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26th Annual Computational Neuroscience Meeting (CNS*2017) of the Organization for Computational Neuroscience Antwerp, Belgium, July 15-20, 2017

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BMC NEUROSCIENCE 2017年第SUPPL 1期18卷 59-59页

作者： [Anonymous] Indiana University Purdue University Indianapolis Indianapolis IN 46032 USA Stark Neurosciences Research Institute Indiana University School of Medicine Indianapolis IN 46032 USA Department of Mathematics East Carolina University Greenville NC 27858 USA Jülich Supercomputing Centre Forschungszentrum Jülich 52425 Jülich Germany Future Systems Swiss National Supercomputing Centre 8092 Zurich Switzerland User Engagement and Support Swiss National Supercomputing Centre 6900 Lugano Switzerland Institut de Neurosciences des Systèmes Aix Marseille Univ 13005 Marseille France Simulation Lab Neuroscience Forschungszentrum Jülich Jülich Germany Department of Experimental Psychology Ghent University 9000 Ghent Belgium Donders Center for Cognitive Neuroimaging Radboud University 6525HR Nijmegen The Netherlands Department of Electrical Computer and Energy Engineering University of Colorado Boulder CO 80309 USA Department of Neurosurgery Johns Hopkins School of Medicine Baltimore MD 21287 USA Department of Neurology Johns Hopkins School of Medicine Baltimore MD 21287 USA Department of Otolaryngology Johns Hopkins School of Medicine Baltimore MD 21287 USA INSERM U968 Paris France Sorbonne Universités UPMC University Paris 06 UMR_S 968 Institut de la Vision Paris France CNRS UMR_7210 Paris France Department of Computer Architecture and Technology University of Granada (CITIC) Granada Spain Sorbonne Universités UPMC Univ Paris 06 INSERM CNRS Institut de la Vision Paris France Department of Adaptive Machine Systems Osaka University Osaka Japan Department of Computer Science University of Cergy-Pontoise Cergy-Pontoise France Department of Physics and Astronomy College of Charleston Charleston SC 29424 USA School of Physics Faculty of Science University of Sydney Sydney NSW 2006 Australia Center of Excellence for Integrative Brain Function Australian Research Council Sydney Australia Max Planck Institute for Human Cognitive and Brain Sciences Saxony Lei

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26th Annual Computational Neuroscience Meeting (CNS*2017): Part 3 Antwerp, Belgium. 15-20 July 2017 Abstracts

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BMC NEUROSCIENCE 2017年第SUPPL 1期18卷 95-176页

作者： [Anonymous] Department of Neuroscience Yale University New Haven CT 06520 USA Department Physiology & Pharmacology SUNY Downstate Brooklyn NY 11203 USA NYU School of Engineering 6 MetroTech Center Brooklyn NY 11201 USA Departament de Matemàtica Aplicada Universitat Politècnica de Catalunya Barcelona 08028 Spain Institut de Neurobiologie de la Méditerrannée (INMED) INSERM UMR901 Aix-Marseille Univ Marseille France Center of Neural Science New York University New York NY USA Aix-Marseille Univ INSERM INS Inst Neurosci Syst Marseille France Laboratoire de Physique Théorique et Modélisation CNRS UMR 8089 Université de Cergy-Pontoise 95300 Cergy-Pontoise Cedex France Department of Mathematics and Computer Science ENSAT Abdelmalek Essaadi’s University Tangier Morocco Laboratory of Natural Computation Department of Information and Electrical Engineering and Applied Mathematics University of Salerno 84084 Fisciano SA Italy Department of Medicine University of Salerno 84083 Lancusi SA Italy Dipartimento di Fisica Università degli Studi Aldo Moro Bari and INFN Sezione Di Bari Italy Data Analysis Department Ghent University Ghent Belgium Coma Science Group University of Liège Liège Belgium Cruces Hospital and Ikerbasque Research Center Bilbao Spain BIOtech Department of Industrial Engineering University of Trento and IRCS-PAT FBK 38010 Trento Italy Department of Data Analysis Ghent University Ghent 9000 Belgium The Wellcome Trust Centre for Neuroimaging University College London London WC1N 3BG UK Department of Electronic Engineering NED University of Engineering and Technology Karachi Pakistan Blue Brain Project École Polytechnique Fédérale de Lausanne Lausanne Switzerland Departement of Mathematics Swansea University Swansea Wales UK Laboratory for Topology and Neuroscience at the Brain Mind Institute École polytechnique fédérale de Lausanne Lausanne Switzerland Institute of Mathematics University of Aberdeen Aberdeen Scotland UK Department of Integrativ

