Drug-target interaction prediction based on spatial consistency constraint and graph convolutional autoencoder

BACKGROUND: Drug-target interaction (DTI) prediction plays an important role in drug discovery and repositioning. However, most of the computational methods used for identifying relevant DTIs do not consider the invariance of the nearest neighbour relationships between drugs or targets. In other words, they do not take into account the invariance of the topological relationships between nodes during representation learning. It may limit the performance of the DTI prediction methods. RESULTS: Here, we propose a novel graph convolutional autoencoder-based model, named SDGAE, to predict DTIs. As the graph convolutional network cannot handle isolated nodes in a network, a pre-processing step was applied to reduce the number of isolated nodes in the heterogeneous network and facilitate effective exploitation of the graph convolutional network. By maintaining the graph structure during representation learning, the nearest neighbour relationships between nodes in the embedding space remained as close as possible to the original space. CONCLUSIONS: Overall, we demonstrated that SDGAE can automatically learn more informative and robust feature vectors of drugs and targets, thus exhibiting significantly improved predictive accuracy for DTIs. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-023-05275-3.