Title: Gene selection and parameter determination of support vector machines based on BPSO algorithm

Authors: Shutao Li, Xixian Wu, Mingkui Tan

Addresses: College of Electrical and Information Engineering, Hunan University, Changsha, 410082, China. ' College of Electrical and Information Engineering, Hunan University, Changsha, 410082, China. ' College of Electrical and Information Engineering, Hunan University, Changsha, 410082, China

Abstract: The advent of microarray technology allows researchers to perform cancer diagnosis on gene level. However, the microarray data usually contains a large quantity of irrelevant, noisy and redundant genes which may seriously deteriorate the prediction accuracy. What|s more, microarray data always suffers from the problem of a relatively small number of samples, which raises the difficulties in diagnosis. Accordingly, gene selection plays an important role in cancer diagnosis using microarray data. As a state-of-the-art classifier, support vector machine (SVM) has been successfully applied in solving the small-sample recognition problems and therefore is very suitable for microarray data processing. However, to improve the recognition accuracy, it is essential to choose certain good enough parameters for SVM in applications. This study proposes a new gene selection method based on a binary version of particle swarm optimisation (BPSO) algorithm and SVM. In the method, the task of gene selection and parameter tuning of SVM is performed simultaneously by BPSO. To verify the proposed method, three benchmark dataset (leukaemia, breast and colon) are studied. The experimental results show that the proposed method is highly effective and competitive compared with other methods.

Keywords: microarray data; cancer diagnosis; gene selection; particle swarm optimisation; PSO; support vector machines; SVM; parameter determination; classifiers; leukaemia; breast cancer; colon cancer.

DOI: 10.1504/IJMIC.2009.030081

International Journal of Modelling, Identification and Control, 2009 Vol.8 No.4, pp.344 - 352

Available online: 09 Dec 2009 *

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