Self-supervised Blending Structural Context of Visual Molecules for Robust Drug Interaction Prediction

Identifying drug-drug interactions (DDIs) is critical for ensuring drug safety and advancing drug development, a topic that has garnered significant research interest. While existing methods have made considerable progress, approaches relying solely on known DDIs face a key challenge when applied to drugs with limited data (e.g., novel and few-shot drugs): insufficient exploration of the space of unlabeled pairwise drugs. To address these issues, we innovatively introduce S2VM, a Selfsupervised Visual pretraining framework for pair-wise Molecules, to fully fuse structural representations and explore the space of drug pairs for DDI prediction. S2VM incorporates the explicit structure and correlations of visual molecules, such as the positional relationships and connectivity between functional substructures. Specifically, we blend the visual fragments of drug pairs into a unified input for joint encoding and then recover molecule-specific visual information for each drug individually.