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An overview of the haplotype problems and algorithms

中国高等学校学术文摘·计算机科学 2007年第3期1卷 272-282页

作者： ZHAO Yuzhong XU Yun ZHANG Qiangfeng CHEN Guoliang Computer Science Department University of Science and Technology of ChinaHefei 230027China Anhui Province-MOST Co-Key Laboratory of High Performance Computing and Its Application Hefei 230027China

A single nucleotide polymorphism (SNP),as the most common form of genetic variation,has been widely studied to help analyze the possible association between diseases and *** gain more information,SNPs on a single chromosome are usually studied together,which constitute a *** haplotypes from biological experiments is usually very costly and time-consuming,which causes people to develop efficient methods to determine haplotypes from the computational *** problems and algorithms about haplotypes have been proposed to reduce the cost of studies of disease *** general,four categories of problems are widely researched:the haplotype assembly problem,the haplotype inference problem,the haplotype block partition problem,and the haplotype tagging SNP selection *** former two problems have been well reviewed by many researchers,whereas the latter two have not been comprehensively surveyed to our *** this paper,we try to make a detailed introduction to the four problems,especially the latter two.

关键词： bioinformatics haplotype single nucleotide polymorphism (SNP) algorithm complexity

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EXPECTED PRESENT VALUE OF TOTAL DIVIDENDS IN THE COMPOUND BINOMIAL MODEL WITH DELAYED CLAIMS AND RANDOM INCOME

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Acta Mathematica Scientia 2013年第6期33卷 1639-1651页

作者：周杰明莫晓云欧辉杨向群 College of Mathematics and Computer Science Key Laboratory of High Performance Computing and Stochastic Information Processing Ministry of Education of ChinaHunan Normal University Department of Mathematics Hunan University of Finance and Economics

In this paper, a compound binomial model with a constant dividend barrier and random income is considered. Two types of individual claims, main claims and by-claims, are defined, where every by-claim is induced by the main claim and may be delayed for one time period with a certain probability. The premium income is assumed to another binomial process to capture the uncertainty of the customer＇s arrivals and payments. A system of difference equations with certain boundary conditions for the expected present value of total dividend payments prior to ruin is derived and solved. Explicit results are obtained when the claim sizes are Kn distributed or the claim size distributions have finite support. Numerical results are also provided to illustrate the impact of the delay of by-claims on the expected present value of dividends.

关键词： compound binomial model main claim by-claim dividend random income

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Study on optimization of agent initial positions in land combat simulation

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自然科学进展(英文版) 2004年第3期14卷 257-261页

作者： WU Chunguo LIANG Yanchun LEE Heow Pueh LU Chun Yang Xiaowei College of Computer Science and Technology Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education Jilin University Changchun 130012 China Institute of High Performance Computing Singapore 117528 Singapore Institute of High Performance Computing Singapore 117528 Singapore Department of Applied Mathematics South China University of Technology Guangzhou 510640 China Centre for ACES Department of Mechanical Engineering National University of Singapore 119260 Singapore

The use of computational-intelligence-based techniques in the optimization of agent initial positions in land combat simulations is studied. A novel method for the reduction of support vectors in the support vector machine (SVM) is presented. The optimization on the width of the Gaussian kernel function and the combination of the SVM with the radial basis function neural network are performed in the proposed method. Simulation results show that the proposed method can improve the running efficiency drastically compared with that using the traditional SVM with the same precision. We also summarize and present some experiences and trends in the study on the optimization problem in land combat simulation.

