Geodesic
Chebyshev acceleration of the GeneRank algorithm
Electronic transactions on numerical analysis, Tome 40 (2013), pp. 311-320
The ranking of genes plays an important role in biomedical research. The GeneRank method of Morrison et al. [BMC Bioinformatics, 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.
Classification : 65F10, 65F50, 92D20
Keywords: generank, computational genomics, Chebyshev semi-iteration, polynomials of best uniform approximation, conjugate gradients 
@article{ETNA_2013__40__a10,
     author = {Benzi,  Michele and Kuhlemann,  Verena},
     title = {Chebyshev acceleration of the {GeneRank} algorithm},
     journal = {Electronic transactions on numerical analysis},
     pages = {311--320},
     year = {2013},
     volume = {40},
     zbl = {1288.65036},
     language = {en},
     url = {http://geodesic.mathdoc.fr/item/ETNA_2013__40__a10/}
}
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AU  - Benzi,  Michele
AU  - Kuhlemann,  Verena
TI  - Chebyshev acceleration of the GeneRank algorithm
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EP  - 320
VL  - 40
UR  - http://geodesic.mathdoc.fr/item/ETNA_2013__40__a10/
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%A Benzi,  Michele
%A Kuhlemann,  Verena
%T Chebyshev acceleration of the GeneRank algorithm
%J Electronic transactions on numerical analysis
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%P 311-320
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%U http://geodesic.mathdoc.fr/item/ETNA_2013__40__a10/
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%F ETNA_2013__40__a10
Benzi,  Michele; Kuhlemann,  Verena. Chebyshev acceleration of the GeneRank algorithm. Electronic transactions on numerical analysis, Tome 40 (2013), pp. 311-320. http://geodesic.mathdoc.fr/item/ETNA_2013__40__a10/