Gene selection from microarray gene expression data for classification of cancer subgroups employing PSO and adaptive K-nearest neighborhood technique

Abstract

These days, microarray gene expression data are playing an essential role in cancer classifications. However, due to the availability of small number of effective samples compared to the large number of genes in microarray data, many computational methods have failed to identify a small subset of important genes. Therefore, it is a challenging task to identify small number of disease-specific significant genes related for precise diagnosis of cancer sub classes. In this paper, particle swarm optimization (PSO) method along with adaptive K-nearest neighborhood (KNN) based gene selection technique are proposed to distinguish a small subset of useful genes that are sufficient for the desired classification purpose. A proper value of K would help to form the appropriate numbers of neighborhood to be explored and hence to classify the dataset accurately. Thus, a heuristic for selecting the optimal values of K efficiently, guided by the classification accuracy is also proposed. This proposed technique of finding minimum possible meaningful set of genes is applied on three benchmark microarray datasets, namely the small round blue cell tumor (SRBCT) data, the acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) data and the mixed-lineage leukemia (MLL) data. Results demonstrate the usefulness of the proposed method in terms of classification accuracy on blind test samples, number of informative genes and computing time. Further, the usefulness and universal characteristics of the identified genes are reconfirmed by using different classifiers, such as support vector machine (SVM).