MDG-DDI: multi-feature drug graph for drug-drug interaction prediction

BACKGROUND: Drug-drug interactions (DDIs) frequently occur in combination therapy and may cause adverse effects or reduced efficacy. Existing computational approaches often fail to capture both the semantic information in drug sequences and the structural properties of drug molecules, limiting predictive power. RESULTS: We propose MDG-DDI, a deep learning framework that integrates a Frequent Consecutive Subsequence (FCS)-based Transformer encoder with a Deep Graph Network (DGN) to extract complementary semantic and structural features. These representations are fused and fed into a Graph Convolutional Network (GCN) for DDI prediction. Experiments on three benchmark datasets under transductive and inductive settings show that MDG-DDI consistently outperforms state-of-the-art methods, with particularly strong gains when predicting interactions involving unseen drugs. CONCLUSION: By jointly modeling substructure-level semantics and molecular graph structure, MDG-DDI achieves robust and accurate DDI prediction. The framework demonstrates improved generalization and offers potential for enhancing drug safety assessment and discovery.