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14th Symposium on Computer Architecture and High Performance Computing (SCAB-PAD'02)
A Parallel Approximation Hitting Set Algorithm for Gene Expression Analysis
Vit?ria, ES, Brazil
October 28-October 30
ISBN: 0-7695-1772-2
With the recent DNA-microarray technology, it is possible to measure the expression levels of thousands of genes simultaneously in the same experiment. A genetic network is a model that describes how the expression level of each gene is affected by the expression levels of other genes in the network. Given the results of an experiment with n genes and m measures over time (m < < n), we consider the problem of finding a subset of genes (k genes, where k < < n) that explain the expression level of a given target gene under study. We consider the coarse-grained multicomputer (CGM) model, with p processors. In this paper we first present a sequential approximation algorithm of O(m4n) time and O(m2n) space. The main result is a new parallel approximation algorithm that determines the k genes in O(m4n/p) local computing time plus O(k) communication rounds, and with space requirement of O(m2n/p). The p factor in the parallel time and space complexities indicates a good parallelization. We also show preliminary promising experimental results on a Beowulf machine. To our knowledge there are no CGM algorithms for the problem considered in this paper.
Citation:
D. Ruchkys, S. Song, "A Parallel Approximation Hitting Set Algorithm for Gene Expression Analysis," sbac-pad, pp.0075, 14th Symposium on Computer Architecture and High Performance Computing (SCAB-PAD'02), 2002
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