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4th Eurographics Workshop on 3D Object Retrieval, 3DOR 2011

作者： Boyer, E. Bronstein, A.M. Bronstein, M.M. Bustos, B. Darom, T. Horaud, R. Hotz, I. Keller, Y. Keustermans, J. Kovnatsky, A. Litman, R. Reininghaus, J. Sipiran, I. Smeets, D. Suetens, P. Vandermeulen, D. Zaharescu, A. Zobel, V. INRIA Grenoble Rhône-Alpes France Department of Electrical Engineering Tel Aviv University Israel Institute of Computational Science Faculty of Informatics Università della Svizzera Italiana Lugano Switzerland Department of Computer Science University of Chile Chile School of Engineering Bar-Ilan University Ramat-Gan Israel Zuse Institut Berlin Germany Department of Electrical Engineering K.U. Leuven Belgium Department of Mathematics Technion - Israel Institute of Technology Haifa Israel Aimetis Corp. Waterloo Canada

ISBN: (纸本)9783905674316

Feature-based approaches have recently become very popular in computer vision and image analysis applications, and are becoming a promising direction in shape retrieval. SHREC'11 robust feature detection and description benchmark simulates the feature detection and description stages of feature-based shape retrieval algorithms. The benchmark tests the performance of shape feature detectors and descriptors under a wide variety of transformations. The benchmark allows evaluating how algorithms cope with certain classes of transformations and strength of the transformations that can be dealt with. The present paper is a report of the SHREC'11 robust feature detection and description benchmark results. © The Eurographics Association 2011.

关键词： Feature extraction

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Experiment of Flow Control Using Laser Energy Deposition Around High Speed Propulsion System

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AIP Conference Proceedings 2011年第1期1402卷 416-423页

作者： HyoungJin Lee InSeuck Jeung SangHun Lee Seihwan Kim aDepartment of Mechanical and Aerospace Engineering & Institute of Advanced Aerospace Technology Seoul Nation University Seoul Korea bInterdisciplinary Program in Computational Science and Technology Seoul National University Seoul Korea

An experimental investigation was conducted to examine the effect of a pulsed Nd:YAG laser energy deposition on the shock structures in supersonic/hypersonic flow and quiescent air. The effect of the laser energy and pressure in the blast wave generation were also investigated. As a result, the strength of plasma and blast wave becomes stronger as pressure or laser energy increase. And the breakdown threshold of air by laser energy deposition is 0.015 bar at 508 mJ laser energy, the blast wave threshold generation in air by laser energy deposition is 0.100 bar at same laser energy. As qualitative analysis, schlieren images are also obtained. After the series of experiments, the effect of laser energy deposition (LED) on high speed flow around the shock—shock interaction created by a wedge and blunt body. By LED, the structure of shock—shock interaction was collapsed momentary and the pressure of the stagnation point was fluctuated while interference of wave.

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Identification of aberrant pathway and network activity from high-throughput data-workshop introduction

Identification of aberrant pathway and network activity from...

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16th Pacific Symposium on Biocomputing, PSB 2011

作者： Ochs, M.F. Karchin, R. Ressom, H. Gentleman, R. Departments of Oncology and Health Science Informatics Johns Hopkins University Baltimore MD 19075 United States Department of Biomedical Engineering Institute for Computational Medicine Johns Hopkins University Baltimore MD 21218 United States Department of Oncology Lombardi Comprehensive Cancer Center Georgetown University Washington DC 20057 United States Bioinformatics and Computational Biology Genentech South San Francisco CA 94080 United States

ISBN: (纸本)9814335053

The workshop focused on approaches to deduce changes in biological activity in cellular pathways and networks that drive phenotype from high-throughput data. Work in cancer has demonstrated conclusively that cancer etiology is driven not by single gene mutation or expression change, but by coordinated changes in multiple signaling pathways. These pathway changes involve different genes in different individuals, leading to the failure of gene-focused analysis to identify the full range of mutations or expression changes driving cancer development. There is also evidence that metabolic pathways rather than individual genes play the critical role in a number of metabolic diseases. Tools to look at pathways and networks are needed to improve our understanding of disease and to improve our ability to target therapeutics at appropriate points in these pathways. © 2011 World Scientific Publishing Co. Pte. Ltd.

