title: Recipe for uncovering predictive genes using support vector machines based on model population analysis.
abstract: Selecting a small number of informative genes for microarray-based tumor classification is central to cancer prediction and treatment. Based on model population analysis, here we present a new approach, called Margin Influence Analysis (MIA), designed to work with support vector machines (SVM) for selecting informative genes. The rationale for performing margin influence analysis lies in the fact that the margin of support vector machines is an important factor which underlies the generalization performance of SVM models. Briefly, MIA could reveal genes which have statistically significant influence on the margin by using Mann-Whitney U test. The reason for using the Mann-Whitney U test rather than two-sample t test is that Mann-Whitney U test is a nonparametric test method without any distribution-related assumptions and is also a robust method. Using two publicly available cancerous microarray data sets, it is demonstrated that MIA could typically select a small number of margin-influencing genes and further achieves comparable classification accuracy compared to those reported in the literature. The distinguished features and outstanding performance may make MIA a good alternative for gene selection of high dimensional microarray data. (The source code in MATLAB with GNU General Public License Version 2.0 is freely available at http://code.google.com/p/mia2009/).
authors.affiliation: Research Center of Modernization of Traditional Chinese Medicines, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, PR China. lhdcsu@gmail.com
authors.forename: Hong-Dong
authors.initials: HD
authors.lastname: Li
authors.forename: Yi-Zeng
authors.initials: YZ
authors.lastname: Liang
authors.forename: Qing-Song
authors.initials: QS
authors.lastname: Xu
authors.forename: Dong-Sheng
authors.initials: DS
authors.lastname: Cao
authors.forename: Bin-Bin
authors.initials: BB
authors.lastname: Tan
authors.forename: Bai-Chuan
authors.initials: BC
authors.lastname: Deng
authors.forename: Chen-Chen
authors.initials: CC
authors.lastname: Lin
mesh_terms: D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D005828:Genetics, Population; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D060388:Support Vector Machine