HyGNN: Drug-Drug Interaction Prediction via Hypergraph Neural Network

Abstract: Drug-Drug Interactions (DDIs) may hamper the functionalities of drugs, and in the worst scenario, they may lead to adverse drug reactions (ADRs). Predicting all DDIs is a challenging and critical problem. Most existing computational models integrate drug-centric information from different sources and leverage them as features in machine learning classifiers to predict DDIs. However, these models have a high chance of failure, especially for the new drugs when all the information is not available. This paper proposes a novel Hypergraph Neural Network (HyGNN) model based on only the SMILES string of drugs, available for any drug, for the DDI prediction problem. To capture the drug similarities, we create a hypergraph from drugs' chemical substructures extracted from the SMILES strings. Then, we develop HyGNN consisting of a novel attention-based hypergraph edge encoder to get the representation of drugs as hyperedges and a decoder to predict the interactions between drug pairs. Furthermore, we conduct extensive experiments to evaluate our model and compare it with several state-of-the-art methods. Experimental results demonstrate that our proposed HyGNN model effectively predicts DDIs and impressively outperforms the baselines with a maximum ROC-AUC and PR-AUC of 97.9% and 98.1%, respectively.