Interpretable bilinear attention network with domain adaptation improves drug-target prediction

Abstract

Predicting drug-target interaction is key for drug discovery. Recent deep learning-based methods show promising performance but two challenges remain (i) how to explicitly model and learn local interactions between drugs and targets for better prediction and interpretation; (ii) how to generalize prediction performance on novel drug-target pairs from different distribution. In this work, we propose DrugBAN, a deep bilinear attention network (BAN) framework with domain adaptation to explicitly learn pair-wise local interactions between drugs and targets, and adapt on out-of-distribution data. DrugBAN works on drug molecular graphs and target protein sequences to perform prediction, with conditional domain adversarial learning to align learned interaction representations across different distributions for better generalization on novel drug-target pairs. Experiments on three benchmark datasets under both in-domain and cross-domain settings show that DrugBAN achieves the best overall performance against five state-of-the-art baselines. Moreover, visualizing the learned bilinear attention map provides interpretable insights from prediction results.

Peizhen Bai

Ph.D. Student

My research interests include deep learning, graph neural networks and drug discovery.