A unified drug–target interaction prediction framework based on knowledge graph and recommendation system

Qing Ye, Chang-Yu Hsieh, Ziyi Yang, Yu Kang, Jiming Chen, Dongsheng Cao (), Shibo He () and Tingjun Hou ()
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Qing Ye: Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University
Chang-Yu Hsieh: Tencent Quantum Laboratory
Ziyi Yang: Tencent Quantum Laboratory
Yu Kang: Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University
Jiming Chen: Zhejiang University
Dongsheng Cao: Central South University
Shibo He: Zhejiang University
Tingjun Hou: Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University

Nature Communications, 2021, vol. 12, issue 1, 1-12

Abstract: Abstract Prediction of drug-target interactions (DTI) plays a vital role in drug development in various areas, such as virtual screening, drug repurposing and identification of potential drug side effects. Despite extensive efforts have been invested in perfecting DTI prediction, existing methods still suffer from the high sparsity of DTI datasets and the cold start problem. Here, we develop KGE_NFM, a unified framework for DTI prediction by combining knowledge graph (KG) and recommendation system. This framework firstly learns a low-dimensional representation for various entities in the KG, and then integrates the multimodal information via neural factorization machine (NFM). KGE_NFM is evaluated under three realistic scenarios, and achieves accurate and robust predictions on four benchmark datasets, especially in the scenario of the cold start for proteins. Our results indicate that KGE_NFM provides valuable insight to integrate KG and recommendation system-based techniques into a unified framework for novel DTI discovery.

Date: 2021
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DOI: 10.1038/s41467-021-27137-3

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