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20th Annual Conference on Research in Computational Molecular Biology, RECOMB 2016

作者： Sahlin, Kristoffer Frånberg, Mattias Arvestad, Lars KTH Royal Institute of Technology Science for Life Laboratory School of Computer Science and Communication Stockholm Sweden Atherosclerosis Research Unit Department of Medicine Solna Sweden Karolinska Institutet Stockholm Sweden Department of Numerical Analysis and Computer Science Stockholm University Stockholm Sweden Stockholm Sweden

ISBN: (纸本)9783319319568

Reads from paired-end and mate-pair libraries are often utilized to find structural variation in genomes, and one common approach is to use their fragment length for detection. After aligning readpairs to the reference, read-pair distances are analyzed for statistically significant deviations. However, previously proposed methods are based on a simplified model of observed fragment lengths that does not agree with data. We show how this model limits statistical analysis of identifying variants and propose a new model, by adapting a model we have previously introduced for contig scaffolding, which agrees with data. From this model we derive an improved null hypothesis that, when applied in the variant caller CLEVER, reduces the number of false positives and corrects a bias that contributes to more deletion calls than insertion calls. A reference implementation is freely available at https://***/ksahlin/GetDistr. © Springer International Publishing Switzerland 2016.

关键词： Scaffolds

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Measuring Inconsistencies Propagation from Change Operation Based on Ontology Partitioning

Measuring Inconsistencies Propagation from Change Operation ...

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International IEEE Conference on Signal-Image Technologies and Internet-Based System

作者： Mouhamadou Gaye Ousmane Sall Mamadou Bousso Moussa Lo Numerical Analysis and Computer Laboratory - UFR Applied Sciences and Technology Gaston Berger University UGB Saint-Louis SENEGAL Department of Computerized Management Organisations UFR Economic and Social Sciences Thies University Thies SENEGAL Department of Computer Science UFR Science and Technology Thies University Thies SENEGAL Numerical Analysis and Computer Laboratory UFR Applied Sciences and Technology Gaston Berger University UGB Saint-Louis SENEGAL

Inconsistency measure is an activity related to the ontology evolution. Being a coherent entity, an ontology must change and a modification operation in ontology could generate inconsistencies in its other parts. It is then important to measure these inconsistencies and follow the impact propagation. In this paper, we propose an inconsistency measure of an ontological change and its propagation effects on the other entities of the ontology. The measure is based on the weight of the dependencies between concepts in a community. Ontology is divided into communities which are a set of concepts that have preferential relations. To follow the impact propagation, we propose a process that uses the Change-and-Fix' approach to mark the impacted entities.

关键词： Ontologies Semantics Weight measurement Knowledge based systems Atomic measurements Engines Wheels

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Genetic analysis of over 1 million people identifies 535 new loci associated with blood pressure traits (vol 50, pg 1412, 2018)

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NATURE GENETICS 2018年第12期50卷 1755-1755页

