AMGDTI: drug-target interaction prediction based on adaptive meta-graph learning in heterogeneous network

• Published in: Briefings in bioinformatics Vol. 25; no. 1
• Main Authors: Su, Yansen, Hu, Zhiyang, Wang, Fei, Bin, Yannan, Zheng, Chunhou, Li, Haitao, Chen, Haowen, Zeng, Xiangxiang
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 22.11.2023
• Subjects: Algorithms; Benchmarking; Drug Delivery Systems; Medicine; Problem Solving Protocol; Semantics; adaptive meta-graph; drug–target interaction; graph convolutional networks; heterogeneous network
• ISSN: 1467-5463; 1477-4054
• DOI: 10.1093/bib/bbad474

Prediction of drug-target interactions (DTIs) is essential in medicine field, since it benefits the identification of molecular structures potentially interacting with drugs and facilitates the discovery and reposition of drugs. Recently, much attention has been attracted to network representation learning to learn rich information from heterogeneous data. Although network representation learning algorithms have achieved success in predicting DTI, several manually designed meta-graphs limit the capability of extracting complex semantic information. To address the problem, we introduce an adaptive meta-graph-based method, termed AMGDTI, for DTI prediction. In the proposed AMGDTI, the semantic information is automatically aggregated from a heterogeneous network by training an adaptive meta-graph, thereby achieving efficient information integration without requiring domain knowledge. The effectiveness of the proposed AMGDTI is verified on two benchmark datasets. Experimental results demonstrate that the AMGDTI method overall outperforms eight state-of-the-art methods in predicting DTI and achieves the accurate identification of novel DTIs. It is also verified that the adaptive meta-graph exhibits flexibility and effectively captures complex fine-grained semantic information, enabling the learning of intricate heterogeneous network topology and the inference of potential drug-target relationship.