A Novel Triple Matrix Factorization Method for Detecting Drug‐Side Effect Association Based on Kernel Target Alignment

Abstract

All drugs usually have side effects, which endanger the health of patients. To identify potential side effects of drugs, biological and pharmacological experiments are done but are expensive and time‐consuming. So, computation‐based methods have been developed to accurately and quickly predict side effects. To predict potential associations between drugs and side effects, we propose a novel method called the Triple Matrix Factorization‐ (TMF‐) based model. TMF is built by the biprojection matrix and latent feature of kernels, which is based on Low Rank Approximation (LRA). LRA could construct a lower rank matrix to approximate the original matrix, which not only retains the characteristics of the original matrix but also reduces the storage space and computational complexity of the data. To fuse multivariate information, multiple kernel matrices are constructed and integrated via Kernel Target Alignment‐based Multiple Kernel Learning (KTA‐MKL) in drug and side effect space, respectively. Compared with other methods, our model achieves better performance on three benchmark datasets. The values of the Area Under the Precision‐Recall curve (AUPR) are 0.677, 0.685, and 0.680 on three datasets, respectively.