Predicting drug side effects by multi-label learning and ensemble learning

BACKGROUND: Predicting drug side effects is an important topic in the drug discovery. Although several machine learning methods have been proposed to predict side effects, there is still space for improvements. Firstly, the side effect prediction is a multi-label learning task, and we can adopt the multi-label learning techniques for it. Secondly, drug-related features are associated with side effects, and feature dimensions have specific biological meanings. Recognizing critical dimensions and reducing irrelevant dimensions may help to reveal the causes of side effects. METHODS: In this paper, we propose a novel method ‘feature selection-based multi-label k-nearest neighbor method’ (FS-MLKNN), which can simultaneously determine critical feature dimensions and construct high-accuracy multi-label prediction models. RESULTS: Computational experiments demonstrate that FS-MLKNN leads to good performances as well as explainable results. To achieve better performances, we further develop the ensemble learning model by integrating individual feature-based FS-MLKNN models. When compared with other state-of-the-art methods, the ensemble method produces better performances on benchmark datasets. CONCLUSIONS: In conclusion, FS-MLKNN and the ensemble method are promising tools for the side effect prediction. The source code and datasets are available in the Additional file 1. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-015-0774-y) contains supplementary material, which is available to authorized users.