Multivariate selection of genetic markers in diagnostic classification

Artificial Intelligence in Medicine
G WeberLucila Ohno-Machado

Abstract

Analysis of gene expression data obtained from microarrays presents a new set of challenges to machine learning modeling. In this domain, in which the number of variables far exceeds the number of cases, identifying relevant genes or groups of genes that are good markers for a particular classification is as important as achieving good classification performance. Although several machine learning algorithms have been proposed to address the latter, identification of gene markers has not been systematically pursued. In this article, we investigate several algorithms for selecting gene markers for classification. We test these algorithms using logistic regression, as this is a simple and efficient supervised learning algorithm. We demonstrate, using 10 different data sets, that a conditionally univariate algorithm constitutes a viable choice if a researcher is interested in quickly determining a set of gene expression levels that can serve as markers for disease. We show that the classification performance of logistic regression is not very different from that of more sophisticated algorithms that have been applied in previous studies, and that the gene selection in the logistic regression algorithm is reasonable in both cases. F...Continue Reading

References

Dec 7, 2000·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·A Ben-DorZ Yakhini
Jun 8, 2001·Proceedings of the National Academy of Sciences of the United States of America·H ZhangM Xiong
Jul 27, 2001·Bioinformatics·C H YeangT Golub
Oct 9, 2001·Bioinformatics·K Y Yeung, W L Ruzzo
Nov 15, 2001·Proceedings of the National Academy of Sciences of the United States of America·A BhattacharjeeM Meyerson
Dec 14, 2001·Proceedings of the National Academy of Sciences of the United States of America·S RamaswamyT R Golub
Jan 5, 2002·Indian Journal of Pediatrics·T DuaM Kabra
Jun 28, 2002·Cancer Cell·Dinesh SinghWilliam R Sellers
Sep 28, 2002·Science·Michelle N ArbeitmanKevin P White
Dec 7, 2002·Nature Genetics·Sridhar RamaswamyTodd R Golub

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Citations

Feb 27, 2013·Cancer Informatics·P T Krishna KumarPuneeth Iyengar
Jul 15, 2015·Advances in Bioinformatics·Zena M Hira, Duncan F Gillies
Oct 7, 2004·Journal of Biomedical Informatics·Winston Patrick KuoLucila Ohno-Machado
Aug 25, 2005·Neonatal Network : NN·Susan Givens Bell

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