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检索条件"任意字段=Seventh International Symposium on Parallel Architectures, Algorithms and Programming"

共 505 条记录，以下是341-350 订阅

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Comparative exon prediction based on heuristic coding region alignment

Comparative exon prediction based on heuristic coding region...

引用

8th international symposium on parallel architectures, algorithms and Networks, I-SPAN 2005

作者： Hsieh, Shu Ju Lin, Chun Yuan Chung, Yun Sheng Tang, Chuan Yi Department of Computer Science National Tsing-Hua University Hsinchu Taiwan Institute of Molecular and Cellular Biology National Tsing-Hua University Hsinchu Taiwan

ISBN: (纸本)0769525091

Identifying protein coding genes is one of most challenging problems in computational molecular biology. With increasing numbers of sequenced eukaryotic genomes and syntenic maps across species, it is possible to apply genomic comparison for gene recognition. Here, we propose a program, EXONALIGN, which simultaneously aligns and predicts exons between homologous genomic sequences. The program applies CORAL (COding Region ALignment), a heuristic linear time alignment tool, to determine whether the regions following the conserved splice signals pairs are significant or not. The approach which combines the intrinsic splice site strength with the conservation of protein coding regions and exon-intron structures reduces the computation time and increases the prediction accuracy. EXONALIGN was tested on ROSETTA data set of 117 human-mouse homologous sequence pairs. At the exon level the sensitivity and specificity of EXONALIGN are respectively 89% and 88%, and both are 98% at the nucleotide level. The rates of missing exons and wrong exons are as low as 2%. © 2005 IEEE.

关键词： Heuristic programming

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Using predictive adaptive parallelism to address portability and irregularity

Using predictive adaptive parallelism to address portability...

引用

international symposium on parallel architectures, algorithms and Networks (ISPAN)

作者： D.L. Wangerin I.D. Scherson School of Computer Science University of California Irvine CA USA

A semi-dynamic system is presented that is capable of predicting the performance of parallel programs at runtime. The functionality given by the system allows for efficient handling of portability and irregularity of ... 详细信息

关键词： parallel processing Yarn Adaptive systems Runtime Resource management Concurrent computing Computer science programming profession parallel programming Network topology

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Theory and practice of programming applied to membrane systems

Theory and practice of programming applied to membrane syste...

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international symposium on Symbolic and Numeric algorithms for Scientific Computing (SYNASC)

作者： G. Ciobanu Research Institute e-Austria Timişoara Institute of Computer Science Romanian Academy Iasi Romania

Following the knowledge provided by the theory of programming, we present an abstract syntax of the membrane systems, and their semantics. We define an appropriate notion of configurations, and sets of inference rules corresponding to the three stages of an evolution step in membrane systems. A notion of bisimulation is defined; bisimulation relations allow to compare the evolution behaviour of two membrane systems. On the other hand, the practice of programming related to membrane systems is given by the presentation of some sequential and parallel software simulators, emphasizing their specific features.

关键词： Biomembranes Functional programming Skin Computer science parallel programming parallel algorithms Turing machines Registers parallel processing Concurrent computing

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Enabling software DSM system for grid computing

Enabling software DSM system for grid computing

引用

international symposium on parallel architectures, algorithms and Networks (ISPAN)

作者： Tyng-Yeu Liang Chun-Yi Wu Jyh-Biau Chang Ce-Kuen Shieh Pei-Hsin Fan Department of Electrical Engineering National Kaohsiung University of Applied Sciences Kaohsiung Taiwan Department of Electrical Engineering National Cheng Kung University Tainan Taiwan

In this study, we have successfully developed a grid-enabled software distributed shared memory called Teamster-G. This system provides users with not only a shared memory programming interface but also a transparent resource allocation service to easily develop applications and aggregate distributed resources for solving their problems on the grid environment. Moreover, since the communication cost of maintaining data-consistency is a big problem for the performance of the DSM applications, Teamster-G exploits a cluster cache scheme and a two-level consistency protocol to minimize the number of data-consistency messages transferred over wide area network. We will present the framework and the performance of Teamster-G in this paper.

关键词： Software systems Grid computing Resource management Wide area networks Yarn Protocols Costs Processor scheduling parallel architectures Computer applications

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Adapting a partitioning-based heuristic load-balancing algorithm to heterogeneous computing environments

Adapting a partitioning-based heuristic load-balancing algor...

引用

international symposium on Symbolic and Numeric algorithms for Scientific Computing (SYNASC)

作者： D. Petcu Computer Science Department Institute e-Austria TimiInstitute e-Austria Timişoara Western University of Timişoara Romania

A graph partitioning-based heuristic load-balancing algorithm known as the largest-task-first-with-minimum-finish-time-and-available-communication-costs from EVAH package by M.J. Djomehri, et. al. (2003) is modified in order to be dynamically adapted to heterogeneous computing environments like a grid. An example is given to show the improvement.

关键词： Heuristic algorithms Partitioning algorithms Load management Grid computing Packaging parallel processing Mathematical programming History Computational fluid dynamics Costs

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A new multi-processor architecture for parallel lazy cyclic reference counting

A new multi-processor architecture for parallel lazy cyclic ...

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international symposium on Computer Architecture and High Performance Computing (SBAC-PAD)

作者： R.D. Lins Departamento de Eletrônica e Sistemas Universidade Federal de Pernambuco Recife Pernambuco Brazil

Reference counting is the memory management technique of most widespread use today. This paper presents a new multi-processor architecture for parallel cyclic reference counting. In this architecture, there is no dire... 详细信息

关键词： Java Memory management Virtual machining Data structures Computer languages parallel programming programming profession Heuristic algorithms Algorithm design and analysis parallel architectures

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A scalable method for predicting network performance in heterogeneous clusters

A scalable method for predicting network performance in hete...