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Domain-knowledge optimized simulated annealing for network-on-chip application mapping

Advances in Intelligent Systems and Computing

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Advances in Intelligent systems and Computing 2013年 187 AISC卷 473-487页

作者： Radu, Ciprian Vinţan, Lucian Advanced Computer Architecture and Processing Systems Research Lab Lucian Blaga University of Sibiu Sibiu Romania

ISBN: (纸本)9783642325472

Network-on-Chip architectures are scalable on-chip interconnection networks. They replace the inefficient shared buses and are suitable for multicore and manycore systems. This paper presents an Optimized Simulated Annealing (OSA) algorithm for the Network-on-Chip application mapping problem. With OSA, the cores are implicitly and dynamically clustered using knowledge about communication demands. We show that OSA is a more feasible Simulated Annealing approach to NoC application mapping by comparing it with a general Simulated Annealing algorithm and a Branch and Bound algorithm, too. Using real applications we show that OSA is significantly faster than a general Simulated Annealing, without giving worse solutions. OSA proves to be feasible for Networks-on-Chip with more than 100 nodes. Also, compared to a Branch and Bound technique, it gives better solutions, as the problem size increases, while in terms of speed and memory consumption the two algorithms are comparable.

关键词： Network-on-chip

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26th Annual Computational Neuroscience Meeting (CNS*2017): Part 1

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BMC Neurosci 2017年第SUPPL 1期18卷 58-58页

作者： Sue Denham Panayiota Poirazi Erik De Schutter Karl Friston Ho Ka Chan Thomas Nowotny Dongqi Han Sungho Hong Sophie Rosay Tanja Wernle Alessandro Treves Sarah Goethals Romain Brette Tomas Van Pottelbergh Rodolphe Sepulchre Alex D. Bird Hermann Cuntz Pedro J. Gonçalves Jan-Matthis Lueckmann Giacomo Bassetto Marcel Nonnenmacher Jakob H. Macke Audrey J. Sederberg Jason N. MacLean Stephanie E. Palmer Ulisse Ferrari Christophe Gardella Olivier Marre Thierry Mora Emina Ibrahimovic Martin Müller Jean-Pascal Pfister Tushar Chauhan Timothée Masquelier Alexandre Montlibert Benoit R. Cottereau Moritz Helias Jannis Schuecker David Dahmen Sven Goedeke Alexandre Hyafil Ainhoa Hermoso-Mendizabal Pavel E. Rueda-Orozco Santiago Jaramillo David Robbe Jaime de la Rocha Marie Rooy Fani Koukouli David DiGregorio Uwe Maskos Boris Gutkin Andrey Yu Verisokin Darya V. Verveyko Dmitry E. Postnov Willy Wong Omid Talakoub Robert Chen Milos Popovic Dmitriy Lisitsyn Eric Drebitz Iris Grothe Sunita Mandon Andreas Kreiter Udo Ernst Peter A. Robinson Xuelong Zhao Kevin M. Aquino John D. Griffiths Grishma Mehta-Pandejee Natasha Gabay James MacLaurin Somwrita Sarkar Tim Kunze Jens Haueisen Thomas R. Knösche Subutai Ahmad Yuwei Cui Marcus Lewis Jeff Hawkins Simona Olmi Spase Petkoski Fabrice Bartolomei Maxime Guye Viktor Jirsa Hazem Toutounji Daniel Durstewitz Matteo Cantarelli Adrian Quintana Boris Marin Matt Earnshaw Padraig Gleeson Robert Court Robert McDougal R. Angus Silver Salvador Dura-Bernal Stephen Larson William W. Lytton Giovanni Idili Lorenzo Posani Simona Cocco Karel Ježek Rémi Monasson School of Psychology Faculty of Health & Human Sciences Plymouth University Plymouth Devon PL4 8AA UK Institute of Molecular Biology and Biotechnology (IMBB) Foundation for Research and Technology-Hellas (FORTH) Heraklion Crete Greece Okinawa Institute of Science and Technology Graduate University Okinawa Japan Wellcome Trust Centre for Neuroimaging Institute of Neurology UCL London WC1N 3BG UK School of Engineering and Informatics University of Sussex Brighton BN1 9QJ UK Graduate School Okinawa Institute of Science and Technology Okinawa 904-0495 Japan Computational Neuroscience Unit Okinawa Institute of Science and Technology Okinawa 904-0495 Japan Cognitive Neuroscience Area Scuola Internazionale Superiore di Studi Avanzati Trieste 34136 Italy Kavli Institute for Systems Neuroscience NTNU Trondheim 7030 Norway Institut de la Vision Sorbonne Universités UPMC Univ Paris 06 INSERM CNRS Paris 75012 France Department of Engineering University of Cambridge Cambridge Cambridgeshire CB2 1PZ UK Ernst Strüngmann Institute for Neuroscience Max Planck Society Frankfurt Germany Frankfurt Institute for Advanced Studies Frankfurt Germany Neural Systems Analysis Research Center Caesar An Associate of the Max Planck Society Bonn Germany Max Planck Institute for Biological Cybernetics Tübingen Germany Bernstein Center for Computational Neuroscience Tübingen Germany Present Address: Biomedical Engineering Department Georgia Institute of Technology Atlanta GA 30306 USA Department of Neurobiology University of Chicago Chicago IL 60637 USA Department of Organismal Biology and Anatomy University of Chicago Chicago IL 60637 USA Committee on Computational Neuroscience University of Chicago Chicago IL 60637 USA Institut de la Vision Sorbonne Universités INSERM Paris France Laboratoire de Physique Statistique Ecole Normale Supérieure Paris France Institute of Molecular Life Sciences University of Zürich 8057 Zürich Switzerland Institute of Neuroinformatics Univer