作者： Evangelou, Evangelos Warren, Helen R. Mosen-Ansorena, David Mifsud, Borbala Pazoki, Raha Gao, He Ntritsos, Georgios Dimou, Niki Cabrera, Claudia P. Karaman, Ibrahim Fu Liang Ng Evangelou, Marina Witkowska, Katarzyna Tzanis, Evan Hellwege, Jacklyn N. Giri, Ayush Edwards, Digna R. Velez Sun, Yan V. Cho, Kelly Gaziano, J. Michael Wilson, Peter W. F. Tsao, Philip S. Kovesdy, Csaba P. Esko, Tonu Magi, Reedik Milani, Lili Almgren, Peter Boutin, Thibaud Debette, Stephanie Ding, Jun Giulianini, Franco Holliday, Elizabeth G. Jackson, Anne U. Li-Gao, Ruifang Lin, Wei-Yu Luan, Jian'an Mangino, Massimo Oldmeadow, Christopher Prins, Bram Peter Qian, Yong Sargurupremraj, Muralidharan Shah, Nabi Surendran, Praveen Theriault, Sebastien Verweij, Niek Willems, Sara M. Zhao, Jing-Hua Amouyel, Philippe Connell, John de Mutsert, Renee Doney, Alex S. F. Farrall, Martin Menni, Cristina Morris, Andrew D. Noordam, Raymond Pare, Guillaume Poulter, Neil R. Shields, Denis C. Stanton, Alice Thom, Simon Abecasis, Goncalo Amin, Najaf Arking, Dan E. Ayers, Kristin L. Barbieri, Caterina M. Batini, Chiara Bis, Joshua C. Blake, Tineka Bochud, Murielle Boehnke, Michael Boerwinkle, Eric Boomsma, Dorret I. Bottinger, Erwin P. Braund, Peter S. Brumat, Marco Campbell, Archie Campbell, Harry Chakravarti, Aravinda Chambers, John C. Chauhan, Ganesh Ciullo, Marina Cocca, Massimiliano Collins, Francis Cordell, Heather J. Davies, Gail de Borst, Martin H. de Geus, Eco J. Deary, Ian J. Deelen, Joris Del Greco, Fabiola M. Demirkale, Cumhur Yusuf Dorr, Marcus Ehret, Georg B. Elosua, Roberto Enroth, Stefan Erzurumluoglu, A. Mesut Ferreira, Teresa Franberg, Mattias Franco, Oscar H. Gandin, Ilaria Gasparini, Paolo Giedraitis, Vilmantas Gieger, Christian Girotto, Giorgia Goel, Anuj Gow, Alan J. Gudnason, Vilmundur Guo, Xiuqing Gyllensten, Ulf Hamsten, Anders Harris, Tamara B. Harris, Sarah E. Hartman, Catharina A. Havulinna, Aki S. Hicks, Andrew A. Hofer, Edith Hofman, Albert Hottenga, Jouke-Jan Huffman, Jennifer E. Hwang, Shih-Jen Ingelsson, Erik James, Alan Jansen Department of Epidemiology and Biostatistics Imperial College London London UK Department of Hygiene and Epidemiology University of Ioannina Medical School Ioannina Greece William Harvey Research Institute Barts and The London School of Medicine and Dentistry Queen Mary University of London London UK National Institute for Health Research Barts Cardiovascular Biomedical Research Center Queen Mary University of London London UK MRC-PHE Centre for Environment and Health Imperial College London London UK Department of Mathematics Imperial College London London UK Division of Epidemiology Department of Medicine Institute for Medicine and Public Health Vanderbilt Genetics Institute Vanderbilt University Medical Center Tennessee Valley Healthcare System (626)/Vanderbilt University Nashville TN USA Vanderbilt Genetics Institute Vanderbilt Epidemiology Center Department of Obstetrics and Gynecology Vanderbilt University Medical Center Tennessee Valley Health Systems VA Nashville TN USA Department of Epidemiology Emory University Rollins School of Public Health Atlanta GA USA Department of Biomedical Informatics Emory University School of Medicine Atlanta GA USA Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC) VA Boston Healthcare System Boston MA USA Division of Aging Department of Medicine Brigham and Women’s Hospital Department of Medicine Harvard Medical School Boston MA USA Atlanta VAMC and Emory Clinical Cardiovascular Research Institute Atlanta GA USA VA Palo Alto Health Care System Division of Cardiovascular Medicine Stanford University School of Medicine Stanford CA USA Nephrology Section Memphis VA Medical Center and University of Tennessee Health Science Center Memphis TN USA Estonian Genome Center University of Tartu Tartu Estonia Program in Medical and Population Genetics Broad Institute of Harvard and MIT Cambridge MA USA Department Clinical Sciences Malmö Lund University Malmö Sweden MRC Human Genetics Un

High blood pressure is a highly heritable and modifiable risk factor for cardiovascular disease. We report the largest genetic association study of blood pressure traits (systolic, diastolic and pulse pressure) to date in over 1 million people of European ancestry. We identify 535 novel blood pressure loci that not only offer new biological insights into blood pressure regulation but also highlight shared genetic architecture between blood pressure and lifestyle exposures. Our findings identify new biological pathways for blood pressure regulation with potential for improved cardiovascular disease prevention in the future.

关键词： Cardiovascular diseases Genome informatics Genome-wide association studies

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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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Solving the Klein-Gordon equation using Fourier spectral methods: A benchmark test for computer performance 23

Solving the Klein-Gordon equation using Fourier spectral met...