关键词： Diseases

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Compaction and Tensile Forces Determine the Accuracy of Folding Landscape Parameters from Single Molecule Pulling Experiments

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Physical Review Letters 2011年第13期106卷 138102-138102页

作者： Greg Morrison Changbong Hyeon Michael Hinczewski D. Thirumalai School of Engineering and Applied Science Harvard University Cambridge Massachusetts 02138 USA Biophysics Program Institute For Physical Science and Technology University of Maryland College Park Maryland 20742 USA School of Computational Sciences Korea Institute for Advanced Study Seoul 130-722 Republic of Korea

We establish a framework for assessing whether the transition state location of a biopolymer, which can be inferred from single molecule pulling experiments, corresponds to the ensemble of structures that have equal probability of reaching either the folded or unfolded states (Pfold=0.5). Using results for the forced unfolding of a RNA hairpin, an exactly soluble model, and an analytic theory, we show that Pfold is solely determined by s, an experimentally measurable molecular tensegrity parameter, which is a ratio of the tensile force and a compaction force that stabilizes the folded state. Applications to folding landscapes of DNA hairpins and a leucine zipper with two barriers provide a structural interpretation of single molecule experimental data. Our theory can be used to assess whether molecular extension is a good reaction coordinate using measured free energy profiles.

关键词： Free energy

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Simultaneous Identification for Synergistic Transcription Factors and their Transcription Factor Binding Sites

Simultaneous Identification for Synergistic Transcription Fa...

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International Conference on Complex, Intelligent and Software Intensive Systems, CISIS

作者： Zing Tsung-Yeh Tsai Grace Tzu-Wei Huang Huai-Kuang Tsai Institute of Information Science Academia Sinica Taipei Taiwan Institute of Biomedical Informatics National Yang-Ming University Taiwan Joint CMU-Pitt PhD Program in Computational Biology University of Pittsburgh Carnegie Mellon University Pittsburgh USA Computer Science and Engineering National Taiwan Ocean University Keelung Taiwan

Identifying transcription factor binding sites (TFBSs) is crucial for understanding the mechanism of transcriptional regulation. It is known that transcription factors (TFs) often cooperate to regulate genes. While traditional approaches can be used to discover binding motifs of a group of co-regulated genes, they often fail to accurately assign motifs to the corresponding TFs. Here, we consider two TFs together to infer their TFBSs and their synergistic relationship simultaneously. The basic idea is that if two TFs interact, their TFBSs, if distinct, would be conserved across species and coincided in the promoter regions of the genes they co-regulated. Applying our method to Saccharomyces cerevisiae chromatin immunoprecipitation data, we predicted 110 TF pairs with statistically significant motif assignments. A majority of these TF pairs have literature support to be synergistic, and the designated motifs to TFs match well with their known consensus. We further examined the synergism of predicted TF pairs in seven experimental conditions using ANOVA, and identified significant interactions.

关键词： Bioinformatics Analysis of variance DNA Databases Gene expression Proteins Stress

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Supporting Instructional Software engineering Activities Using CODILA: Some Latin American Experiences

Supporting Instructional Software Engineering Activities Usi...

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2011 2nd International Conference on Education and Educational Technology(EET 2011)

作者： Fáber Giraldo Sergio F.Ochoa Laura Aballay Clifton Clunie Andrés Neyem Raquel Anaya System and Computer Engineering University of Quindío Computer Science Department University of Chile Informatics Institute National University of San Juan Computational Systems Engineering Technological University of Panama Computer Science Department Pontifical Catholic University of Chile System Engineering Department Universidad EAFIT

Computer science students must be able to support the global software development phenomena;therefore they should enhance their teamwork, communication, negotiation, leadership and collaboration skills. It pushes the educational institutions to rethink the way in which they are transferring the soft skills, e.g. collaboration capabilities, to the new software engineers. Advances in developing platforms, wideband communications, global markets, technological trends and outsourcing promote the conception of a global software engineering. Trying to help address this issue, this paper describes the results of two experiences where a CODILA(Collaborative and Distributed Learning Activity) was used to solve a software engineering problem in a distributed way. These experiences involved students and instructors of eight Latin American universities. We have measured the development of collaboration skills and satisfaction level of computer science students participating in these distributed collaborative practices, and the obtained results are highly encouraging.

关键词： CODILA,distributed CSCL experience,interaction and communication design,experimental software engineering

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Fast streaming 3D level set segmentation on the GPU for smooth multi-phase segmentation

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Lecture Notes in Computer science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2011年 6750 LNCS卷 72-91页

作者： Sharma, Ojaswa Zhang, Qin Anton, François Bajaj, Chandrajit Department of Computer Science and Engineering Indian Institute of Technology Bombay Mumbai 400076 India DTU Informatics Technical University of Denmark Lyngby 2800 Denmark Computational Visualization Center University of Texas at Austin Austin TX 78712-0027 United States

ISBN: (纸本)9783642226182

Level set method based segmentation provides an efficient tool for topological and geometrical shape handling, but it is slow due to high computational burden. In this work, we provide a framework for streaming computations on large volumetric images on the GPU. A streaming computational model allows processing large amounts of data with small memory footprint. Efficient transfer of data to and from the graphics hardware is performed via a memory manager. We show volumetric segmentation using a higher order, multi-phase level set method with speedups of the order of 5 times. © 2011 Springer-Verlag Berlin Heidelberg.