关键词： multi-agent support vector machine radial basis function genetic algorithm regression

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Understanding co-run performance on CPU-GPU integrated processors： observations, insights, directions

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Frontiers of computer Science 2017年第1期11卷 130-146页

作者： Qi ZHU Bo WU Xipeng SHEN Kai SHEN Li SHEN Zhiying WANG National Key Laboratory of High Performance Computing National University of Defense Technology Changsha 410073 China Department of Computer Science North Carolina State University Raleigh NC 27695 USA Department of Electrical Engineering & Computer Science Colorado School of Mines Golden CO 80401 USA Department of Computer Science University of Rochester Rochester NY 14627 USA

Recent years have witnessed a processor develop- ment trend that integrates central processing unit （CPU） and graphic processing unit （GPU） into a single chip. The inte- gration helps to save some host-device data copying that a discrete GPU usually requires, but also introduces deep re- source sharing and possible interference between CPU and GPU. This work investigates the performance implications of independently co-running CPU and GPU programs on these platforms. First, we perform a comprehensive measurement that covers a wide variety of factors, including processor ar- chitectures, operating systems, benchmarks, timing mecha- nisms, inputs, and power management schemes. These mea- surements reveal a number of surprising observations. We an- alyze these observations and produce a list of novel insights, including the important roles of operating system （OS） con- text switching and power management in determining the program performance, and the subtle effect of CPU-GPU data copying. Finally, we confirm those insights through case studies, and point out some promising directions to mitigate anomalous performance degradation on integrated heteroge- neous processors.

关键词： performance analysis GPGPU co-run degrada-tion fused processor program transformation

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A comparative study on dynamic and static sparsity patterns in parallel sparse approximate inverse preconditioning

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Journal of Mathematical Modelling and Algorithms 2003年第3期2卷 203-215页

作者： Wang, Kai Kim, Sangbae Zhang, Jun Laboratory for High Performance Scientific Computing and Computer Simulation Department of Computer Science University of Kentucky Lexington KY 40506-0046 United States

Sparse approximate inverse (SAI) techniques have recently emerged as a new class of parallel preconditioning techniques for solving large sparse linear systems on high performance computers. The choice of the sparsity pattern of the SAI matrix is probably the most important step in constructing an SAI preconditioner. Both dynamic and static sparsity pattern selection approaches have been proposed by researchers. Through a few numerical experiments, we conduct a comparable study on the properties and performance of the SAI preconditioners using the different sparsity patterns for solving some sparse linear systems. © 2004 Kluwer Academic Publishers. Printed in the Netherlands.

关键词： Dynamic and static sparsity pattern Parallel preconditioning Sparse approximate inverse Sparse matrices

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Developing an Automated Mechanism for Cluster computing in computerized Classroom

Developing an Automated Mechanism for Cluster Computing in C...

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International Conference on Computational Science (ICCS) on the Ascent of Computational Excellence

作者： Wang, Shuen-Tai Li, Chin-Hung Chang, Hsi-Ya Chen, Ying-Chuan Hsu, Ching-Hsien National Center for High-Performance Computing Taiwan Department of Computer Science and Information Engineering Chung Hua University Taiwan

Scientific computing has become one of the key players in the advance of modern science and technologies. In the meantime, due to the success of developments in processor fabrication, the computing power of Personal computer (PC) is not to be ignored as well. Lots of high throughput type of applications can be satisfied by using the current desktop PCs, especially for those in computerized classrooms, and leave the supercomputers for the demands from large scale high performance parallel computations. The goal of this work is to develop an automated mechanism for cluster computing to utilize the computing power such as resides in computerized classroom. The PCs in computerized classroom are usually setup for education and training purpose during the daytime, and shut down at night. After well deployment, these PCs can be transformed into a pre-configured cluster computing resource immediately without touching the existing education/training environment installed on these PCs. Thus, the training activities will not be affected by this additional activity to harvest idle computing cycles. To echo today's energy saving issues, a dynamic power management is also developed to minimize energy cost. This development not only greatly reduces the management efforts and time to build a cluster, but also implies the reduction of the power consumption by such a mechanism.

关键词： Personal computer cluster computing computerized classroom dynamic power management

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Scheduling user-level threads on distributed shared-memory multiprocessors

Scheduling user-level threads on distributed shared-memory m...

