Predicting disease risks using feature selection based on random forest and support vector machine

Abstract

Disease risk prediction is an important task in biomedicine and bioinformatics. To resolve the problem of high-dimensional features space and highly feature redundancy and to improve the intelligibility of data mining results, a new wrapper method of feature selection based on random forest variables importance measures and support vector machine was proposed. The proposed method combined sequence backward searching approach and sequence forward searching approach. Feature selection starts with the entire set of features in the dataset. At every iteration, two feature subsets are gained. One feature subset removes those most unimportant features and the most important feature at the same time, which is used to train random forest and to compute feature importance for next feature selection. Another feature subset removes only those most unimportant features while remains the most important feature, which is used as the optimal feature subset to train SVM classifier. Finally, the feature subset with the highest SVM classification accuracy was regarded as optimal feature subset. The experimental results on 11 UCI datasets, a real clinical data sets and a gene expression dataset show that the proposed algorithm can generate the smaller feature subset while improve the classification accuracy. © 2014 Springer International Publishing Switzerland.