Improved machine learning models for predicting selective compounds

Xia Ning, Michael A. Walters, George Karypis

Abstract: The identification of small potent compounds that selectively bind to the target under consideration with high affinities is a critical step towards successful drug discovery. However, there still lacks efficient and accurate computational methods to predict compound selectivity properties. In this paper, we propose a set of machine learning methods to do compound selectivity prediction. In particular, we propose a novel cascaded learning method and a multi-task learning method. The cascaded method decomposes the selectivity prediction into two steps, one model for each step, so as to effectively filter out non-selective compounds. The multi-task method incorporates both activity and selectivity models into one multi-task model so as to better differentiate compound selectivity properties. We conducted a comprehensive set of experiments and compared the results with other conventional selectivity prediction methods, and our results demonstrated that the cascaded and multi-task methods significantly improve the selectivity prediction performance.