Parallel Mutual Information Based Construction of Whole-Genome Networks on the Intel (R) Xeon Phi (TM) Coprocessor

Sanchit Misra, Kiran Pamnany, Srinivas Aluru
2014 2014 IEEE 28th International Parallel and Distributed Processing Symposium  
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 wholegenome scale, and the few that can, require large clusters. In this paper, we present a solution on the Intel R Xeon Phi TM coprocessor, taking advantage of its multi-level parallelism including many x86-based cores, multiple threads per core, and vector processing units. We
more » ... present a solution on the Intel R Xeon R 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.
doi:10.1109/ipdps.2014.35 dblp:conf/ipps/MisraPA14 fatcat:zbkz7kentrbarpefrzjf7ruuba