检索结果-内蒙古大学图书馆

International Symposium on Parallel and Distributed Processing (IPDPS)

作者： Sanchit Misra Kiran Pamnany Srinivas Aluru Parallel Computing Lab Intel Corporation Bangalore India School of Computational Science and Engineering Georgia Institute of Technology Atlanta USA

Construction of whole-genome networks from large-scale gene expression data is an important problem in systems biology. While several techniques have been developed, most cannot handle network reconstruction at the whole-genome scale, and the few that can, require large clusters. In this paper, we present a solution on the Intel (R) Xeon Phi (TM) coprocessor, taking advantage of its multi-level parallelism including many x86-based cores, multiple threads per core, and vector processing units. We also present a solution on the Intel (R) Xeon (R) processor. Our solution is based on TINGe, a fast parallel network reconstruction technique that uses mutual information and permutation testing for assessing statistical significance. We demonstrate the first ever inference of a plant whole genome regulatory network on a single chip by constructing a 15,575 gene network of the plant Arabidopsis thaliana from 3,137 microarray experiments in only 22 minutes. In addition, our optimization for parallelizing mutual information computation on the Intel Xeon Phi coprocessor holds out lessons that are applicable to other domains.

关键词： Vectors Joints Coprocessors Mutual information Optimization Splines (mathematics) Arrays

来源：评论

学校读者我要写书评

暂无评论

Hydrodynamic interaction between overlapping domains during recurrence of registration within planar lipid bilayer membranes

引用

Physical Review E 2014年第3期89卷 032717-032717页

作者： Tao Han Trevor P. Bailey Mikko Haataja Department of Mechanical and Aerospace Engineering Princeton Institute for the Science and Technology of Materials (PRISM) and Program in Applied and Computational Mathematics (PACM) Princeton University Princeton New Jersey 08544 USA

Due to a thermodynamic coupling between the two leaflets comprising a lipid bilayer, compositional lipid domains residing within opposing leaflets are often found in registry. If the system is perturbed by displacing one domain relative to the other, diffusive and advective lipid fluxes are established to restore equilibrium and reestablish domain overlap. In this work, we focus on the advective part of the process, and first derive an analytical expression for the hydrodynamic drag coefficient associated with the advective flow for the special case of perfect domain overlap. The resulting expression identifies parameter regions where sliding friction between the leaflets dominates over viscous dissipation within the leaflets or vice versa. It is shown that in all practically relevant cases, sliding friction between the leaflets is the dominant factor. Finally, we investigate the domain separation dependence of the hydrodynamic drag coefficient via direct simulations of a continuum diffuse interface model, and provide useful empirical expressions for its behavior.

关键词： Drag coefficient

来源：评论

学校读者我要写书评

暂无评论

Anatomy of High-Performance Many-Threaded Matrix Multiplication

Anatomy of High-Performance Many-Threaded Matrix Multiplicat...

引用

IEEE International Parallel and Distributed Processing Symposium

作者： Tyler M. Smith Robert van de Geijn Mikhail Smelyanskiy Jeff R. Hammond Field G. Van Zee Institute for Computational Engineering and Sciences and Department of Computer Science The University of Texas at Austin Parallel Computing Lab Intel Corporation Leadership Computing Facility Argonne National Lab

ISBN: (纸本)9781479938018

BLIS is a new framework for rapid instantiation of the BLAS. We describe how BLIS extends the "GotoBLAS approach" to implementing matrix multiplication (GEMM). While GEMM was previously implemented as three loops around an inner kernel, BLIS exposes two additional loops within that inner kernel, casting the computation in terms of the BLIS micro-kernel so that porting GEMM becomes a matter of customizing this micro-kernel for a given architecture. We discuss how this facilitates a finer level of parallelism that greatly simplifies the multithreading of GEMM as well as additional opportunities for parallelizing multiple loops. Specifically, we show that with the advent of many-core architectures such as the IBM PowerPC A2 processor (used by Blue Gene/Q) and the Intel Xeon Phi processor, parallelizing both within and around the inner kernel, as the BLIS approach supports, is not only convenient, but also necessary for scalability. The resulting implementations deliver what we believe to be the best open source performance for these architectures, achieving both impressive performance and excellent scalability.

