An enhanced feature selection filter for classification of microarray cancer data

Abstract

The main aim of this study is to select the optimal set of genes from microarray cancer datasets that contribute to the prediction of specific cancer types. This study proposes the enhancement of the feature selection filter algorithm based on Joe's normalized mutual information and its use for gene selection. The proposed algorithm is implemented and evaluated on seven benchmark microarray cancer datasets, namely, central nervous system, leukemia (binary), leukemia (3 class), leukemia (4 class), lymphoma, mixed lineage leukemia, and small round blue cell tumor, using five well‐known classifiers, including the naive Bayes, radial basis function network, instance‐based classifier, decision‐based table, and decision tree. An average increase in the prediction accuracy of 5.1% is observed on all seven datasets averaged over all five classifiers. The average reduction in training time is 2.86 seconds. The performance of the proposed method is also compared with those of three other popular mutual information–based feature selection filters, namely, information gain, gain ratio, and symmetric uncertainty. The results are impressive when all five classifiers are used on all the datasets.

Keywords

• cancer classification
• feature selection
• gene expression
• microarray
• normalized mutual information