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A comparison of multi-objective algorithms for the automatic design space exploration of a superscalar system

Advances in Intelligent Systems and Computing

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Advances in Intelligent systems and Computing 2013年 187 AISC卷 489-502页

作者： Calborean, Horia Jahr, Ralf Ungerer, Theo Vintan, Lucian Advanced Computer Architecture and Processing Systems Research Lab Lucian Blaga University of Sibiu E. Cioran Str. No. 4 Sibiu 550025 Romania Institute of Computer Science University of Augsburg Universitaetsstr. 6a 86159 Augsburg Germany

ISBN: (纸本)9783642325472

In today's computer architectures the design spaces are huge, thus making it very difficult to find optimal configurations. One way to cope with this problem is to use Automatic Design Space Exploration (ADSE) techniques. We developed the Framework for Automatic Design Space Exploration (FADSE) which is focused on microarchitectural optimizations. This framework includes several state-of-the art heuristic algorithms. In this paper we selected three of them, NSGA-II and SPEA2 as genetic algorithms as well as SMPSO as a particle swarm optimization, and compared their performance. As test case we optimize the parameters of the Grid ALU Processor (GAP) microarchitecture and then GAP together with the post-link code optimizer GAPtimize. An analysis of the simulation results shows a very good performance of all the three algorithms. SMPSO reveals the fastest convergence speed. A clear winner between NSGA-II and SPEA2 cannot be determined.

关键词： Heuristic algorithms

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Highlights from the 11th ISCB Student Council Symposium 2015. Dublin, Ireland. 10 July 2015

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BMC bioinformatics 2016年第3期17 Suppl 3卷 95页

