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Lecture Notes in computational science and engineering 2013年 91卷 73-84页

作者： Hu, Qiya Shu, Shi Zou, Jun LSEC Institute of Computational Mathematics and Scientific/Engineering Computing Academy of Mathematics and Systems Science The Chinese Academy of Sciences Beijing 100080 China School of Mathematics and Computational Science Xiangtan University Hunan 411105 China Department of Mathematics The Chinese University of Hong Kong Shatin N.T. Hong Kong

ISBN: (纸本)9783642352744

We propose a new nonoverlapping domain decomposition preconditioner for the discrete system arising from the edge element discretization of the three-dimensional Maxwell's equations. This preconditioner uses the simplest coarse edge element space induced by the coarse triangulation. We will show that the rate of the PCG convergence with this substructuring preconditioner is quasi-optimal, and is independent of large variations of the coefficients across the local interfaces. © Springer-Verlag Berlin Heidelberg 2013.

关键词： Maxwell equations

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Scaling and correlation of human movements in cyberspace and physical space

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Physical Review E 2014年第5期90卷 050802(R)-050802(R)页

作者： Zhi-Dan Zhao Zi-Gang Huang Liang Huang Huan Liu Ying-Cheng Lai Web Sciences Center University of Electronic Science and Technology of China Chengdu 610054 China School of Electrical Computer and Energy Engineering Arizona State University Tempe Arizona 85287 USA Institute of Computational Physics and Complex Systems and Key Laboratory for Magnetism and Magnetic Materials of MOE Lanzhou University Lanzhou Gansu 730000 China School of Computing Informatics and Decision Systems Engineering Arizona State University Tempe Arizona 85287 USA Department of Physics Arizona State University Tempe Arizona 85287 USA

Understanding the dynamics of human movements is key to issues of significant current interest such as behavioral prediction, recommendation, and control of epidemic spreading. We collect and analyze big data sets of human movements in both cyberspace (through browsing of websites) and physical space (through mobile towers) and find a superlinear scaling relation between the mean frequency of visit 〈f〉 and its fluctuation σ:σ∼〈f〉β with β≈1.2. The probability distribution of the visiting frequency is found to be a stretched exponential function. We develop a model incorporating two essential ingredients, preferential return and exploration, and show that these are necessary for generating the scaling relation extracted from real data. A striking finding is that human movements in cyberspace and physical space are strongly correlated, indicating a distinctive behavioral identifying characteristic and implying that the behaviors in one space can be used to predict those in the other.

关键词： CYBERSPACE CORRELATION (Statistics) HUMAN mechanics BEHAVIORAL research PREDICTION models EPIDEMIOLOGY -- Mathematical models

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Development of Lattice QCD Simulation Code Set “Bridge++” on Accelerators

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Procedia Computer science 2014年 29卷 1701-1710页

作者： S. Motoki S. Aoki T. Aoyama K. Kanaya H. Matsufuru Y. Namekawa H. Nemura Y. Taniguchi S. Ueda N. Ukita Graduate School of Computer Science and Engineering University of Aizu Japan Yukawa Institute for Theoretical Physics Kyoto University Japan Kobayashi-Maskawa Institute for the Origin of Particles and the Universe (KMI) Nagoya University Japan Graduate School of Pure and Applied Sciences University of Tsukuba Japan Computing Research Center High Energy Accelerator Research Organization (KEK) Japan Center for Computational Sciences University of Tsukuba Japan Theory Center IPNS High Energy Accelerator Research Organization (KEK) Japan

We are developing a new code set “Bridge++” for lattice QCD (Quantum Chromodynamics) simulations. It aims at an extensible, readable, and portable workbench, while achieving high performance. Bridge++ covers popular lattice actions and numerical algorithms. The code set is constructed in C++ with an object oriented programming. In this paper, we describe our code design focusing on the use of accelerators such as GPGPUs. For portability our implemen- tation employs OpenCL to control the devices while encapsulates the details of manipulation by providing generalized interfaces. The code is successfully applied to several recent accelerators.

