures for intelligent theory-based agents, comprising languages, knowledge representation methodologies, reasoning algorithms, and control loops. The Creative Intelligent systems symposium included five major discussion sessions and a general poster session (in which all contributing papers were presented). The purpose of this symposium was to explore the synergies between creative cognition and intelligent systems. The goal of the Emotion, Personality, and Social Behavior symposium was to examine fundamental issues in affect and personality in both biological and artificial agents, focusing on the roles of these factors in mediating social behavior. The Semantic Scientific Knowledge Integration symposium brought together the semantic technologies community with the scientific information technology community in an effort to build the general semantic science information community. The Social Information Processing symposium's goal was to

关键词： Knowledge representation

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Signature-based Microprocessor Power Modeling for Rapid System-level Design Space Exploration

Signature-based Microprocessor Power Modeling for Rapid Syst...

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Embedded systems for Real-Time Multimedia (ESTIMedia)

作者： Peter van Stralen Andy D. Pimentel Computer Systems Architecture group Informatics Institute University of Amsterdam Computer Systems Architecture group Informatics Institute University of Amsterdam Netherlands

This paper presents a technique for high-level power estimation of microprocessors. The technique, which is based on abstract execution profiles called 'event signatures', operates at a higher level of abstraction than commonly-used instruction-level power simulators and should thus be capable of achieving good evaluation performance. We have compared our power estimation results to those from the instruction-level simulator Wattch. In these experiments, we demonstrate that with a good underlying power model, the signature-based power modeling technique can yield accurate estimations (a mean error of 5.5 percent compared to Wattch in our experiments). At the same time, the power estimations based on our event signature technique are at least an order of magnitude faster than with Wattch.

关键词： Microprocessors Power system modeling System-level design Space exploration computer architecture Application software Computational modeling Hardware Discrete event simulation Analytical models

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Orient-2: A realtime wireless posture tracking system using local orientation estimation 07

Orient-2: A realtime wireless posture tracking system using ...

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4th Workshop on Embedded Networked Sensors, EmNets 2007

作者： Young, A.D. Ling, M.J. Arvind, D.K. Institute of Computer Systems Architecture School of Informatics University of Edinburgh Mayfield Road Edinburgh EH9 3JZ United Kingdom

ISBN: (纸本)9781595936943

A realtime posture tracking system has been developed using a network of compact wireless sensor devices worn by the user. Each device is a complete inertial/magnetic tracking unit which performs in situ orientation estimation based on its own sensor readings, using a complementary quaternion-based filter. Compared to existing systems which transmit raw sensor data to a PC for processing, it is shown that this technique reduces bandwidth requirements by 79% for typical usage. In combination with a time division multiple access scheme, this reduction allows for full-body tracking using 15 devices at a 64Hz update rate through a single 250kbps receiver. The data is applied to a rigid body model of the subject to provide a realtime display, and can be exported for use in major animation packages.

关键词： Wireless sensor networks

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Evaluating the Design of Biological Cells Using a computer Workbench

Evaluating the Design of Biological Cells Using a Computer W...

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Annual Symposium on Simulation

作者： Tessa E. Pronk Simon Polstra Andy D. Pimentel Timo M. Breit Integrative BioInformatics Unit Swammerdam Institute for Life Sciences University of Amsterdam Netherlands Computer Systems Architecture Group Informatics Institute University of Amsterdam Netherlands

For embedded systems as well as for biological cell systems, design is a feature that defines their identity. The assembly of different components in designs of both systems can vary widely. Given the similarities between computers and cellular systems, methods and models of computation from the domain of computer systems engineering might be applied to modeling cellular systems. Our aim is to construct a framework that focuses on understanding the design options and consequences within a cell, taking an in silico (forward-) engineering approach rather than a reverse engineering approach that is used in this domain as a default now. We take our ideas from the domain of embedded computer systems. The most important features of our approach, as taken from this domain, are a variable abstraction level of components that allows for addition of components when detailed information is lacking, and a separation of concerns between function and performance by components in the design. This allows for efficient and flexible modeling. Also, there is a strict separation between computation within- and communication between components, reducing complexity. As a proof of principle, we show that we can make a statement regarding the design of the gene expression machinery of the cell to produce a protein, using such a method

关键词： Biological cells Biology computing Biological system modeling Embedded system Assembly systems Computational modeling systems engineering and theory Design engineering Reverse engineering Embedded computing

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Data access and management in ACGT: tools to solve syntactic and semantic heterogeneities between clinical and image databases 07

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Proceedings of the 2007 conference on Advances in conceptual modeling: foundations and applications

作者： Luis Martín Erwin Bonsma Alberto Anguita Jeroen Vrijnsen Miguel García-Remesal José Crespo Manolis Tsiknakis Víctor Maojo Biomedical Informatics Group Artificial Intelligence Laboratory School of Computer Science Universidad Politécnica de Madrid Boadilla del Monte Madrid Spain Phillips Research Healthcare System Architecture Eindhoven The Netherlands Center of eHealth Technologies Institute of Computer Science Foundation for Research and Technology-Hellas Heraklion Crete Greece