作者： Katie Wilkins Mehedi Hassan Margherita Francescatto Jakob Jespersen R. Gonzalo Parra Bart Cuypers Dan DeBlasio Alexander Junge Anupama Jigisha Farzana Rahman Griet Laenen Sander Willems Lieven Thorrez Yves Moreau Nagarajan Raju Sonia Pankaj Chothani C. Ramakrishnan Masakazu Sekijima M. Michael Gromiha Paddy J Slator Nigel J Burroughs Przemysław Szałaj Zhonghui Tang Paul Michalski Oskar Luo Xingwang Li Yijun Ruan Dariusz Plewczynski Giulia Fiscon Emanuel Weitschek Massimo Ciccozzi Paola Bertolazzi Giovanni Felici Pieter Meysman Manu Vanaerschot Maya Berg Hideo Imamura Jean-Claude Dujardin Kris Laukens Westa Domanova James R. Krycer Rima Chaudhuri Pengyi Yang Fatemeh Vafaee Daniel J. Fazakerley Sean J. Humphrey David E. James Zdenka Kuncic Plant Pathology and Plant-Microbe Biology Section School of Integrative Plant Science Cornell University Ithaca USA Graduate Field of Computational Biology Cornell University Ithaca USA School of Computing & Mathematics University of South Wales Cardiff UK Department of Genome Biology for Neurodegenerative Diseases German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association ᅟ Germany Department of Surgery Massachusetts General Hospital The Broad Institute of MIT and Harvard Boston USA Department of Systems Biology Technical University of Denmark Kemitorvet Denmark Protein Physiology Lab Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Buenos Aires Argentina Molecular Parasitology Unit (MPU) Institute of Tropical Medicine Antwerp Belgium Advanced Database Research and Modeling (ADReM) research group University of Antwerp Antwerpen Belgium Department of Computer Science University of Arizona Tucson USA Department of Veterinary Clinical and Animal Sciences Center for non-coding RNA in Technology and Health University of Copenhagen Copenhagen Denmark University College Dublin Dublin Ireland Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems Signal Processing and Data Analytics KU Leuven Leuven Belgium Minds Medical IT Department Leuven Belgium Scientific Institute of Public Health (WIV-ISP) Platform of Biotechnology and Molecular Biology (PBB) Brussels Belgium Department of Development and Regeneration @ Kulak KU Leuven Kortrijk Belgium Department of Biotechnology Bhupat and Jyoti Metha School of Biosciences Indian Institute of Technology Madras Chennai India Philips Research North America Briarcliff Manor USA Global Scientific Information and Computing Center (GSIC) Tokyo Institute of Technology Tokyo Japan Systems Biology Centre University of Warwick Senate House Coventry UK Systems Biology Doctoral Training Centre University of Warwick Senate House Coventry UK Center for B

A1 Highlights from the eleventh ISCB Student Council Symposium 2015 Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan DeBlasio, Alexander Junge, Anupama Jigisha, Farzana Rahman O1 Prioritizing a drug’s targets using both gene expression and structural similarity Griet Laenen, Sander Willems, Lieven Thorrez, Yves Moreau O2 Organism specific protein-RNA recognition: A computational analysis of protein-RNA complex structures from different organisms Nagarajan Raju, Sonia Pankaj Chothani, C. Ramakrishnan, Masakazu Sekijima; M. Michael Gromiha O3 Detection of Heterogeneity in Single Particle Tracking Trajectories Paddy J Slator, Nigel J Burroughs O4 3D-NOME: 3D NucleOme Multiscale Engine for data-driven modeling of three-dimensional genome architecture Przemysław Szałaj, Zhonghui Tang, Paul Michalski, Oskar Luo, Xingwang Li, Yijun Ruan, Dariusz Plewczynski O5 A novel feature selection method to extract multiple adjacent solutions for viral genomic sequences classification Giulia Fiscon, Emanuel Weitschek, Massimo Ciccozzi, Paola Bertolazzi, Giovanni Felici O6 A systems Biology Compendium for Leishmania donovani Bart Cuypers, Pieter Meysman, Manu Vanaerschot, Maya Berg, Hideo Imamura, Jean-Claude Dujardin, Kris Laukens O7 Unravelling signal coordination from large scale phosphorylation kinetic data Westa Domanova, James R. Krycer, Rima Chaudhuri, Pengyi Yang, Fatemeh Vafaee, Daniel J. Fazakerley, Sean J. Humphrey, David E. James, Zdenka Kuncic

关键词： Visceral Leishmaniasis Feature Selection Method Frequent Itemset Mining Leishmania Donovani Student Council

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Iterative methods in large field electron microscope tomography

Iterative methods in large field electron microscope tomogra...

