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检索条件"主题词=Parallel algorithms"

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parallel algorithm for multiple genome alignment on the Grid environment

Parallel algorithm for multiple genome alignment on the Grid...

引用

International Symposium on parallel and Distributed Processing (IPDPS)

作者： N. Ahmed Y. Pan A. Vandenberg Department of Computer Science Georgia State University Atlanta GA USA Information Systems & Technology Georgia State University Atlanta GA USA

The multiple genome sequence alignment problem falls in the domain of problems that can be parallelized to address large sequence lengths. Although there is communication required for the computation of the aligned sequences, the proper distribution can reduce the overall problem to a set of tasks to be solved independently and then merged. A parallel algorithm for the alignment of multiple genome sequences is described. The algorithm is experimentally evaluated in a distributed Grid environment that provides very scalable and low cost computation performance. The Grid environment is evaluated with respect to a traditional cluster environment and results are compared to evaluate the effectiveness of a Grid environment for large computational biology.

关键词： parallel algorithms Genomics Bioinformatics Sequences Distributed computing Clustering algorithms Computational efficiency Biology computing Grid computing Computational biology

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Approximate String Matching Algorithm Using parallel Methods for Molecular Sequence Camparisons

Approximate String Matching Algorithm Using Parallel Methods...

引用

Portuguese Conference on Artificial Intelligence, EPIA

作者： Carla Correa Tavares dos Reis Oswaldo Cruz Foundation Brazil

This work presents the development of algorithms for approximate string matching using parallel methods. It intends to do the maximum of molecular sequences comparisons per unity of time. The parallel program implementation has carried out in C on an available twenty processing nodes clustering architecture using a model of parallel programming systems, the MPI (message-passing interface), which is as library of subroutines. In this paper we are also concerned with reporting the speedup and efficiency measures. More precisely, we present a parallel algorithm for approximate sequence matching, showing its implementation and reporting its measures in comparison to its sequential version. We use one of the possible approaches to reduce the time spent on comparisons of molecular database sequences by distributing the data among processors, which achieves a linear speedup (time) and requires constant space memory per processor (Reis, 2001)

关键词： Sequences Databases Clustering algorithms parallel programming Velocity measurement parallel algorithms DNA Proteins Libraries Algorithm design and analysis

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parallel multiple sequences alignment in SMP cluster

Parallel multiple sequences alignment in SMP cluster

引用

International Conference on High Performance Computing in the Asia-Pacific Region

作者： Guangming Tan Shengzhong Feng Ninghui Sun Graduate School of Chinese Academy of Sciences China Institute of Computing Technology Chinese Academy and Sciences China

Multiple sequences alignment is a fundamental and challenging problem in computational molecular biology. It is commonly used to analyse the DNA/protein sequences. To develop a high efficient parallel algorithm is a very important solution to speedup this time consuming problem. However, due to the irregular computation behaviors based on tree, it is difficult to achieve good load balancing, so the utilization of processor is very low. This paper presents a parallel multiple sequences alignment algorithm featuring a mixed fine and coarse grained parallelization approach. The parallel algorithm is suitable to be implemented in SMP cluster, which is the main architecture of current cluster systems. We implemented the parallel algorithm in SMP cluster using a hybrid MPI/OpenMP method and the experimental results shows that the mixed fine and coarse algorithm achieves higher speedup

关键词： Sequences parallel algorithms Clustering algorithms Approximation algorithms Biology computing DNA Proteins Polynomials Concurrent computing Sun

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parallel Algorithm for Computing Reversal Distance

Parallel Algorithm for Computing Reversal Distance

引用

IEEE International Conference on parallel and Distributed Computing, Applications and Technologies (PDCAT)

作者： Yi-Fei She Guo-Liang Chen University of Science and Technology of China National High Performance Computing Center Department of Computer Science University of Science and Technology Hefei Anhui China National High Performance Computing Center University of Science and Technology of China Hefei Anhui China

Computing reversal distance of two signed permutations has gained increasing attention over the last decade with the study of genome rearrangements in computational molecular biology. In this paper, we present a parallel algorithm to computing reversal distance of two signed permutations. Our algorithm consists three parts and runs in O(lg2(n)) time using O(n2) processors in SIMD-CREW model.

关键词： parallel algorithms Concurrent computing Biology computing High performance computing Genomics Bioinformatics Computational biology Computer science Sequences Sorting

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A Poly-Algorithm for Efficient parallel Matrix Multiplication on Metacomputing Platforms

A Poly-Algorithm for Efficient Parallel Matrix Multiplicatio...

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IEEE International Conference on Cluster Computing

作者： Sana Jeddi Wahid Nasri ESSTT Département d'Informatique Tunis Tunisia

There is today an increasing diversity of parallel execution supports. New characteristics are influencing the execution of parallel applications, like for instance the hierarchical structure and the heterogeneity of the processors. Designing efficient software that takes full advantages of such systems remains difficult Indeed, solving a target problem by using a single algorithm is not always efficient on any computational support. We present in this paper a poly-algorithmic approach for selecting the most suitable algorithm among various ones for given problem size and available metacomputing platform, like hierarchical clusters of SMPs (Symmetric Multi-Processors) which become more and more popular. Our principal objective here is to illustrate such an approach on the well-known matrix multiplication problem which is one of the most important basic numerical kernels

关键词： Metacomputing Clustering algorithms Concurrent computing Matrix decomposition parallel algorithms Multiprocessor interconnection networks Symmetric matrices Costs Computer networks Computer architecture

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A parallel algorithm for correlating event streams

A parallel algorithm for correlating event streams

引用

International Symposium on parallel and Distributed Processing (IPDPS)

作者： D.M. Zimmerman K.M. Chandy Computer Science 256-80 California Institute of Technology Pasadena CA USA

This paper describes a parallel algorithm for correlating or "fusing" streams of data from sensors and other sources of information. The algorithm is useful for applications where composite conditions over multiple data streams must be detected rapidly, such as intrusion detection or crisis management. The implementation of this algorithm on a multithreaded system and the performance of this implementation are also briefly described.

