Managing memory and reducing I/O cost for correlation matrix calculation in bioinformatics
Krishnajith, Anaththa P. D., Kelly, Wayne A., Hayward, Ross F., & Tian, Yu-Chu (2013) Managing memory and reducing I/O cost for correlation matrix calculation in bioinformatics. In Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, IEEE, Grand Copthorne Waterfront Hotel, Singapore, pp. 36-43.
The generation of a correlation matrix from a large set of long gene sequences is a common requirement in many bioinformatics problems such as phylogenetic analysis. The generation is not only computationally intensive but also requires significant memory resources as, typically, few gene sequences can be simultaneously stored in primary memory. The standard practice in such computation is to use frequent input/output (I/O) operations. Therefore, minimizing the number of these operations will yield much faster run-times. This paper develops an approach for the faster and scalable computing of large-size correlation matrices through the full use of available memory and a reduced number of I/O operations. The approach is scalable in the sense that the same algorithms can be executed on different computing platforms with different amounts of memory and can be applied to different problems with different correlation matrix sizes. The significant performance improvement of the approach over the existing approaches is demonstrated through benchmark examples.
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|Item Type:||Conference Paper|
|Keywords:||Correlation matrix, Bioinformatics computing, Scalable computing, memory management, phylogenetic analysis, Data shared scheduling|
|Subjects:||Australian and New Zealand Standard Research Classification > INFORMATION AND COMPUTING SCIENCES (080000) > COMPUTATION THEORY AND MATHEMATICS (080200) > Computation Theory and Mathematics not elsewhere classified (080299)
Australian and New Zealand Standard Research Classification > INFORMATION AND COMPUTING SCIENCES (080000) > COMPUTER SOFTWARE (080300) > Bioinformatics Software (080301)
|Divisions:||Current > Schools > School of Electrical Engineering & Computer Science
Current > QUT Faculties and Divisions > Science & Engineering Faculty
|Copyright Owner:||Copyright 2013 IEEE|
|Deposited On:||13 May 2013 04:46|
|Last Modified:||13 Jan 2014 03:45|
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