Software Note: A hierarchical clustering algorithm for MIMD architecture

Authors:
Zhihua Du;Feng Lin
Affiliations:
BioInformatics Research Centre, Nanyang Technological University, Nanyang Avenue, Singapore 639798, Singapore;BioInformatics Research Centre, Nanyang Technological University, Nanyang Avenue, Singapore 639798, Singapore
Venue:
Computational Biology and Chemistry
Year:
2004

Citing 2
Cited 1

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Abstract

Hierarchical clustering is the most often used method for grouping similar patterns of gene expression data. A fundamental problem with existing implementations of this clustering method is the inability to handle large data sets within a reasonable time and memory resources. We propose a parallelized algorithm of hierarchical clustering to solve this problem. Our implementation on a multiple instruction multiple data (MIMD) architecture shows considerable reduction in computational time and inter-node communication overhead, especially for large data sets. We use the standard message passing library, message passing interface (MPI) for any MIMD systems.