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IEEE/ACM Trans Comput Biol Bioinform. 2009 Apr-Jun;6(2):344-52. doi: 10.1109/TCBB.2007.70272.

Parallel clustering algorithm for large data sets with applications in bioinformatics.

Author information

1
Department of Biochemistry and Molecular Biology, Computational System Biology Laboratory, Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, USA. olman@csbl.bmb.uga.edu

Abstract

Large sets of bioinformatical data provide a challenge in time consumption while solving the cluster identification problem, and that is why a parallel algorithm is so needed for identifying dense clusters in a noisy background. Our algorithm works on a graph representation of the data set to be analyzed. It identifies clusters through the identification of densely intraconnected subgraphs. We have employed a minimum spanning tree (MST) representation of the graph and solve the cluster identification problem using this representation. The computational bottleneck of our algorithm is the construction of an MST of a graph, for which a parallel algorithm is employed. Our high-level strategy for the parallel MST construction algorithm is to first partition the graph, then construct MSTs for the partitioned subgraphs and auxiliary bipartite graphs based on the subgraphs, and finally merge these MSTs to derive an MST of the original graph. The computational results indicate that when running on 150 CPUs, our algorithm can solve a cluster identification problem on a data set with 1,000,000 data points almost 100 times faster than on single CPU, indicating that this program is capable of handling very large data clustering problems in an efficient manner. We have implemented the clustering algorithm as the software CLUMP.

PMID:
19407357
DOI:
10.1109/TCBB.2007.70272
[Indexed for MEDLINE]
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