A Drug-Drug Interaction Prediction Method Based on Atomic 3D Position Encoding and Elastic Message Passing Graph Neural Network

Drug-drug interaction (DDI) refers to the inhibitory or enhancing effects between different drugs. Existing DDI prediction methods primarily use graph neural networks (GNNs) to directly represent drug molecular features. However, they often ignore the 3D structures of different atoms within drug molecules and the impact of noise in GNNs on DDI prediction. Consequently, the accuracy of GNN-based DDI prediction remains unsatisfactory. To address these limitations, this study proposes a DDI prediction method based on atomic 3D position encoding and an elastic message passing graph neural network (A3DPE-EMPGNN). Firstly, we construct an atomic feature network based on an attention mechanism and a message passing neural network. This network leverages 3D position encoding based on the molecular centroid to learn the features of different atoms and their associated chemical bonds, thereby constructing a graph-based molecular representation. Secondly, we design a molecular feature network that incorporates an attention mechanism, utilizing multi-head attention to capture interaction information between different drug molecules. Thirdly, we employ an adversarial attack detection and defense strategy, integrating supervised and contrastive loss learning to optimize the model and enhance its robustness while performing DDI prediction. Lastly, we evaluate the effectiveness of A3DPE-EMPGNN on two real-world datasets. Experimental results clearly demonstrate that our method achieves over 98% accuracy across ACC, AUC, AP, and F1-score, outperforming state-of-the-art GNN-based models.