A general hypergraph learning algorithm for drug multi-task predictions in micro-to-macro biomedical networks

Shuting Jin, Yue Hong, Li Zeng, Yinghui Jiang, Yuan Lin, Leyi Wei, Zhuohang Yu, Xiangxiang Zeng, Xiangrong Liu

Abstract: Author summary Drugs containing the same functional groups may have similar pharmacochemical properties. However, how to effectively combine chemical information of drugs from molecular fragments containing functional groups into the biomolecular network is challenging and rarely explored. we decompose drugs’ SMILES string and construct a drug-centric heterogeneous network that integrates drug substructure and molecular interactions information. Based on the heterogeneous network, we proposed an end-to-end hypergraph attention network framework for the drug multi-task predictions, termed as HGDrug. The efficiency and generalization of the proposed HGDrug have been demonstrated by the state-of-the-art performance in four drug-related interaction predictions tasks with huge improvement compared to previous general-purpose classical models and task-specific models. In addition, HGDrug can effectively identify potential drug-related interactions and the drug-sub-structure networks are able to help to improve the performance of other GNN models. These conclusions present important insights on how to introduce the drug’ substructure information for multiple drug-related interactions tasks on biomedical networks. In summary, HGDrug offers a general and powerful tool for the identification of drug-related interactions by constructing the micro-to-macro drug-centric heterogeneous network.