Heterogenous biological network multi-task learning model for ncRNA-disease-drug association prediction

• Published in: Knowledge-based systems 2024-09, Vol.300, p.112222, Article 112222
• Main Authors: Yuan, Yongna, Liu, Jiahui, Pan, Xiaohang, Zhang, Ruisheng, Su, Wei
• Format: Article
• Language: English
• Subjects: Graph attention networks; Heterogenous biological network; Multi-task learning; ncRNA-disease-drug associations; Network medicine
• ISSN: 0950-7051
• DOI: 10.1016/j.knosys.2024.112222

•We propose a novel end-to-end model HBNMM to simultaneously predict three potential associations with multi-task learning.•We gather diverse biomedical data to establish a sophisticated heterogeneous network, which contains ncRNA-disease-drug association networks, similarity networks and gaussian similarity networks.•Compared with state-of-the-art models, HBNMM achieves the best performance using graph attention networks.•Five case studies validated by dbDEMC, ncRNADrug and CTD show effectiveness of HBNMM. Traditional medical research is characterised by lengthy duration, significant financial investment, and substantial risk of failure. In response to these challenges, network medicine, combined with medicine and computer technology, has become an important development direction, and computational methods have been proposed to predict potential associations. However, most of the current computational methods focus on single-potential association prediction tasks, which face issues of association sparsity and weak generalisation ability. To address these challenges, we developed a heterogeneous biological network multi-task learning model (HBNMM). Unlike previous methods based on bipartite graphs, HBNMM constructs a complex heterogeneous biological network, including ncRNA-disease-drug association networks and diverse similarity networks. HBNMM applies graph attention networks to aggregate node neighbourhood information and acquire node feature embeddings, and is then trained with a multi-task learning strategy to simultaneously predict potential ncRNA-disease, ncRNA-drug, and drug-disease associations. As a result, the HBNMM achieves an excellent performance that is higher than that of the state-of-the-art models. Furthermore, five case studies supported by experiments showed powerful predictive ability for drug discovery and disease treatment.