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5th International Conference on Parallel Processing, Euro-Par 1999

作者： Polychronopoulos, Eleftherios D. Papatheodorou, Theodore S. High Performance Computing Information Systems Laboratory Department of Computer Engineering and Informatics University of Patras Rio 26 500 Patras Greece

ISBN: (纸本)3540664432

In this paper we present Dynamic Bisectioning or DBS, a simple but powerful comprehensive scheduling policy for user-level threads, which unifies the exploitation of (multidimensional) loop and nested functional (or task) parallelism. Unlike other schemes that have been proposed and used thus far, DBS is not constrained to scheduling DAGs or singly nested parallel loops. Rather, our policy encompasses the most general type of parallel program model that allows arbitrary mix of nested loops and nested DAGs (directed acyclic task-graphs) or any combination of the above. DBS employs a simple but powerful two-level dynamic policy which is adaptive and sensitive to the type and amount of parallelism at hand. On one extreme DBS approximates static scheduling, hence facilitating locality of data, while at the other extreme it resorts to dynamic thread migration in order to balance uneven loads. Even the latter is done in a controlled way so as to minimize network latency. © Springer-Verlag Berlin Heidelberg 1999.

关键词： Scheduling

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Parallel fdtd computing for EMC simulation in high-speed electronics

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International Journal of Computational engineering Science 2004年第3期5卷 575-588页

作者： Jin, Hongfan Li, Erping Yuan, Weiliang Li, Lewei Computational Electromagnetics and Electronics Division Institute of High Performance Computing Singapore 117528 Department of Electrical and Computer Engineering National University of Singapore Kent Ridge Singapore 119260

The paper presents and discusses the parallelized 3D finite-difference time-domain algorithm based on single-program multiple-data architecture using the MPI protocol for electromagnetic compatibility and signal integrity analysis and evaluation in high-speed designs. The efficiency for parallelization is verified through numerical experiments at IBM P640 and P690 multiprocessor high performance computers with up to 20 processors at different sizes of the problems. © Imperial College Press.

关键词： Electromagnetic compatibility

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An e-learning platform based on grid architecture

An e-learning platform based on grid architecture

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作者： Yang, Chao-Tung Ho, Hsin-Chuan High-Performance Computing Laboratory Department of Computer Science and Information Engineering Tunghai University Taichung 407 Taiwan Department of Computer Science and Information Engineering Tunghai University Lizen High School Taichung Taiwan

The overall popularity of the Internet has helped e-learning become a hot method for learning in recent years. Over the Internet, learners can freely absorb new knowledge without restrictions on time or place. Many companies have adopted e-learning to train their employees. An e-learning system can make an enterprise more competitive by increasing the knowledge of its employees. E-learning has been shown to have impressive potential in e-commerce. At present, most e-learning environment architectures use single computers or servers as their structural foundations. As soon as their work loads increase, their software and hardware must be updated or renewed. This is a big burden on organizations that lack sufficient funds. Thus, in this study we employ a kind of Grid computing technology, called the "Data Grid" to integrate idle computer resources in enterprises into e-learning platforms, thus eliminating the need to purchase costly high-level servers and other equipment.

关键词： Learning systems

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Using a performance-based skeleton to implement divisible load applications on grid computing environments

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Journal of Information Science and engineering 2009年第1期25卷 59-81页

作者： Shih, Wen-Chung Yang, Chao-Tung Tseng, Shian-Shyong Department of Information Science and Applications Asia University Taichung 413 Taiwan High-Performance Computing Laboratory Department of Computer Science and Information Engineering Tunghai University Taichung 407 Taiwan Department of Computer Science National Chiao Tung University Hsinchu 300 Taiwan

Applications with divisible loads have such a rich source of parallelism that their parallelization can significantly reduce their total completion time on grid computing environments. However, it is a challenge for grid users, probably scientists and engineers, to develop their applications which can exploit the computing power of the grid. We propose a performance-based skeleton algorithm for implementing divisible load applications on grids. Following this skeleton, novice grid programmers can easily develop a high performance grid application. To examine the performance of programs developed by this approach, we apply this skeleton to implement three kinds of applications and conduct experiments on our grid test-bed. Experimental results show that programs implemented by this approach run more rapidly than those using conventional scheduling schemes.

关键词： Grid computing

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