Supervised Graph Co-contrastive Learning for Drug-Target Interaction Prediction.

Yang Li, Guanyu Qiao, Xin Gao, Guohua Wang

Research output: Contribution to journalArticlepeer-review

31 Scopus citations


Motivation Identification of Drug-Target Interactions (DTIs) is an essential step in drug discovery and repositioning. DTI prediction based on biological experiments is time-consuming and expensive. In recent years, graph learning based methods have aroused widespread interest and shown certain advantages on this task, where the DTI prediction is often modeled as a binary classification problem of the nodes composed of drug and protein pairs. Nevertheless, in many real applications, labeled data are very limited and expensive to obtain. With only a few thousand labeled data, models could hardly recognize comprehensive patterns of DPP node representations, and are unable to capture enough commonsense knowledge, which is required in DTI prediction. Supervised contrastive learning gives an aligned representation of DPP node representations with the same class label. In embedding space, DPP node representations with the same label are pulled together, and those with different labels are pushed apart. Results We propose an end-to-end supervised graph co-contrastive learning model for DTI prediction directly from heterogeneous networks. By contrasting the topology structures and semantic features of the drug-protein-pair network, as well as the new selection strategy of positive and negative samples, SGCL-DTI generates a contrastive loss to guide the model optimization in a supervised manner. Comprehensive experiments on three public datasets demonstrate that our model outperforms the SOTA methods significantly on the task of DTI prediction, especially in the case of cold start. Furthermore, SGCL-DTI provides a new research perspective of contrastive learning for DTI prediction. Availability The research shows that this method has certain applicability in the discovery of drugs, the identification of drug-target pairs and so on.
Original languageEnglish (US)
JournalBioinformatics (Oxford, England)
StatePublished - Mar 21 2022

Bibliographical note

KAUST Repository Item: Exported on 2022-03-24
Acknowledgements: We thank the anonymous reviewers for their constructive suggestions. This work was supported by the National Natural Science Foundation of China [62072095,61806049,61771165] and the Heilongjiang Postdoctoral Science Foundation [LBH-Z20104].

ASJC Scopus subject areas

  • Biochemistry
  • Computational Theory and Mathematics
  • Computational Mathematics
  • Molecular Biology
  • Statistics and Probability
  • Computer Science Applications


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