关键词： Linear algebra Libraries High-performance Matrix BLAS Multicore

来源：评论

学校读者我要写书评

暂无评论

Solution structures of the DNA-binding domains of immune-related zinc-finger protein ZFAT

引用

Journal of Structural and Functional Genomics 2015年第2期16卷 55-65页

作者： Tochio, Naoya Umehara, Takashi Nakabayashi, Kazuhiko Yoneyama, Misao Tsuda, Kengo Shirouzu, Mikako Koshiba, Seizo Watanabe, Satoru Kigawa, Takanori Sasazuki, Takehiko Shirasawa, Senji Yokoyama, Shigeyuki RIKEN Systems and Structural Biology Center 1-7-22 Suehiro-cho Tsurumi Yokohama 230-0045 Japan Department of Mathematical and Life Sciences Research Center for the Mathematics on Chromatin Live Dynamics Graduate School of Science Hiroshima University 1-3-1 Kagamiyama Higashi-Hiroshima 739-8530 Japan RIKEN Center for Life Science Technologies 1-7-22 Suehiro-cho Tsurumi Yokohama 230-0045 Japan PRESTO Japan Science and Technology Agency (JST) 1-7-22 Suehiro-cho Tsurumi Yokohama 230-0045 Japan Department of Maternal-Fetal Biology National Research Institute for Child Health and Development Tokyo 157-8535 Japan Department of Integrative Genomics Tohoku Medical Megabank Organization Tohoku University 2-1 Seiryo-machi Aoba-ku Sendai 980-8573 Japan RIKEN Quantitative Biology Center 1-7-22 Suehiro-cho Tsurumi Yokohama 230-0045 Japan Department of Computational Intelligence and Systems Science Interdisciplinary Graduate School of Science and Engineering Tokyo Institute of Technology 4259 Nagatsuta-cho Midori Yokohama 226-8502 Japan Institute for Advanced Studies Kyushu University 6-10-1 Hakozaki Higashi-ku Fukuoka 812-8582 Japan Department of Cell Biology Faculty of Medicine Fukuoka University Fukuoka 814-0180 Japan Center for Advanced Molecular Medicine Fukuoka University Fukuoka 814-0180 Japan RIKEN Structural Biology Laboratory 1-7-22 Suehiro-cho Tsurumi Yokohama 230-0045 Japan

ZFAT is a transcriptional regulator, containing eighteen C2H2-type zinc-fingers and one AT-hook, involved in autoimmune thyroid disease, apoptosis, and immune-related cell survival. We determined the solution structur... 详细信息

ZFAT is a transcriptional regulator, containing eighteen C₂H₂-type zinc-fingers and one AT-hook, involved in autoimmune thyroid disease, apoptosis, and immune-related cell survival. We determined the solution structures of the thirteen individual ZFAT zinc-fingers (ZF) and the tandemly arrayed zinc-fingers in the regions from ZF2 to ZF5, by NMR spectroscopy. ZFAT has eight uncommon bulged-out helix-containing zinc-fingers, and six of their structures (ZF4, ZF5, ZF6, ZF10, ZF11, and ZF13) were determined. The distribution patterns of the putative DNA-binding surface residues are different among the ZFAT zinc-fingers, suggesting the distinct DNA sequence preferences of the N-terminal and C-terminal zinc-fingers. Since ZFAT has three to five consecutive tandem zinc-fingers, which may cooperatively function as a unit, we also determined two tandemly arrayed zinc-finger structures, between ZF2 to ZF4 and ZF3 to ZF5. Our NMR spectroscopic analysis detected the interaction between ZF4 and ZF5, which are connected by an uncommon linker sequence, KKIK. The ZF4–ZF5 linker restrained the relative structural space between the two zinc-fingers in solution, unlike the other linker regions with determined structures, suggesting the involvement of the ZF4–ZF5 interfinger linker in the regulation of ZFAT function. © 2015, The Author(s).

