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| Parameters selection in gene selection using Gaussian kernel support vector machines by genetic algorithm |
| MAO Yong, ZHOU Xiao-bo, PI Dao-ying, SUN You-xian, WONG Stephen T.C. |
| National Laboratory of Industrial Control Technology, Institute of Modern Control Engineering, Zhejiang University, Hangzhou 310027, China; Harvard Center for Neurodegeneration and Repair, Harvard Medical School and Brigham and Women’s Hospital, Harvard Medical School, Harvard University, Boston, MA 02115, USA |
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Abstract In microarray-based cancer classification, gene selection is an important issue owing to the large number of variables and small number of samples as well as its non-linearity. It is difficult to get satisfying results by using conventional linear statistical methods. Recursive feature elimination based on support vector machine (SVM RFE) is an effective algorithm for gene selection and cancer classification, which are integrated into a consistent framework. In this paper, we propose a new method to select parameters of the aforementioned algorithm implemented with Gaussian kernel SVMs as better alternatives to the common practice of selecting the apparently best parameters by using a genetic algorithm to search for a couple of optimal parameter. Fast implementation issues for this method are also discussed for pragmatic reasons. The proposed method was tested on two representative hereditary breast cancer and acute leukaemia datasets. The experimental results indicate that the proposed method performs well in selecting genes and achieves high classification accuracies with these genes.
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Received: 08 December 2004
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