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作者： Wan, Xiaohua Phan, Sébastien Lawrence, Albert Zhang, Fa Han, Renmin Liu, Zhiyong Ellisman, Mark Key Lab of Intelligent Information Processing and Advanced Computing Research Lab Institute of Computing Technology Chinese Academy of Sciences Beijing China National Center for Microscopy and Imaging Research University of California San Diego CA 92093 United States Chinese Academy of Sciences Graduate University Beijing China State Key Lab for Computer Architecture Institute of Computing Technology Chinese Academy of Sciences Beijing China

Electron tomography (ET) is a powerful technology allowing the three-dimensional (3D) imaging of cellular ultrastructure. These structures are reconstructed from a set of micrographs taken at different sample orientations, the final volume being the solution of a general inverse problem. Two different approaches are used in this context: iterative methods and filtered backprojection. Iterative methods are known to provide high-resolution 3D reconstructions for ET under noisy and incomplete data conditions. However, all previous implementations have been restricted to the straight-line projection models. This is not accurate since electron trajectories in electron microscopes do not follow the straight-line optics assumed for X-rays, and biological samples may warp as a result of being exposed to an electron beam. Compensation for curvilinear trajectories, nonlinear electron optics, and sample warping constitutes a major advance in large-field ET and has made possible resolution down to the molecular level in reconstructions of whole cells. At present these advances are limited to filtered backprojection and have been implemented in the software package TxBR. As the next step in this development, we have modified the ASART method in conjunction with a 3D model. By employing alignment based on general curvilinear trajectories we have been able to show that further improvements can be achieved with iterative methods. We also discuss a unified treatment of the alignment and reconstruction problems within the framework of iterative methods, and the relationship between formulas employed in the update step and cross-validation methods. Copyright © by SIAM. Unauthorized reproduction of this article is prohibited.

关键词： Iterative methods

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Optimizing application mapping algorithms for NoCs through a unified framework

Optimizing application mapping algorithms for NoCs through a...

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作者： Radu, Ciprian Vintan, Lucian Advanced Computer Architecture and Processing Systems Research Lab. Lucian Blaga University Sibiu Romania

ISBN: (纸本)9781424473359

This paper presents a preliminary PhD research towards developing a framework to evaluate and optimize application mapping algorithms for Network-on-Chip architectures. Several such algorithms have been proposed for mapping the threads of a parallel application on a NoC architecture. However, the performance of those algorithms is evaluated only on some specific NoC designs. A unified approach for evaluating such algorithms allows a better comparison of their performance and can potentially lead to some optimizations. The proposed framework is intended to be flexible so that the algorithms can be tested on different NoC designs. To this end, a scalable and flexible Network-on-Chip simulator is proposed. Some preliminary results obtained with this simnlator are presented, too. They show the flexibility of this simulator and that it is feasible for addressing the application mapping problem in a unified manner.

关键词： Network-on-chip

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An automatic design space exploration framework for multicore architecture optimizations

An automatic design space exploration framework for multicor...

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作者： Calborean, Horia Vinţan, Lucian Advanced Computer Architecture and Processing Systems Research Lab. Lucian Blaga University of Sibiu Romania

ISBN: (纸本)9781424473359

During the last years, especially due to the computing systems complexity growth, the need for tools which perform automatic design space exploration becomes more and more stringent. This paper presents a new initiated project having as the main aim developing a software tool, called FADSE (Framework for Automatic Design Space Exploration), that comes to meet this need. It is intended to provide out-of-the- box algorithms capable of solving single and multiobjective optimization problems. It focuses on automatic design space exploration for multicore and manycore systems. This tool is intended to be ftexible, to provide easy development and portability.

关键词： Multiobjective optimization

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An automatic design space exploration framework for multicore architecture optimizations

An automatic design space exploration framework for multicor...

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Roedunet International Conference (RoEduNet)

作者： Horia Calborean Lucian Vinţan Advanced Computer Architecture & Processing Systems Research Lab “Lucian Blaga” University of Sibiu Romania

ISBN: (纸本)9781424473359

During the last years, especially due to the computing systems complexity growth, the need for tools which perform automatic design space exploration becomes more and more stringent. This paper presents a new initiated project having as the main aim developing a software tool, called FADSE (Framework for Automatic Design Space Exploration), that comes to meet this need. It is intended to provide out-of-the-box algorithms capable of solving single and multiobjective optimization problems. It focuses on automatic design space exploration for multicore and manycore systems. This tool is intended to be flexible, to provide easy development and portability.

关键词： Space exploration Multicore processing Design optimization computer architecture Ant colony optimization Microarchitecture Software tools Software design Heuristic algorithms Machine learning algorithms

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