NDLI: Parallel Mutual Information Based Construction of Genome-Scale Networks on the Intel®Xeon Phi™ Coprocessor

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Parallel Mutual Information Based Construction of Genome-Scale Networks on the Intel®Xeon Phi™ Coprocessor

Content Provider	IEEE Xplore Digital Library
Author	Misra, S. Pamnany, K. Aluru, S.
Copyright Year	2004
Abstract	Construction of whole-genome networks from large-scale gene expression data is an important problem in systems biology. While several techniques have been developed, most cannot handle network reconstruction at the whole-genome scale, and the few that can, require large clusters. In this paper, we present a solution on the Intel Xeon Phi coprocessor, taking advantage of its multi-level parallelism including many x86-based cores, multiple threads per core, and vector processing units. We also present a solution on the Intel^® Xeon^® processor. Our solution is based on TINGe, a fast parallel network reconstruction technique that uses mutual information and permutation testing for assessing statistical significance. We demonstrate the first ever inference of a plant whole genome regulatory network on a single chip by constructing a 15,575 gene network of the plant Arabidopsis thaliana from 3,137 microarray experiments in only 22 minutes. In addition, our optimization for parallelizing mutual information computation on the Intel Xeon Phi coprocessor holds out lessons that are applicable to other domains.
Sponsorship	IEEE Computer Society
Starting Page	1008
Ending Page	1020
Page Count	13
File Size	1579347
File Format	PDF
ISSN	15455963
Volume Number	12
Issue Number	5
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2015-09-01
Publisher Place	U.S.A.
Access Restriction	One Nation One Subscription (ONOS)
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Bioinformatics Mutual information Splines (mathematics) Computational biology systems biology gene networks mutual information Xeon Phi Gene networks
Content Type	Text
Resource Type	Article
Subject	Applied Mathematics Genetics Biotechnology

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
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Parallel Information-Theory-Based Construction of Genome-Wide Gene Regulatory Networks

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Heterogeneous computing architecture for fast detection of SNP-SNP interactions

Explicit Fourth-Order Runge–Kutta Method on Intel Xeon Phi Coprocessor

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Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters

Parallel Mutual Information Based Construction of Genome-Scale Networks on the Intel®Xeon Phi™ Coprocessor

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