Matrix factorization with denoising autoencoders for prediction of drug–target interactions

Drug–target interaction is crucial in the discovery of new drugs. Computational methods can be used to identify new drug–target interactions at low costs and with reasonable accuracy. Recent studies pay more attention to machine-learning methods, ranging from matrix factorization to deep learning, in the DTI prediction. Since the interaction matrix is often extremely sparse, DTI prediction performance is significantly decreased with matrix factorization-based methods. Therefore, some matrix factorization methods utilize side information to address both the sparsity issue of the interaction matrix and the cold-start issue. By combining matrix factorization and autoencoders, we propose a hybrid DTI prediction model that simultaneously learn the hidden factors of drugs and targets from their side information and interaction matrix. The proposed method is composed of two steps: the pre-processing of the interaction matrix, and the hybrid model. We leverage the similarity matrices of both drugs and targets to address the sparsity problem of the interaction matrix. The comparison of our approach against other algorithms on the same reference datasets has shown good results regarding area under receiver operating characteristic curve and the area under precision–recall curve. More specifically, experimental results achieve high accuracy on golden standard datasets (e.g., Nuclear Receptors, GPCRs, Ion Channels, and Enzymes) when performed with five repetitions of tenfold cross-validation. Graphical abstract: [Figure not available: see fulltext.]Display graphical of the hybrid model of Matrix Factorization with Denoising Autoencoderswith the help side information of drugs and targets for Prediction of Drug-Target Interactions.