Gene selection in cancer classification using PSO/SVM and GA/SVM hybrid algorithms

• Published in: 2007 IEEE Congress on Evolutionary Computation pp. 284 - 290
• Main Authors: Alba, E., Garcia-Nieto, J., Jourdan, L., Talbi, E.-G.
• Format: Conference Proceeding
• Language: English
• Published: IEEE 01.09.2007
• Subjects: Cancer; DNA; Filters; Gene expression; Genetic algorithms; Neoplasms; Particle swarm optimization; Space exploration; Support vector machine classification; Support vector machines
• ISBN: 1424413397; 9781424413393
• ISSN: 1089-778X
• DOI: 10.1109/CEC.2007.4424483

In this work we compare the use of a particle swarm optimization (PSO) and a genetic algorithm (GA) (both augmented with support vector machines SVM) for the classification of high dimensional microarray data. Both algorithms are used for finding small samples of informative genes amongst thousands of them. A SVM classifier with 10- fold cross-validation is applied in order to validate and evaluate the provided solutions. A first contribution is to prove that PSOsvm is able to find interesting genes and to provide classification competitive performance. Specifically, a new version of PSO, called Geometric PSO, is empirically evaluated for the first time in this work using a binary representation in Hamming space. In this sense, a comparison of this approach with a new GAsvm and also with other existing methods of literature is provided. A second important contribution consists in the actual discovery of new and challenging results on six public datasets identifying significant in the development of a variety of cancers (leukemia, breast, colon, ovarian, prostate, and lung).