Supervised feature selection on gene expression microarray datasets using manifold learning

Abstract

In recent decades, the ultimate output from microarray assay, has produced enormous numbers of microarray datasets, regardless of the used technology. These datasets include complex and high dimensional samples and genes that the number of samples is much smaller than the number of genes (features). Due to the redundant dimensions in these datasets, processing them directly not only leads to poor performance but also increases computation time and memory usage. Feature selection reduces computational expense while improving or maintaining diagnosis accuracy. In this study, we propose a new supervised feature selection method based on a manifold learning approach. We focus in two different directions to address this issue. First, maximum relevancy criterion that achieves by integrating Supervised Laplacian Eigenmaps (S-LE) and a matrix, which can realize the process of feature selection. The applied criterion simultaneously opts the features that make same-class samples closer to each other and ignores the features that cause different-class samples be near. Second, minimum redundancy among selected features by applying the Pearson correlation coefficient. In the test phase, the proposed method is compared with ten state-of-the-art algorithms on seven microarray datasets. Reported results show that the proposed method has more promising performance than the other methods.