DTGHAT: multi-molecule heterogeneous graph transformer based on multi-molecule graph for drug-target identification.

Introduction: Drug target identification is a fundamental step in drug discovery and plays a pivotal role in new therapies development. Existing computational methods focus on the direct interactions between drugs and targets, often ignoring the complex interrelationships between drugs, targets and various biomolecules in the human system. Method: To address this limitation, we propose a novel prediction model named DTGHAT (Drug and Target Association Prediction using Heterogeneous Graph Attention Transformer based on Molecular Heterogeneous). DTGHAT utilizes a graph attention transformer to identify novel targets from 15 heterogeneous drug-gene-disease networks characterized by chemical, genomic, phenotypic, and cellular networks. Result: In a 5-fold cross-validation study, DTGHAT achieved an area under the receiver operating characteristic curve (AUC) of 0.9634, which is at least 4% higher than current state-of-the-art methods. Characterization ablation experiments highlight the importance of integrating biomolecular data from multiple sources in revealing drug-target interactions. In addition, a case study on cancer drugs further validates DTGHAT's effectiveness in predicting novel drug target identification. DTGHAT is free and available at: https://github.com/stella-007/DTGHAT.git.