ISBN: (纸本)9783540762911

Recent changes in data management within post-genomic clinical trials have emphasized the need for novel methods and tools to solve semantic and syntactic heterogeneities among distributed sources of information. ACGT is an Integrated Project funded by the European Commission that aims at building a GRID-based platform comprised by a set of tools to support multicentric post-genomic clinical trials on cancer. The main goal of ACGT is to provide seamless access to heterogeneous sources of information. For this purpose, two core tools were developed and included in the ACGT architecture: the ACGT Semantic Mediator (ACGT-SM), and the Data Access Wrappers (ACGT-DAWs). The ACGT-SM addresses semantics and schema integration, while the ACGT-DAWs cope with syntactic heterogeneities. Once the sources are bridged together, they can be seamlessly accessed using the RDQL query *** tested our tools using a set of three relational and DICOM based image sources obtaining promising results.

关键词： DICOM ontologies semantic mediation database integration clinical trial databases

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REQUIREMENTS FOR AN EVENT-BASED SIMULATION PACKAGE FOR GRID systems

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Journal of Interconnection Networks 2007年第2期8卷 163-178页

作者： FATOS XHAFA JAVIER CARRETERO LEONARD BAROLLI ARJAN DURRESI Polytechnic University of Catalonia Department of Languages and Informatics Systems C/Jordi Girona 1-3 08034 Barcelona Spain . Polytechnic University of Catalonia Department of Computer Architecture C/Jordi Girona 1-3 08034 Barcelona Spain Department of Information and Communication Engineering Fukuoka Institute of Technology (FIT) 3-30-1 Wajiro-higashi Higashi-ku Fukuoka 811-0295 Japan Department of Computer Science Louisiana State University 298 Coates Hall Baton Rouge LA 70803 USA

In this paper we present a study on the requirements for the design and implementation of simulation packages for Grid systems. Grids are emerging as new distributed computing systems whose main objective is to manage and allocate geographically distributed computing resources to applications and users in an efficient and transparent manner. Grid systems are at present very difficult and complex to use for experimental studies of large-scale distributed applications. Although the field of simulation of distributed computing systems is mature, recent developments in large-scale distributed systems are raising needs not present in the simulation of the traditional distributed systems. Motivated by this, we present in this work a set of basic requirements that any simulation package for Grid computing should offer. This set of functionalities is obtained after a careful review of most important existing Grid simulation packages and includes new requirements not considered in such simulation packages. Based on the identified set of requirements, a Grid simulator is developed and exemplified for the Grid scheduling problem.

关键词： Grid systems event-based simulation requirements scheduling

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Comparison of seven approaches for holter ECG clustering and classification

Comparison of seven approaches for holter ECG clustering and...

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29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBS 2007), vol.10

作者： Vaclav Chudacek Milan Petrik George Georgoulas Miroslav Cepek Lenka Lhotska Chrysostomos Stylios Gerstner laboratory at Department of Cybernetics Czech Technical University Czech Republic Czech Republic Department of Cybernetics Center for Machine Perception Czech Technical University Czech Republic Intelligent Control Systems Laboratory Georgia Technology Research Institute Atlanta USA Czech Republic Department of Computer Science and Engineering Neural Computing Group Czech Technical University Czech Republic Czech Republic Department of Cybernetics Gerstner Laboratory Czech Technical University Czech Republic Department of Informatics and Communications Technology TEI Epirus Artas Greece

In this work we present a comparative study, testing selected methods for clustering and classification of holter electrocardiogram (ECG). More specifically we focus on the task of discriminating between normal 'N' beats and premature ventricular 'V' beats. Some of the tested methods represent the state of the art in pattern analysis, while others are novel algorithms developed by us. All the algorithms were tested on the same datasets, namely the MIT-BIH and the AHA databases. The results for all the employed methods are compared and evaluated using the measures of sensitivity and specificity.

关键词： Electrocardiography Testing Decision trees Laboratories Cybernetics Sensitivity and specificity Heart rate variability Clustering algorithms Spatial databases Computational complexity

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On the Calibration of Abstract Performance Models for System-level Design Space Exploration

On the Calibration of Abstract Performance Models for System...

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International Conference on Embedded computer systems: architectures, Modeling and Simulation (IC-SAMOS)

作者： Andy D. Pimentel Mark Thompson Simon Polstra Cagkan Erbas Computer Systems Architecture group Informatics Institute University of Amsterdam Amsterdam Netherlands

High-level performance modeling and simulation has become a key ingredient of system-level design as they facilitate early architectural design space exploration. An important precondition for such high-level modeling and simulation methods is that they should yield trustworthy performance estimations. This requires validation (if possible) and calibration of the simulation models, which are two aspects that have not yet been widely addressed in the system-level community. This paper presents an initial attempt to provide support for calibrating various model components of a system-level performance model. We discuss these model calibration mechanisms in the context of our Sesame system-level simulation framework. An illustrative case study is also presented to indicate the merits of model calibration

关键词： Calibration System-level design Space exploration computer architecture Context modeling Predictive models Computational modeling Embedded system Documentation Virtual prototyping

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