Predicting Drug-Target Interactions via Dual-Stream Graph Neural Network.

Abstract

Drug target interaction prediction is a crucial stage in drug discovery. However, brute-force search over a compound database is financially infeasible. We have witnessed the increasing measured drug-target interactions records in recent years, and the rich drug/protein-related information allows the usage of graph machine learning. Despite the advances in deep learning-enabled drug-target interaction, there are still open challenges: (1) rich and complex relationship between drugs and proteins can be explored; (2) the intermediate node is not calibrated in the heterogeneous graph. To tackle with above issues, this paper proposed a framework named DSG-DTI. Specifically, DSG-DTI has the heterogeneous graph autoencoder and heterogeneous attention network-based Matrix Completion. Our framework ensures that the known types of nodes (e.g., drug, target, side effects, diseases) are precisely embedded into high-dimensional space with our pretraining skills. Also, the attention-based heterogeneous graph-based matrix completion achieves highly competitive results via effective long-range dependencies extraction. We verify our model on two public benchmarks. The result of two publicly available benchmark application programs show that the proposed scheme effectively predicts drug-target interactions and can generalize to newly registered drugs and targets with slight performance degradation, outperforming the best accuracy compared with other baselines.