Enhancing Drug-Drug Interaction Prediction by Knowledge Graph Embedding

Drug-drug interactions (DDIs) refer to the synergistic or antagonistic effects between different drugs. Synergistic effects can enhance therapeutic efficacy, while antagonistic effects may reduce efficacy or even trigger adverse reactions, worsening the patient's condition. Most existing DDI prediction studies overlook the features of chemical bonds between atoms within drug molecules and the interaction types between drug pairs, which to some extent limits the accuracy and reliability of the predictions. In view of this, we have designed a novel framework called KGE-DDI, which leverages knowledge graph embedding (KGE) technology to enhance the prediction of DDIs. Specifically, for individual drug molecules, KGE-DDI first integrates the features of atoms and chemical bond. Then, by introducing attention mechanisms and graph neural network technology, it learns representations of the drug molecules. For pairs of drug molecules, KGE-DDI models their interactions utilizing atom-level Pearson correlation matrices. Finally, it predicts the interactions between drug pairs by employing our designed scoring function. We conducted comprehensive experiments under both transductive and inductive settings, and the results demonstrate the effectiveness and superiority of KGE-DDI in three scenarios: (existing drug, existing drug), (new drug, new drug), and (new drug, existing drug).