Multi-scale biomedical knowledge networks are expanding with emerging experimental technologies  . Link prediction is increasingly used especially in bipartite biomedical networks  . We propose a Graph Neural Networks (GNN) method, namely Graph Pair based Link Prediction model (GPLP), for predicting biomedical network links simply based on their topological interaction information. In GPLP, 1-hop subgraphs extracted from known network interaction matrix is learnt to predict missing links. To evaluate our method, three heterogeneous biomedical networks were used, i.e. Drug-Target Interaction network (DTI), Compound-Protein Interaction network (CPI) from NIH Tox21, and Compound-Virus Inhibition network (CVI). In 5-fold cross validation, our proposed GPLP method significantly outperforms over the state-of-the-art baselines. Besides, robustness is tested with different network incompleteness  . Our method has the potential applications in other biomedical networks.
Multi-scale biomedical knowledge networks are expanding with emerging experimental technologies that generates multi-scale biomedical big data . Link prediction is increasingly used especially in bipartite biomedical networks to identify hidden biological interactions and relationshipts between key entities such as compounds, targets, gene and diseases . We propose a Graph Neural Networks (GNN) method, namely Graph Pair based Link Prediction model (GPLP), for predicting biomedical network links simply based on their topological interaction information. In GPLP, 1-hop subgraphs extracted from known network interaction matrix is learnt to predict missing links. To evaluate our method, three heterogeneous biomedical networks were used, i.e. Drug-Target Interaction network (DTI), Compound-Protein Interaction network (CPI) from NIH Tox21, and Compound-Virus Inhibition network (CVI). Our proposed GPLP method significantly outperforms over the state-of-the-art baselines. In addition, different network incompleteness is analysed with our devised protocol, and we also design an effective approach to improve the model robustness towards incomplete networks . Our method demonstrates the potential applications in other biomedical networks.
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