关键词： parallel algorithms Temperature sensors Power system modeling Hurricanes Condition monitoring Intrusion detection Noise generators Diseases Hospitals History

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parallel strategies for a multi-criteria GRASP algorithm

Parallel strategies for a multi-criteria GRASP algorithm

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Computer Science Society (SCCC) International Conference Chilean FLAGGED

作者： D.S. Vianna J.E.C. Arroyo P.S. Vieira T.R. de Azeredo Nucleo de Pesquisa e Desenvolvimento em Informática-NPDI Universidade Candido Mendes-UCAM-Campos Campos Dos Goytacazes Brazil

This paper proposes different strategies of parallelizing a multi-criteria GRASP (greedy randomized adaptive search problem) algorithm. The parallel GRASP algorithm is applied to the multi-criteria minimum spanning tree problem, which is NP-hard. In this problem, a vector of costs is defined for each edge of the graph and the goal is to find all the efficient or Pareto optimal spanning trees (solutions). Each process finds a subset of efficient solutions. These subsets are joined using different strategies to obtain the final set of efficient solutions. The multi-criteria GRASP algorithm with the different parallel strategies are tested on complete graphs with n = 20, 30 and 50 nodes and r = 2 and 3 criteria. The computational results show that the proposed parallel algorithms reduce the execution time and the results obtained by the sequential version were improved.

关键词： Tree graphs Cost function Search problems Testing Concurrent computing parallel algorithms Design optimization Telecommunication traffic Cities and towns Large-scale systems

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parallel algorithm for mining frequent itemsets

Parallel algorithm for mining frequent itemsets

引用

International Conference on Machine Learning and Cybernetics (ICMLC)

作者： You-Lin Ruan Gan Liu Qing-Hua Li School of Information Engineering Huazhong University of Science and Technology Wuhan China School of Information Engineering Wuhan University of Technology Wuhan China

parallel mining frequent itemsets is a key issue in data mining research. A parallel mining algorithm PMFI in distributed database is proposed in this paper, which attempts to make each processor to do independently and decrease the number of candidate of global frequent itemsets according to the relation between local frequent itemsets and global frequent itemsets. Thus, PMFI uses far less communication overhead and fewer synchronization steps, improves efficiency of mining global frequent itemsets.

关键词： parallel algorithms Data mining Itemsets Distributed databases Iterative algorithms Frequency synchronization Transaction databases Machine learning algorithms Gallium nitride Data engineering

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An O(1) Time parallel Algorithm for the Dominance Counting and 3D Block-Based Medial Axis Transform on AROB

An O(1) Time Parallel Algorithm for the Dominance Counting a...

引用

IEEE International Conference on parallel and Distributed Computing, Applications and Technologies (PDCAT)

作者： Shih-Ying Lin Shi-Jinn Horng Tzong-Wann Kao Yuh-Rau Wang Lan Yang Institute of Technology Taiwan National Taiwan University of Science and Technology Taipei Taiwan Northern Taiwan Institute of Science and Technology Taipei Taiwan Saint Johns and Saint Marys University of Technology Taipei Taiwan

In this paper, we present a constant time algorithm for solving three dimensional block-based medial axis transform (3D BB-MAT, for short) on the array with reconfigurable optical buses (AROB). The main contribution of this work is to exploit the dominance counting method for solving the 3D BB-MAT that was never done previously in the literature. With the advantages of both optical transmission and electronic computation on the AROB model, the constant algorithm is proposed for the medial axis transform of a 3D N x N x N binary image on a 4D AROB using N^4 processors. To the best of our knowledge, this presented result of the dominance counting technique for medial axis transform of block-based is the best O(1) time algorithm known.

关键词： parallel algorithms Optical arrays Image processing Concurrent computing Optical computing Shape Computer vision Application software Pixel Phase change random access memory

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A modified word serial bit parallel algorithm for FPGA implementation of digital ionospheric radar

A modified word serial bit parallel algorithm for FPGA imple...

引用

Asia-Pacific Conference on Microwave

Digital signal processing (DSP) has become an integral part of wireless communication systems and equivalent traditional analog systems can be developed with required fidelity at reasonable cost. In a previous work, a DSP technique is employed for radar upconversion using combinations of upsampling and narrow band FIR filtering. An efficient FPGA implementation of the DSP modulator is possible exploiting filter symmetry since symmetrical properties of word serial bits parallel (WSBP) FIR filters improve system throughput. However arithmetic processing rate for the WSBP symmetric models is higher than that of the non-symmetric models. In this paper we present a modified WSBP symmetrical algorithm to reduce the arithmetic processing for implementation of direct conversion ionospheric radar. In WSBP approach processing is performed in integers as block of bits. Matching and buffering criterion are used to reduce computations up to fifty percent. The algorithm can be extended to applications with similar characteristics particularly for system on chip (SOC) techniques.

关键词： parallel algorithms Field programmable gate arrays Radar Digital signal processing Finite impulse response filter Arithmetic Signal processing algorithms Wireless communication Costs Narrowband

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