An embedded feature selection method based on generalized classifier neural network for cancer classification

Abstract

The selection of relevant genes plays a vital role in classifying high-dimensional microarray gene expression data. Sparse group Lasso and its variants have been employed for gene selection to capture the interactions of genes within a group. Most of the embedded methods are linear sparse learning models that fail to capture the non-linear interactions. Additionally, very less attention is given to solving multi-class problems. The existing methods create overlapping groups, which further increases dimensionality. The paper proposes a neural network-based embedded feature selection method that can represent the non-linear relationship. In an effort toward an explainable model, a generalized classifier neural network (GCNN) is adopted as the model for the proposed embedded feature selection. GCNN has well-defined architecture in terms of the number of layers and neurons within each layer. Each layer has a distinct functionality, eliminating the obscure nature of most neural networks. The paper proposes a feature selection approach called Weighted GCNN (WGCNN) that embeds feature weighting as a part of training the neural network. Since the gene expression data comprises a large number of features, to avoid overfitting of the model a statistical guided dropout is implemented at the input layer. The proposed method works for binary as well as multi-class classification problems likewise. Experimental validation is carried out on seven microarray datasets on three learning models and compared with six state-of-art methods that are popularly employed for feature selection. The WGCNN performs well in terms of the F1 score and the number of features selected.