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23rd High Performance Computing Symposium, HPC 2015, Part of the 2015 Spring Simulation Multi-Conference, SpringSim 2015

作者： Aseeri, S. Batrašev, O. Icardi, M. Leu, B. Liu, A. Li, N. Muite, B.K. Müller, E. Palen, B. Quell, M. Servat, H. Sheth, P. Speck, R. Van Moer, M. Vienne, J. KAUST Supcrcomputing Laboratory 4700 King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia Arvutitcaduse Instituut Tartu Ülikool Liivi 2 Tartu50409 Estonia Stochastic Numerics Group 4700 King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia Electrical and Computer Engineering University of Michigan Ann ArborMI48109-2122 United States Numerical Algorithms Group Wilkinson House Jordan Hill Road Oxford0X2 8DR United Kingdom Numerical Mathematics Group 4700 King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia Department of Mathematical Sciences University of Bath BathBA2 7 AY United Kingdom CAEN Advanced Computing University of Michigan Ann ArborMI48109-2094 United States Lnstitut für Analysis und Scientific Computing Technische Universität Wien Wiedner Haupstrasse 8-10 Wien1040 Austria Compulcr Sciences Department BSC UPC c/Jordi Girona Barcelona Calalunya08034 Spain Biomedical Engineering University of Michigan Ann ArborMI48109-2122 United States Jülich Supercomputing Centre Forschungszentrum Jülich GmbH Germany Germany National Center for Supercomputing Applications University of Illinois at Urbiina-Chanipaign UrbanaIL61801 United States Texas Advanced Computing Center University of Texas at Austin AustinTX78758-4497 United States

ISBN: (纸本)9781510810600

The cubic Klein-Gordon equation is a simple but non-trivial partial differential equation whose numerical solution has the main building blocks required for the solution of many other partial differential equations. In this study, the library 2DE-COMP&FFT is used in a Fourier spectral scheme to solve the Klein-Gordon equation and strong scaling of the code is examined on thirteen different machines for a problem size of 5123. The results are useful in assessing likely performance of other parallel fast Fourier transform based programs for solving partial differential equations. The problem is chosen to be large enough to solve on a workstation, yet also of interest to solve quickly on a supercomputer, in particular for parametric studies. Unlike the Linpack benchmark, a high ranking will not be obtained by simply building a bigger computer. © 2015 Aseeri et al.

关键词： Fast Fourier transforms

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Single straddle carrier routing problem in port container terminals: Mathematical model and solving approaches

Single straddle carrier routing problem in port container te...

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作者： Ndiaye, Babacar Mbaye Le Thi, Hoai An Dinh, Tao Pham Laboratory of Mathematics of Decision and Numerical Analysis University of Cheikh Anta Diop BP 45087 Dakar-Fann 99000 Dakar Senegal Laboratory of Theoretical and Applied Computer Science UFR MIM University of Lorraine Metz Ile du Saulcy 57045 Metz France Laboratory of Mathematics National Institute for Applied Sciences - Rouen University Avenue 76801 Saint-Etienne-du-Rouvray France

This paper treats the problem of routing straddle carriers during the loading operations of export containers. The straddle carrier (SC) travel distance will be much longer if two consecutive containers must be collected far from one another instead of from consecutive yard-bays. So, finding the minimum straddle carrier travel distance will guarantee port efficiency and allow cost savings. Our objective is to minimise the total travel distance of a straddle carrier. A SC performs a so called partial tour to pick-up containers of a same group, according to the work schedule. This problem is formulated as a mixed-integer linear programming problem, which is hard to solve optimally. In this paper, we reformulate the problem, thanks to exact penalty techniques in DC programming, as a continuous polyhedral DC programme. A combination of the local algorithm DCA and a global optimisation approach based on cutting plane techniques is proposed. Our algorithm, consisting in solving a finite number of linear programmes, converges to a global solution. Computational experiments indicate its efficiency. Copyright © 2012 Inderscience Enterprises Ltd.

关键词： Containers

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DC programming and DCA for large-scale two-dimensional packing problems

DC programming and DCA for large-scale two-dimensional packi...

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4th Asian Conference on Intelligent Information and Database Systems, ACIIDS 2012

作者： Ndiaye, Babacar Mbaye An, Le Thi Hoai Tao, Pham Dinh Niu, Yi Shuai Laboratory of Mathematics of Decision and Numerical Analysis Cheikh Anta Diop University - Dakar BP 45087 Dakar-Fann Senegal Laboratory of Theoretical and Applied Computer Science UFR MIM University of Paul Verlaine Metz Ile du Saulcy Metz 57045 France Laboratory of Mathematics National Institute for Applied Sciences - Rouen University Avenue Saint-Etienne-du-Rouvray 76801 France

ISBN: (纸本)9783642284892

In this paper, we propose a global optimization method based on DC (Difference of Convex functions) programming and DCA (DC Algorithm) involving cutting plane techniques for solving two-dimensional Bin packing and Strip packing problems. Given a set of rectangular items, we consider problems of allocating each item to larger rectangular standardized units. In two-dimensional bin packing problem, these units are finite rectangles, and the objective is to pack all the items into the minimum number of units. In two-dimensional strip packing problem, there is a single standardized unit of given width, and the objective is to pack all the items within the minimum height. These problems are characterized as BLP (Binary Linear Programming) problems. Thanks to exact penalty technique in DC Programming, the BLP can be reformulated as polyhedral DC program which can be efficiently solved via the proposed DC programming approach. Computational experiments on large-scale dataset involving up to 200 items show the good performance of our algorithm. © 2012 Springer-Verlag.