关键词： Graphics processing unit

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Continuum model of irradiation-induced spinodal decomposition in the presence of dislocations

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Physical Review B 2011年第17期83卷 174106-174106页

作者： J. J. Hoyt M. Haataja Department of Materials Science and Engineering McMaster University Hamilton Ontario Canada L8S4L7 Department of Mechanical and Aerospace Engineering Princeton Institute for the Science and Technology of Materials (PRISM) Program in Applied and Computational Mathematics (PACM) Princeton University Princeton New Jersey 08544

A model of phase-separation kinetics in systems exposed to energetic particle irradiation has been extended to include the effects of mobile dislocations. It is shown that when dislocations are allowed to participate in the decomposition reaction, phase separation can occur at temperatures above the coherent spinodal, which is in agreement with several experiments on irradiated alloys. A linear stability analysis of the governing kinetic equations is performed and three regimes of microstructural evolution are identified within the parameter space of damage cascade size vs incident flux: complete phase separation, solid-solution behavior, and compositional patterning. In addition, numerical simulations of the evolving dislocation density and composition fields are performed. The numerical results provide the amplitude and wavelength of the stable patterns that can form under irradiation and elucidate the role of misfit dislocations in reducing the coherency strain due to atomic size mismatch.

关键词： PHASE transformations (Physics) THERMODYNAMICS PARTICLES (Nuclear physics) ALLOYS IRRADIATION STRAINS & stresses (Mechanics)

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Independent Component Analysis Based Seeding Method for K-Means Clustering

Independent Component Analysis Based Seeding Method for K-Me...

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IEEE WIC ACM International Conference on Web Intelligence (WI)

作者： Takashi Onoda Miho Sakai Seiji Yamada System Engineering Laboratory Central Research Institute Electric Power Industry Tokyo Japan Department of Computational Intelligence and Systems Science Tokyo Institute of Technology Yokohama Japan Digital Content and Media Sciences Research Division National Institute of Informatics (NII) Tokyo Japan

The k-means clustering method is a widely used clustering technique for the Web because of its simplicity and speed. However, the clustering result depends heavily on the chosen initial clustering centers, which are chosen uniformly at random from the data points. We propose a seeding method based on the independent component analysis for the k-means clustering method. We evaluate the performance of our proposed method and compare it with other seeding methods by using benchmark datasets. We applied our proposed method to a Web corpus, which is provided by ODP. The experiments show that the normalized mutual information of our proposed method is better than the normalized mutual information of k-means clustering method and k-means++ clustering method. Therefore, the proposed method is useful for Web corpus.

关键词： Clustering methods Principal component analysis Iris Mutual information Electronic mail Measurement Independent component analysis

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Meeting report from the first meetings of the computational Modeling in Biology Network (COMBINE)

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Standards in Genomic sciences 2011年第2期5卷 230-242页

作者： le Novère, Nicolas Hucka, Michael Anwar, Nadia Bader, Gary D Demir, Emek Moodie, Stuart Sorokin, Anatoly EMBL-EBI Hinxton CB10 1SD United Kingdom Division of Engineering and Applied Science California Institute of Technology Pasadena CA United States General Bioinformatics Limited Reading United Kingdom The Donnelly Centre University of Toronto Toronto ON M5S Canada MSKCC - Computational Biology Center New York NY United States Eight Pillars Ltd Edinburgh 19 Redford Walk United Kingdom School of Informatics University of Edinburgh Edinburgh United Kingdom

The computational Modeling in Biology Network (COMBINE), is an initiative to coordinate the development of the various community standards and formats in computational systems biology and related fields. This report summarizes the activities pursued at the first annual COMBINE meeting held in Edinburgh on October 6-9 2010 and the first HARMONY hackathon, held in New York on April 18-22 2011. The first of those meetings hosted 81 attendees. Discussions covered both official COMBINE standards-(BioPAX, SBGN and SBML), as well as emerging efforts and interoperability between different formats. The second meeting, oriented towards software developers, welcomed 59 participants and witnessed many technical discussions, development of improved standards support in community software systems and conversion between the standards. Both meetings were resounding successes and showed that the field is now mature enough to develop representation formats and related standards in a coordinated manner.

关键词： Flux Balance Analysis Plenary Session Glyph System Biology Markup Language Exit Survey

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