LRSSL: predict and interpret drug–disease associations based on data integration using sparse subspace learning
Xujun Liang, Pengfei Zhang, Yan Lü, Ying Fu, Peng Fang, Lingzhi Qu, Meiying Shao, Yongheng Chen, Zhuchu Chen · Bioinformatics · 2016
Motivation: : Exploring the potential curative effects of drugs is crucial for effective drug development. Previous studies have indicated that integration of multiple types of information could be conducive to discovering novel indications of drugs. However, how to efficiently identify the mechanism behind drug-disease associations while integrating data from different sources remains a challenging problem. Results: : In this research, we present a novel method for indication prediction of both new drugs and approved drugs. This method is based on Laplacian regularized sparse subspace learning (LRSSL), which integrates drug chemical information, drug target domain information and target annotation information. Experimental results show that the proposed method outperforms several recent approaches for predicting drug-disease associations. Some drug therapeutic effects predicted by the method could be validated by database records or literatures. Moreover, with L1-norm constraint, important drug features have been extracted from multiple drug feature profiles. Case studies suggest that the extracted drug features could be beneficial to interpretation of the predicted results. Availability and Implementation: https://github.com/LiangXujun/LRSSL. Contact: [email protected]. Supplementary information: Supplementary data are available at Bioinformatics online.