MPGNN-DSA: A Meta-path-based Graph Neural Network for drug-side effect association prediction

Abstract

Drug side effect is an important entity in the biomedical field, and identifying the association of the drug-side effects is a very important issue in pharmacological studies and drug risk-benefit. Traditional side effect discovery methods are mainly based on pharmacological experiments. These methods can detect the side effects of some drugs, but the identification process is time-consuming, expensive, and fails to identify some rare side effects. In recent years, with the expansion of massive biomedical data, computational-based methods are widely developed and applied for the task of drug-side effect association(DSA) prediction. However, existing methods cannot fully utilize public biomedical databases, and the complex semantic associations between drugs and side effects are not effectively captured, which leads to suboptimal model prediction performance. In this study, we develop a novel meta-path-based graph neural network model for drug-side effect association prediction. In the proposed model, we first construct a heterogeneous information network(HIN) by fusing multiple biological datasets. And then, a novel meta-path-based feature learning module is designed to learn high-quality representations of drugs and side effects. Finally, with the learned features, the prediction module utilizes a fully connected neural network to make prediction. In addition, comprehensive experiments is conducted, the results demonstrate the effectiveness of our model, indicating that the method will be a viable approach for DSA prediction tasks.