关键词： Gene expression NMR Transcription Zinc-finger

来源：评论

学校读者我要写书评

暂无评论

Framework and modular infrastructure for automation of architectural adaptation and performance optimization for HPC systems 1

引用

29th International Supercomputing Conference, ISC 2014

作者： Fialho, Leonardo Browne, James Institute for Computational Engineering and Sciences Austin TX 78712 United States Texas Advanced Computing Center Austin TX 78712 United States Department of Computer Science Austin TX 78712 United States University of Texas at Austin Austin TX 78712 United States

ISBN: (数字)9783319075181

ISBN: (纸本)9783319075174

High performance systems have complex, diverse and rapidly evolving architectures. The span of applications, workloads, and resource use patterns is rapidly diversifying. Adapting applications for efficient execution on this spectrum of execution environments is effort intensive. There are many performance optimization tools which implement some or several aspects of the full performance optimization task but almost none are comprehensive across architectures, environments, applications, and workloads. This paper presents, illustrates, and applies a modular infrastructure which enables composition of multiple open-source tools and analyses into a set of workflows implementing comprehensive end-to-end optimization of a diverse spectrum of HPC applications on multiple architectures and for multiple resource types and parallel environments. It gives results from an implementation on the Stampede HPC system at the Texas Advanced computing Center where a user can submit an application for optimization using only a single command line and get back an at least, partially optimized program without manual program modification for two different chips. Currently, only a subset of the possible optimizations is completely automated but this subset is rapidly growing. Case studies of applications of the workflow are presented. The implementations currently available for download as the PerfExpert tool version 4.0 supports both Sandy Bridge and Intel Phi chips. © Springer International Publishing Switzerland 2014.

关键词： Application programs

来源：评论

学校读者我要写书评

暂无评论

Lifetime of the yrast Iπ=5− state and E1 hindrance in the transitional nucleus Ce58136

引用

Physical Review C 2015年第2期91卷 027302-027302页

作者： T. Alharbi P. H. Regan N. Mărginean Zs. Podolyák O. J. Roberts A. M. Bruce N. Alkhomashi R. Britton D. Bucurescu D. Deleanu D. Filipescu D. Ghită T. Glodariu C. Mihai K. Mulholland R. Lica R. Mărginean M. Nakhostin A. Negret C. R. Nita L. Stroe T. Sava C. Townsley N. V. Zamfir Department of Physics Almajmaah University P.O. Box 66 11952 Saudi Arabia Department of Physics University of Surrey Guildford GU2 7XH United Kingdom National Physical Laboratory Teddington Middlesex TW11 0LW United Kingdom Horia Hulubei - National Institute for Physics and Nuclear Engineering (IFIN-HH) RO-077125 Bucharest Romania School of Computing Engineering and Mathematics University of Brighton Brighton BN2 4GJ United Kingdom King Abdulaziz City for Science and Technology (KACST) P.O. Box 6086 Riyadh 11442 Saudi Arabia School of Engineering and Computing University of the West of Scotland High Street Paisley PA1 2BE United Kingdom

The half-lives of the Iπ=5− and Iπ=7− yrast states with Ex=1978 keV and Ex=2307 keV in the N=78 isotone Ce136, have been measured to be 496(23) ps and 270(24) ps, respectively, using the coincident fast-timing spectroscopy technique following population by a Sn124(O16,4n) fusion-evaporation reaction at an incident beam energy of 68 MeV. The extracted B(E1;5−→4+)=1.8(3)×10−6 W.u. value is compared with the systematics of the region and is found to be in line with typical E1 strengths for single-particle-type decays, rather than showing any evidence for the additional E1 decay hindrance associated with K-quantum number violation in axially deformed systems observed in lighter Ce isotopes.

关键词：

来源：评论

学校读者我要写书评

暂无评论

First-principles study of vibrational modes and Raman spectra in P-doped Si nanocrystals

引用

Physical Review B 2014年第19期89卷 195309-195309页

作者： K. H. Khoo James R. Chelikowsky Institute of High Performance Computing Agency for Science Technology and Research 1 Fusionopolis Way #16-16 Connexis Singapore 138632 Center for Computational Materials Institute for Computational Engineering and Sciences Departments of Physics and Chemical Engineering The University of Texas at Austin Austin Texas 78712 USA

We have studied the vibrational modes and Raman spectra of P-doped Si nanocrystals using pseudopotential density functional theory and the Placzek approximation. We find that Si nanocrystal vibrations are largely unaffected by the introduction of P dopants. However, the Raman spectra of doped nanocrystals are enhanced relative to those of pristine nanocrystals, and demonstrate a strong dependence on dopant position. Thus, Raman has the potential of being developed as a tool for probing the location of the dopant within the nanocrystal. Our analysis shows that vibrational modes involving atoms in the vicinity of the dopant give the largest contributions to the Raman spectra.