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international symposium on parallel architectures, algorithms and Networks (ISPAN)

作者： D. Katramatos S.J. Chapin Department of Computer Science University of Virginia Charlottesville VA USA Department of Electrical Engineering and Computer Science Syracuse University Syracuse NY USA

An important requirement for the effective scheduling of parallel applications on large heterogeneous clusters is a current view of system resource availability. Maintaining such a view is a time consuming problem, potentially O(N/sup 2/). Although CPU availability is relatively easy to monitor, interconnecting network bandwidth varies not only with network topology, but also with message size and even with respect to the load of the communicating nodes. This paper describes a method for predicting a cluster's network performance for the purpose of scheduling parallel applications. The method generates a cluster-specific network model which can predict the latency of communications between any pair of nodes in linear time and under any computational and/or communication load conditions. The paper also presents the models generated for the Centurion cluster at the University of Virginia and the Orange Grove cluster at Syracuse University. A study of the prediction accuracy of the method under various load conditions by comparison to experimental measurements indicates an average prediction error of approximately 5% with the maximum encountered prediction error of less than 9%.

关键词： Intelligent networks Availability Delay Processor scheduling Network topology Computer networks programming environments Bandwidth Condition monitoring Computer science

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Impact of instruction re-ordering on the correctness of shared-memory programs

Impact of instruction re-ordering on the correctness of shar...

引用

international symposium on parallel architectures, algorithms and Networks (ISPAN)

作者： L. Higha J. Kawash Dept. of Comput. Sci. Calgary Univ. Alta. Canada Department of Computer Science American University of Sharjah UAE University of Calgary

Sequential consistency is an intuitive consistency model that simplifies reasoning about concurrent multiprocessor programs. Most implementations of high-performance multiprocessors, however, utilize mechanisms that al low instructions to execute out of order resulting in consistency models that are weaker than sequential consistency and further complicating the job of programmers. This paper invests all possible combinations of re-ordering of read and write instructions and their effects on the correctness of programs that are designed for sequential consistency. It shows that with certain combinations of re-orderings, any program that accesses shared memory through only reads and writes and that is correct assuming sequential consistency, can be transformed to a new program that does not use any explicit synchronization, and that remains correct in spite of the instruction re-ordering. With other combinations of re-ordering, such transformations do not exist, and even solutions to the mutual exclusion problem are impossible without resorting to explicit synchronization.

关键词： Read-write memory Computer science Out of order programming profession Algorithm design and analysis Councils Hardware Optimizing compilers Java Virtual machining

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parallelizing image analysis algorithms: ANET solution and performances

Parallelizing image analysis algorithms: ANET solution and p...

引用

Computer architectures for Machine Perception (CAMP)

作者： B. Ducourthial A. Merigot N. Sicard Laboratory Heudiasyc (UMR CNRS 6599) Université de Technologie de Compiegne Compiegne France Institut Electronique Fondamentale Université de Paris Sud Orsay France

Several hard problems have to be addressed in order to parallelize image analysis algorithms. Indeed, at the region level, these algorithms handle irregular (and sometimes strongly dynamic) data-structures. Moreover, they often lead to an unbalanced amount of computations, which is quite impossible to foresee offline. This paper focus on the parallelization of the ANET image analysis programming environment. Thanks to graph related data structures and efficient computing primitives, ANET allows rapid image algorithm prototyping. But in return, these primitives are difficult to parallelize. We present a solution for powerful implicit parallelization of the ANET environment, without any change in the application programming interface. The ANET API is summarized and illustrated with some examples. Several parallelization experimentations are reported. The solution we propose is detailed, and results are given on complete image analysis applications. ANET appears as a powerful environment, both for its expressiveness that allows rapid prototyping and for its implicit parallelization that allows good computation time.

关键词： Image analysis Concurrent computing Prototypes programming environments Data structures Pixel Image coding Shape Libraries parallel programming

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Comparative exon prediction based on heuristic coding region alignment

Comparative exon prediction based on heuristic coding region...

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international symposium on parallel architectures, algorithms and Networks (ISPAN)

作者： Shu Ju Hsieh Chun Yuan Lin Yun Sheng Chung Chuan Yi Tang Department of Computer Science National Tsing Hua University Hsinchu Taiwan Institute of Molecular and Cellular Biology National Tsing Hua University Hsinchu Taiwan

Identifying protein coding genes is one of most challenging problems in computational molecular biology. With increasing numbers of sequenced eukaryotic genomes and syntenic maps across species, it is possible to apply genomic comparison for gene recognition. Here, we propose a program, EXONALIGN, which simultaneously aligns and predicts exons between homologous genomic sequences. The program applies CORAL (coding region alignment), a heuristic linear time alignment tool, to determine whether the regions following the conserved splice signals pairs are significant or not. The approach which combines the intrinsic splice site strength with the conservation of protein coding regions and exon-intron structures reduces the computation time and increases the prediction accuracy. EXONALIGN was tested on ROSETTA data set of 117 human-mouse homologous sequence pairs. At the exon level the sensitivity and specificity of EXONALIGN are respectively 89% and 88%, and both are 98% at the nucleotide level. The rates of missing exons and wrong exons are as low as 2%.

关键词： Genomics Bioinformatics Mice Proteins Sequences Simultaneous localization and mapping Cells (biology) Computational biology Accuracy Dynamic programming

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