GCNGAT: Drug–disease association prediction based on graph convolution neural network and graph attention network

Abstract

Predicting drug–disease associations can contribute to discovering new therapeutic potentials of drugs, and providing important association information for new drug research and development. Many existing drug–disease association prediction methods have not distinguished relevant background information for the same drug targeted to different diseases. Therefore, this paper proposes a drug–disease association prediction model based on graph convolutional network and graph attention network (GCNGAT) to reposition marketed drugs under the distinguishment of background information. Firstly, in order to obtain initial drug–disease information, a drug–disease heterogeneous graph structure is constructed based on all known drug–disease associations. Secondly, based on the heterogeneous graph structure, the corresponding subgraphs of each group of drug–disease association pairs are extracted to distinguish different background information for the same drug from different diseases. Finally, a model combining Graph neural network with global Average pooling (GnnAp) is designed to predict potential drug–disease associations by learning drug–disease interaction feature representations. The experimental results show that adding subgraph extraction can effectively improve the prediction performance of the model, and the graph representation learning module can fully extract the deep features of drug–disease. Using the 5-fold cross-validation, the proposed model (GCNGAT) achieves AUC (Area Under the receiver operating characteristic Curve) values of 0.9182 and 0.9417 on the PREDICT dataset and CDataset dataset, respectively. Compared with other predictors on the same dataset (PREDICT dataset), GCNGAT outperforms the existing best-performing model (PSGCN), with a 1.58% increase in the AUC value. It is anticipated that this model can provide experimental reference for drug repositioning and further promote the drug research and development process.