GraphDDI: Graph Neural Network for Prediction of Drug-Drug Interaction

Drug-Drug Interactions (DDI) can trigger unexpected pharmacological consequences, including adverse drug events (ADE). The rise in polypharmacy underscores the importance of understanding how different drug molecules influence each other’s pharmacological activities and necessitates the investigation of potential interactions between newly developed drugs and existing medications. Traditional laboratory methods for DDI detection are time-consuming, making the development of computational prediction methods crucial. This study introduces GraphDDI, a machine learning method utilizing Graph Neural Networks (GNN) to predict DDI accurately. The proposed methodology, trained end-to-end, comprises three stages. (1) Featurization stage: A GNN extracts atomic features from two drugs separately. (2) Interaction stage: an interaction map is calculated between all atom pairs of the drugs. (3) Prediction stage: the model combines the interaction map and drug features to create a unified representation of the drug molecules. Subsequently, the model concatenates these representations and employs a feed-forward neural network to predict the DDI. We demonstrate the efficacy of our proposed model in predicting both the presence of DDI and the specific types of interactions (DDI events). Comparative analysis reveals that our framework surpasses existing models, achieving an F1 score of 0.98 in predicting the existence of drug-drug interactions and 0.90 in categorizing DDI event types. The code is available in our GitHub repository ( https://github.com/devalab/GraphDDI ).