关键词： Global optimization

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Integrating object and grasp recognition for dynamic scene interpretation

Integrating object and grasp recognition for dynamic scene i...

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International Conference on Advanced Robotics (ICAR)

作者： S. Ekvall D. Kragic Computational Vision and Active Perception Laboratory Centre for Autonomous Systems Department of Numerical Analysis and Computer Science Royal Institute of Technology Stockholm Sweden

Understanding and interpreting dynamic scenes and activities is a very challenging problem. In this paper, we present a system capable of learning robot tasks from demonstration. Classical robot task programming requires an experienced programmer and a lot of tedious work. In contrast, programming by demonstration is a flexible framework that reduces the complexity of programming robot tasks, and allows end-users to demonstrate the tasks instead of writing code. We present our recent steps towards this goal. A system for learning pick-and-place tasks by manually demonstrating them is presented. Each demonstrated task is described by an abstract model involving a set of simple tasks such as what object is moved, where it is moved, and which grasp type was used to move it

关键词： Layout Robot programming Writing Humans Sensor phenomena and characterization Object recognition computer vision Laboratories numerical analysis computer science

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Object recognition using composed receptive field histograms of higher dimensionality

Object recognition using composed receptive field histograms...

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International Conference on Pattern Recognition

作者： O. Linde T. Lindeberg Department of Numerical Analysis and Computer Science KTH Computational Vision and Active Perception Laboratory Stockholm Sweden

Effective methods for recognising objects or spatio-temporal events can be constructed based on receptive field responses summarised into histograms or other histogram-like image descriptors. This work presents a set of composed histogram features of higher dimensionality, which give significantly better recognition performance compared to the histogram descriptors of lower dimensionality that were used in the original papers by Swain & Bollard (1991) or Schiele & Crowley (2000). The use of histograms of higher dimensionality is made possible by a sparse representation for efficient computation and handling of higher-dimensional histograms. Results of extensive experiments are reported, showing how the performance of histogram-based recognition schemes depend upon different combinations of cues, in terms of Gaussian derivatives or differential invariants applied to either intensity information, chromatic information or both. It is shown that there exist composed higher-dimensional histogram descriptors with much better performance for recognising known objects than previously used histogram features. Experiments are also reported of classifying unknown objects into visual categories.

关键词： Object recognition Histograms Image recognition Statistics Wavelet coefficients computer vision Laboratories numerical analysis computer science Councils

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Many-to-many feature matching using spherical coding of directed graphs 8

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8th European Conference on computer Vision, ECCV 2004

作者： Fatili Demirci, M. Shokoufandeh, Ali Dickinson, Sven Keselman, Yakov Bretzner, Lars Department of Computer Science Drexel University PhiladelphiaPA19104 United States Department of Computer Science University of Toronto TorontoONM5S 3G4 Canada School of Computer Science Telecommunications and Information Systems DePaul University ChicagoIL60604 United States Computational Vision and Active Perception Laboratory Department Of Numerical Analysis and Computer Science KTH Stockholm Sweden

ISBN: (纸本)3540219846

Abstract. In recent work, we presented a framework for many-to-many matching of multi-scale feature hierarchies, in which features and their relations were captured in a vertex-labeled, edge-weighted directed graph. The algorithm was based on a metric-tree representation of labeled graphs and their metric embedding into normed vector spaces, using the embedding algorithm of Matousek [13]. However, the method was limited by the fact that two graphs to be matched were typically embedded into vector spaces with different dimensionality. Before the embeddings could be matched, a dimensionality reduction technique (PCA) was required, which was both costly and prone to error. In this paper, we introduce a more efficient embedding procedure based on a spherical coding of directed graphs. The advantage of this novel embedding technique is that it prescribes a single vector space into which both graphs are embedded. This reduces the problem of directed graph matching to the problem of geometric point matching, for which efficient many-to-many matching algorithms exist, such as the Earth Mover's Distance. We apply the approach to the problem of multi-scale, view-based object recognition, in which an image is decomposed into a set of blobs and ridges with automatic scale selection. © Springer-Verlag Berlin Heidelberg 2004.

关键词： Directed graphs

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