Improved Regularized Multi-class Logistic Regression for Gene Classification with Optimal Kernel PCA and HC Algorithm.

Abstract

A significant challenge in high-dimensional and big data analysis is related to the classification and prediction of the variables of interest. The massive genetic datasets are complex. Gene expression datasets are enriched with useful genes that are associated with specific diseases such as cancer. In this study, we used two gene expression datasets from the Gene Expression Omnibus and preprocessed them before classification. We used optimal kernel principal component analysis in which the optimal kernel function was chosen for dataset dimensionality reduction and extraction of the most important features. The gene sets with a high validity index were collected using a combined hieratical clustering and optimal kernel principal component analysis (KHC-RLR) algorithm. Logistic regression is one of the most common methods for classification, and it has been shown to be a useful classification approach for gene expression data analysis. In this study, we used multi-class logistic regression to classify the collected gene sets. We found that ordinary logistic regression caused a major overfitting problem; therefore, we used regularized multi-class logistic regression to classify the gene sets. The proposed KHC-RLR algorithm showed a high performance and satisfied accuracy measures.