NDLI: A parallel approximation hitting set algorithm for gene expression analysis

Content Provider	IEEE Xplore Digital Library
Author	Ruchkys, D.P. Song, S.W.
Copyright Year	2002
Description	Author affiliation: Instituto de Matematica e Estatistica, Sao Paulo Univ., Brazil (Ruchkys, D.P.; Song, S.W.)
Abstract	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(m/sup 4/n) time and O(m/sup 2/n) space. The main result is a new parallel approximation algorithm that determines the k genes in O(m/sup 4/n/p) local computing time plus O(k) communication rounds, and with space requirement of O(m/sup 2/n/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.
Sponsorship	SBC IFIP - International Federation for Inf. Process. IEEE Comput. Soc
Starting Page	75
Ending Page	81
File Size	660518
Page Count	7
File Format	PDF
ISBN	0769517722
DOI	10.1109/CAHPC.2002.1180762
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2002-10-28
Publisher Place	Brazil
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Approximation algorithms Gene expression Algorithm design and analysis Genetics User-generated content Time measurement Space technology DNA computing Monitoring Computer networks
Content Type	Text
Resource Type	Article

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