One of the most important problems in data mining is dis- covery of association rules in large database. In our previous study, we proposed parallel algorithms and candidate duplication based load bal- ancing strategi...
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Given two genomic DNA sequences, the syntenic alignment problem is to compute an ordered list of subsequences for each sequence such that the corresponding subsequence pairs exhibit a high degree of similarity. Synten...
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ISBN:
(纸本)3540003037
Given two genomic DNA sequences, the syntenic alignment problem is to compute an ordered list of subsequences for each sequence such that the corresponding subsequence pairs exhibit a high degree of similarity. Syntenic alignments are useful in comparing genomic DNA from related species and in identifying conserved genes. In this paper, we present a parallel algorithm for computing syntenic alignments that runs in O ((p)-(mn)) time and O (m + (p)-(n)) memory per processor, where m and n P P are the respective lengths of the two genomic sequences. Our algorithm is time optimal with respect to the corresponding sequential algorithm and can use 0 ( n) processors, where n is the length of the larger log n sequence. Using an implementation of this parallel algorithm, we report the alignment of human chromosome 12p13 and its syntenic region in mouse chromosome 6 (both over 220, 000 base pairs in length) in under 24 minutes on a 64-processor IBM xSeries cluster.
The B-tree is a fundamental data structure that is used to access and update a large number of keys. In this paper we present a parallel algorithm on the EREW PRAM that deletes keys in a B-tree. Our algorithm runs in ...
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This paper describes an implementation for Shared Memory Multiprocessor of a parallel algorithm to extract all cycles from a graph, using the cyclic conjunction operator. Validation of the parallel code was done using...
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This paper describes the parallel implementation of a preconditioned iterative solver based on the coupling of a differential (FEM) and an integral approach (BEM). Applying a domain decomposition scheme splits the pro...
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This paper describes the parallel implementation of a preconditioned iterative solver based on the coupling of a differential (FEM) and an integral approach (BEM). Applying a domain decomposition scheme splits the problem into separate ITEM and BEM parts and preserves the typical advantages of both methods. In particular, an independent parallelization with respect to the properties of both methods is possible. The limitations regarding computer resources that arise on sequential computers can therefore be overcome. The parallel implementation of the iterative framework is discussed with focus on the mechanisms for sharing and distributing information among the involved processes. A three-dimensional eddy current problem is presented as an example for discussing performance issues.
The main objective of this work is to highlight the advantages of coupling Java FDTD implementation with the mobile-agent computing paradigm, and to promote this approach as a flexible and valuable tool for the distri...
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The main objective of this work is to highlight the advantages of coupling Java FDTD implementation with the mobile-agent computing paradigm, and to promote this approach as a flexible and valuable tool for the distributed solution of complex and large-scale problems. Therefore, we present key issues related to the distributed implementation of a Finite-Difference Time-Domain (FDTD) code using Java mobile agents. The Java object-oriented FDTD code is described, and special agent communication and synchronization aspects related to FDTD are presented in detail.
The paper describes a new stochastic heuristic algorithm for global optimization. The new optimization algorithm, called Intelligent-Particle Swarm Optimization (IPSO), offers more intelligence to particles by using c...
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The paper describes a new stochastic heuristic algorithm for global optimization. The new optimization algorithm, called Intelligent-Particle Swarm Optimization (IPSO), offers more intelligence to particles by using concepts such as: group experiences, unpleasant memories (tabu to be avoided), local landscape models based on virtual neighbors, and memetic replication of successful behavior parameters. The new individual complexity is amplified at the group level and consequently generates a more efficient optimization procedure. A simplified version of the IPSO algorithm was implemented and compared with the classical PSO algorithm for a simple test function and for the Loney's solenoid.
A parallelised max-Log-MAP model (P-max-Log-MAP) that exploits the sub-word parallelism and very long instruction word architecture of a microprocessor or a digital signal processor (DSP) is presented. The proposed mo...
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A parallelised max-Log-MAP model (P-max-Log-MAP) that exploits the sub-word parallelism and very long instruction word architecture of a microprocessor or a digital signal processor (DSP) is presented. The proposed model reduces considerably the computational complexity of the max-Log-MAP algorithm;and therefore facilitates easy implementation.
The exponential increase in expressed sequence tag (EST) sequence data amplifies the computational cost of clustering sequences such that new algorithms are required to analyze data at a greater rate. We have pa-ralle...
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The exponential increase in expressed sequence tag (EST) sequence data amplifies the computational cost of clustering sequences such that new algorithms are required to analyze data at a greater rate. We have pa-rallelized d2-cluster on a SGI Origin 2000 multiprocessor and observed a speedup of approximately 100X on 126 processors when processing a 15,876 EST dataset. The parallelized d2-cluster code is obtainable from the SANBI website (http://w,A,***/CODES).
In order to understand details in the seismic wave field observed on regional and global scales on the Earth's surface accurate modeling of 3D wave propagation is necessary. While numerical techniques are now rout...
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In order to understand details in the seismic wave field observed on regional and global scales on the Earth's surface accurate modeling of 3D wave propagation is necessary. While numerical techniques are now routinely applied to local seismic wave propagation, only recently has the possibility of simulating wave propagation on larger scales in spherical geometry been investigated. We apply a high-order staggered-grid finite-difference scheme to the elastic wave equations in spherical coordinates [phi, theta, r]. Using regular grid spacing in a single domain the physical space is limited to spherical sections which do not include the axis theta = 0. While the staggering of the space-dependent fields improves the overall accuracy of the scheme, some of the tensor elements have to be interpolated to the required grid locations. By comparing with quasi-analytical solutions for layered Earth models we demonstrate the accuracy of the algorithm. Finally, the technique is used to study the effects of a source located in a simplified slab structure. The 3D technique will allow us to study the wave field due to laterally heterogeneous structures, such as subduction zones, plumes or oceanic ridges. (C) 2002 Elsevier Science B.V. All rights reserved.
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