Gene selection via BPSO and Backward generation for cancer classification

Abstract

Gene expression data (DNA microarray) enable researchers to simultaneously measure the levels of expression of several thousand genes. These levels of expression are very important in the classification of different types of tumors. In this work, we are interested in gene selection, which is an essential step in the data pre-processing for cancer classification. This selection makes it possible to represent a small subset of genes from a large set, and to eliminate the redundant, irrelevant or noisy genes. The combinatorial nature of the selection problem requires the development of specific techniques such as filters and Wrappers, or hybrids combining several optimization processes. In this context, we propose two hybrid approaches (RBPSO-1NN and FBPSO-SVM) for the gene selection problem, based on the combination of the filter methods (the Fisher criterion and the ReliefF algorithm), the BPSO metaheuristic algorithms and the Backward algorithm using the classifiers (SVM and 1NN) for the evaluation of the relevance of the candidate subsets. In order to verify the performance of our methods, we have tested them on eight well-known microarray datasets of high dimensions varying from 2308 to 11225 genes. The experiments carried out on the different datasets show that our methods prove to be very competitive with the existing works.