关键词： Lattice QCD HPC GPGPU OpenCL

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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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LOD-MS for Gross-Pitaevskii Equation in Bose-Einstein Condensates

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Communications in computational Physics 2013年第6期14卷 219-241页

作者： Linghua Kong Jialin Hong Jingjing Zhang School of Mathematics and Information Science Jiangxi Normal UniversityNanchangJiangxi 330022P.R.China State Key Laboratory of Scientific and Engineering Computing Institute of Computational Mathematics and Scientific/Engineering ComputingAcademy of Mathematics and System ScienceChinese Academy of SciencesP.O.Box 2719Beijing 100190P.R.China School of Mathematics and Information Science Henan Polytechnic UniversityJiaozuoHenan 454000P.R.China

The local one-dimensional multisymplectic scheme(LOD-MS)is developed for the three-dimensional(3D)Gross-Pitaevskii(GP)equation in Bose-Einstein *** idea is originated from the advantages of multisymplectic integrators and from the cheap computational cost of the local one-dimensional(LOD)*** 3D GP equation is split into three linear LOD Schrodinger equations and an exactly solvable nonlinear Hamiltonian *** three linear LOD Schrodinger equations are multisymplectic which can be approximated by multisymplectic integrator(MI).The conservative properties of the proposed scheme are *** is ***,the scheme preserves the discrete local energy conservation laws and global energy conservation law if the wave function is variable *** is impossible for conventional MIs in nonlinear Hamiltonian *** numerical results show that the LOD-MS can simulate the original problems very *** are consistent with the numerical analysis.

关键词： LOD-MS Gross-Pitaevskii equation local one-dimensional method midpoint method conservation laws

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Efficient sparse matrix-vector multiplication on x86-based many-core processors 13

Efficient sparse matrix-vector multiplication on x86-based m...

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27th ACM International Conference on Supercomputing, ICS 2013

作者： Liu, Xing Smelyanskiy, Mikhail Chow, Edmond Dubey, Pradeep School of Computational Science and Engineering Georgia Institute of Technology Atlanta GA United States Parallel Computing Lab. Intel Corporation Santa Clara CA United States

ISBN: (纸本)9781450321303

Sparse matrix-vector multiplication (SpMV) is an important kernel in many scientific applications and is known to be memory bandwidth limited. On modern processors with wide SIMD and large numbers of cores, we identify and address several bottlenecks which may limit performance even before memory bandwidth: (a) low SIMD efficiency due to sparsity, (b) overhead due to irregular memory accesses, and (c) load-imbalance due to non-uniform matrix structures. We describe an efficient implementation of SpMV on the Intel® Xeon Phi™ Coprocessor, codenamed Knights Corner (KNC), that addresses the above challenges. Our implementation exploits the salient architectural features of KNC, such as large caches and hardware support for irregular memory accesses. By using a specialized data structure with careful load balancing, we attain performance on average close to 90% of KNC's achievable memory bandwidth on a diverse set of sparse matrices. Furthermore, we demonstrate that our implementation is 3.52x and 1.32x faster, respectively, than the best available implementations on dual Intel® Xeon™ Processor E5-2680 and the NVIDIA Tesla K20X architecture. © 2013 ACM.

关键词： Bandwidth

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A Cone Constrained Convex Program:Structure and Algorithms

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Journal of the Operations Research Society of China 2013年第1期1卷 37-53页

作者： Liqun Qi Yi Xu Ya-Xiang Yuan Xinzhen Zhang Department of Applied Mathematics The Hong Kong Polytechnic UniversityHung HomKowloonHong KongChina State Key Laboratory of Scientific/Engineering Computing Institute of Computational Mathematics and Scientific/Engineering ComputingAMSSChinese Academy of SciencesZhong Guan Cun Donglu 55Beijing100190P.R.China Department of Mathematics School of ScienceTianjin UniversityTianjin300072China

In this paper,we consider the positive semi-definite space tensor cone constrained convex program,its structure and *** study defining functions,defining sequences and polyhedral outer approximations for this positive semidefinite space tensor cone,give an error bound for the polyhedral outer approximation approach,and thus establish convergence of three polyhedral outer approximation algorithms for solving this *** then study some other approaches for solving this structured convex *** include the conic linear programming approach,the nonsmooth convex program approach and the bi-level program *** numerical examples are presented.

关键词： Convex program Space tensor Positive semi-definiteness Cone Algorithms

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Multifractal computation for nuclear classification and hepatocellular carcinoma grading

Multifractal computation for nuclear classification and hepa...

