A Novel Method to Predict Drug-Target Interactions Based on Large-Scale Graph Representation Learning.

Abstract

Simple SummaryThe traditional process of drug development is lengthy, time-consuming, and costly, whereas very few drugs ever make it to the clinic. The use of computational methods to detect drug side effects greatly reduces the deficiencies in drug clinical trials. Prediction of drug-target interactions is a key step in drug discovery and repositioning. In this article, we proposed a novel method for the prediction of drug-target interactions based on large-scale graph representation learning. This method can be helpful to researchers in clinical trials and drug research and development.Identification of drug-target interactions (DTIs) is a significant step in the drug discovery or repositioning process. Compared with the time-consuming and labor-intensive in vivo experimental methods, the computational models can provide high-quality DTI candidates in an instant. In this study, we propose a novel method called LGDTI to predict DTIs based on large-scale graph representation learning. LGDTI can capture the local and global structural information of the graph. Specifically, the first-order neighbor information of nodes can be aggregated by the graph convolutional network (GCN); on the other hand, the high-order neighbor information of nodes can be learned by the graph embedding method called DeepWalk. Finally, the two kinds of feature are fed into the random forest classifier to train and predict potential DTIs. The results show that our method obtained area under the receiver operating characteristic curve (AUROC) of 0.9455 and area under the precision-recall curve (AUPR) of 0.9491 under 5-fold cross-validation. Moreover, we compare the presented method with some existing state-of-the-art methods. These results imply that LGDTI can efficiently and robustly capture undiscovered DTIs. Moreover, the proposed model is expected to bring new inspiration and provide novel perspectives to relevant researchers.