A multitask multiple kernel learning algorithm for survival analysis with application to cancer biology

Abstract

Predictive performance of machine learning algorithms on related problems can be improved using multitask learning approaches. Rather than performing survival analysis on each data set to predict survival times of cancer patients, we developed a novel multitask approach based on multiple kernel learning (MKL). Our multitask MKL algorithm both works on multiple cancer data sets and integrates cancer-related pathways/gene sets into survival analysis. We tested our algorithm, which is named as Path2MSurv, on the Cancer Genome Atlas data sets analyzing gene expression profiles of 7,655 patients from 20 cancer types together with cancer-specific pathway/gene set collections. Path2MSury obtained better or comparable predictive performance when benchmarked against random survival forest, survival support vector machine, and single-task variant of our algorithm. Path2MSury has the ability to identify key pathways/gene sets in predicting survival times of patients from different cancer types.