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10th IASTED International Conference on Biomedical engineering, BioMed 2013

作者： Atupelage, Chamidu Nagahashi, Hiroshi Yamaguchi, Masahiro Kimura, Fumikazu Abe, Tokiya Hashiguchi, Akinori Sakamoto, Michiie Department of Computational Intelligence and Systems Science Tokyo Institute of Technology Japan Imaging Science and Engineering Laboratory Tokyo Institute of Technology Japan Global Scientific Information and Computing Center Tokyo Institute of Technology Japan Department of Pathology School of Medicine Keio University Japan

ISBN: (纸本)9780889869530

Hepatocellular carcinoma (HCC) is graded mainly based on the characteristics of liver cell nuclei. This paper proposes a textural feature descriptor and a novel computational method for classifying liver cell nuclei and grading the HCC histological images. The proposed textural feature descriptor observes local and spatial characteristics of the texture patterns by using multifractal computation. The textural features are utilized for nuclear segmentation, fiber region detection, and liver cell nuclei classification. Four categories of nuclear features are computed such as texture, geometry, spatial distribution, and surrounding texture, for HCC classification. Significance of liver cell nuclei classification method is evaluated by classifying non-neoplastic and tumor tissues. Furthermore, characteristics of the liver cell nuclei were utilized for grading a set of HCC images into four classes and obtained 97.77% classification accuracy.

关键词： Grading

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One variant of a （2 ＋ 1）-dimensional Volterra system and its （1 ＋ 1）-dimensional reduction

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Frontiers of Mathematics in China 2013年第5期8卷 1085-1097页

作者： Yingnan ZHANG Yi HE Hon-Wah TAM LSEC Institute of Computational Mathematics and Scientific Engineering ComputingAcademy of Mathematics and System Sciences Chinese Academy of SciencesBeijing 100190 China University of Chinese Academy of Sciences Beijing 100049 China Wuhan Institute of Physics and Mathematics Chinese Academy of Sciences Wuhan 430071 China Department of Computer Science Hong Kong Baptist University Hong Kong China

A new system is generated from a multi-linear form of a （2＋1）- dimensional Volterra system. Though the system is only partially integrable and needs additional conditions to possess two-soliton solutions, its （1＋1）- dimensional reduction gives an integrable equation which has been studied via reduction skills. Here, we give this （1＋1）-dimensional reduction a simple bilinear form, from which a Backlund transformation is derived and the corresponding nonlinear superposition formula is built.

关键词： Integrability soliton solution Bgcklund transformation （BT）,nonlinear superposition formula

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High-resolution contrast enhanced multi-phase hepatic Computed Tomography data fromaporcine Radio-Frequency Ablation study

High-resolution contrast enhanced multi-phase hepatic Comput...

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IEEE International Symposium on Biomedical Imaging

作者： Bernhard Kainz Philip Voglreiter Michael Sereinigg Iris Wiederstein-Grasser Ursula Mayrhauser Sonja Köstenbauer Mika Pollari Rostislav Khlebnikov Matthias Seise Tuomas Alhonnoro Yrjö Häme Daniel Seider Ronan Flanagan Claire Bost Judith Mühl David O'Neill Tingying Peng Stephen Payne Daniel Rueckert Dieter Schmalstieg Michael Moche Marina Kolesnik Philipp Stiegler Rupert H. Portugaller Department of Computing Imperial College London UK Institute for Computer Graphics and Vision (ICG) Graz University of Technology AUT Department for Surgery Medical University Graz AUT Division of Biomedical Research and Section for Surgical Research Medical University Graz AUT Medizinische Universitat Graz Graz Steiermark AT Department of Biomedical Engineering and Computational Science Aalto University FI Schloss Birlinghoven Fraunhofer Institute for Applied Information Technology GER Department of Diagnostic and Interventional Radiology Leipzig University Hospital Leipzig GER NUMA Engineering Services Ltd. Dundalk Co. Louth IRE Department of Engineering Science Keble College Oxford UK University Clinic of Radiology Medical University Graz AUT

Data below 1 mm voxel size is getting more and more common in the clinical practice but it is still hard to obtain a consistent collection of such datasets for medical image processing research. With this paper we provide a large collection of Contrast Enhanced (CE) Computed Tomography (CT) data from porcine animal experiments and describe their acquisition procedure and peculiarities. We have acquired three CE-CT phases at the highest available scanner resolution of 57 porcine livers during induced respiratory arrest. These phases capture contrast enhanced hepatic arteries, portal venous veins and hepatic veins. Therefore, we provide scan data that allows for a highly accurate reconstruction of hepatic vessel trees. Several datasets have been acquired during Radio-Frequency Ablation (RFA) experiments. Hence, many datasets show also artificially induced hepatic lesions, which can be used for the evaluation of structure detection methods.

关键词： Lesions Computed tomography Veins Biomedical imaging Animals Liver Educational institutions

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