HINGRL: predicting drug–disease associations with graph representation learning on heterogeneous information networks

• Published in: Briefings in bioinformatics Vol. 23; no. 1
• Main Authors: Zhao, Bo-Wei, Hu, Lun, You, Zhu-Hong, Wang, Lei, Su, Xiao-Rui
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 17.01.2022; Oxford Publishing Limited (England)
• Subjects: Algorithms; Computational Biology - methods; Computer applications; Disease; Drug development; Drug Repositioning - methods; Drugs; Graph representations; Graphical representations; Humans; Information Services; Learning; Machine Learning; Models, Theoretical; Network topologies; Neural Networks, Computer; Pharmaceutical Preparations; Proteins; R&D; Research & development; Topology; prediction; heterogeneous information network; graph representation learning; drug repositioning; drug–disease associations
• ISSN: 1467-5463; 1477-4054; 1477-4054
• DOI: 10.1093/bib/bbab515

Abstract Identifying new indications for drugs plays an essential role at many phases of drug research and development. Computational methods are regarded as an effective way to associate drugs with new indications. However, most of them complete their tasks by constructing a variety of heterogeneous networks without considering the biological knowledge of drugs and diseases, which are believed to be useful for improving the accuracy of drug repositioning. To this end, a novel heterogeneous information network (HIN) based model, namely HINGRL, is proposed to precisely identify new indications for drugs based on graph representation learning techniques. More specifically, HINGRL first constructs a HIN by integrating drug–disease, drug–protein and protein–disease biological networks with the biological knowledge of drugs and diseases. Then, different representation strategies are applied to learn the features of nodes in the HIN from the topological and biological perspectives. Finally, HINGRL adopts a Random Forest classifier to predict unknown drug–disease associations based on the integrated features of drugs and diseases obtained in the previous step. Experimental results demonstrate that HINGRL achieves the best performance on two real datasets when compared with state-of-the-art models. Besides, our case studies indicate that the simultaneous consideration of network topology and biological knowledge of drugs and diseases allows HINGRL to precisely predict drug–disease associations from a more comprehensive perspective. The promising performance of HINGRL also reveals that the utilization of rich heterogeneous information provides an alternative view for HINGRL to identify novel drug–disease associations especially for new diseases.