An improved Binary Particle Swarm Optimization (iBPSO) for Gene Selection and Cancer Classification using DNA Microarrays

Abstract

DNA Microarrays enable the detection of genetic changes attributable to cancer by simultaneously analyzing the expression of thousands of genes. However, the identification of most relevant genes from thousands of gene expressions available in each biological sample, for cancer classification pose a great challenge. Although researchers have applied BPSO based wrapper approaches to get most relevant genes prior to cancer classification, these approaches didn’t achieve good classification accuracy due to the premature convergence caused by local stagnation problem. This paper proposes an improved Binary Particle Swarm Optimization (iBPSO) to tackle these issues. The proposed iBPSO based wrapper is examined using Naive-Bayes (NB), k-Nearest Neighbor (kNN), and Support Vector Machines (SVM) classifiers with stratified 5-fold cross-validation. The proposed iBPSO exhibited its efficacy in terms of classification accuracy and the number of selected genes in comparison to standard BPSO on six benchmark cancer microarray datasets. Our proposed iBPSO also effectively escapes from local minima stagnation.