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Chebyshev acceleration of the GeneRank algorithm. (English) Zbl 1288.65036
Summary: The ranking of genes plays an important role in biomedical research. The GeneRank method of J. L. Morrison et al. [“GeneRank: Using search engine technology for the analysis of microarray experiments”, BMC Bioinformatics, No. 6, 233 (2005)] ranks genes based on the results of microarray experiments combined with gene expression information, for example from gene annotations. The algorithm is a variant of the well known PageRank iteration, and can be formulated as the solution of a large, sparse linear system. Here we show that classical Chebyshev semi-iteration can considerably speed up the convergence of GeneRank, outperforming other acceleration schemes such as conjugate gradients.

65F10 Iterative numerical methods for linear systems
65F50 Computational methods for sparse matrices
68P10 Searching and sorting
92D10 Genetics and epigenetics
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