关键词：

来源：评论

学校读者我要写书评

暂无评论

Sensitivity Analysis for Time Dependent Problems: Optimal Checkpoint-Recompute HPC Workflows

Sensitivity Analysis for Time Dependent Problems: Optimal Ch...

引用

Workshop on Workflows in Support of Large-Scale science (WORKS)

作者： Varis Carey Hasan Abbasi Ivan Rodero Hemanth Kolla Institute of Computational Engineering and Science University of Texas at Austin Computer Science and Mathematics Division Oak Ridge National Laboratory Rutgers Discovery Informatics Institute and NSF Cloud and Autonomic Computing Center Rutgers University Scalable Modeling and Analysis Sandia National Laboratories

Sensitivity analysis (SA) is a fundamental tool of uncertainty quantification(UQ). Adjoint-based SA is the optimal approach in many large-scale applications, such as the direct numerical simulation (DNS) of combustion. However, one of the challenges of the adjoint workflow for time-dependent applications is the storage and I/O requirements for the application state. During the time-reversal portion of the workflow, forward state is required in last-in-first-out order. The resulting requirements for storage at exascale are enormous. To mitigate this requirement, application state is regenerated from checkpoints over short windows of application time. This approach drastically reduces the total volume of stored data, allows the caching of state in the regeneration window in memory and on local SSDs, may accelerate the application execution by reducing output frequency, and reduces the power overhead from I/O. We explore variations to this workflow, applied to a proxy for the SA of turbulent combustion, by varying checkpoint number, state storage, and other regeneration options to find efficient implementations for minimizing compute time or power consumption.

关键词： computational modeling Mathematical model Sensitivity analysis Combustion Analytical models Checkpointing

来源：评论

学校读者我要写书评

暂无评论

In search of perfect reads

In search of perfect reads

引用

IEEE International Conference on computational Advances in Bio and Medical sciences (ICCABS)

作者： Soumitra Pal Srinivas Aluru Department of Computer Science and Engineering Indian Institute of Technology Bombay Powai Mumbai India School of Computational Science and Engineering College of Computing Georgia Institute of Technology 266 Ferst Drive Atlanta GA USA

Continued advances in next generation short-read sequencing technologies are increasing throughput and read lengths, while driving down the error rates, for example within 1% for Illumina HiSeq reads. Moreover, the errors are not uniformly distributed in all reads, and a large percentage of reads are indeed error-free. Ability to predict such perfect reads can have significant impact on run-time complexity of applications. In this paper, we present a simple and fast k-spectrum analysis based method to identify error-free reads. Our experiments show that if around 80% of the reads in a dataset are perfect, then our method retains almost 99.9% of them with more than 90% precision rate. Though filtering out reads identified as erroneous by our method reduces the coverage by about 7% on an average, coverage pattern across genome remains similar. The filtration process can be customized at several levels of stringency depending upon the downstream application need.

关键词： Bioinformatics Genomics Error correction Sequential analysis Next generation networking Accuracy Prediction algorithms

来源：评论

学校读者我要写书评

暂无评论

A method of grammar learning for questions in nature Chinese language

A method of grammar learning for questions in nature Chinese...

引用

2014 International Conference on Advanced Control, Automation and Robotics (ACAR2014)

作者： H.Song J.W.Zhu T.Lin W.C.Chen B.Chen Institute of Information Engineering Yangzhou University Department of Computer Science and Engineering Guelph University Institute of Computing Technology Chinese Academy of Sciences Computer Science and Applied Mathematics University of Evansville

ISBN: (纸本)9781784660468

NLU-based question understanding is one of the key technologies in the application and promotion of the Q&A system. Due to limitations of the method of artificial acquisition on grammar, it failed to meet the practical demands of creation of large-scale grammar library. This paper proposes and implements a method of machine grammar learning, using 2-frequent sequences with gap condition covering grammar. Firstly, this method gets all the 2-frequent sequences with gap condition and assesses its quality according to its coverage and continuity. And then, considering the expansibility and accuracy of grammar, we compare the structure and set option elements of grammar, and remove the structures in the grammar which caused ambiguity referred to the existing standard grammar. The results of experiments on text-corpus China Telecom show that the efficiency of grammars acquired by this method is more than 95.2%. Compared with existing methods, the proposed method in this paper does not rely on the composition and structure of grammar, but clarify the semantic association between the grammar elements.

关键词： grammar learning 2-frequent sequences with gap condition option element ambiguous element

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：