Medication Recommendation via Dual Molecular Modalities and Multi-Substructure Distillation

Medication recommendation combines patient medical history with biomedical knowledge to assist doctors in determining medication combinations more accurately and safely. Existing approaches based on molecular knowledge overlook the atomic geometric structure of molecules, failing to capture the high-dimensional characteristics and intrinsic physical properties of medications, leading to structural confusion and the inability to extract useful substructures from individual patient visits. To address these limitations, we propose BiMoRec, which overcomes the inherent lack of molecular essential information in 2D molecular structures by incorporating 3D molecular structures and atomic properties. To retain the fast response required of recommendation systems, BiMoRec maximizes the mutual information between the two molecular modalities through bimodal graph contrastive learning, achieving the integration of 2D and 3D molecular graphs, and finally distills substructures through interaction with single patient visits. Specifically, we use deep learning networks to construct a pre-training method to obtain representations of 2D and 3D molecular structures and substructures, and we use contrastive learning to derive mutual information. Subsequently, we generate fused molecular representations through a trained GNN module, re-determining the relevance of substructure representations in conjunction with the patient's clinical history information. Finally, we generate the final medication combination based on the extracted substructure sequences. Our implementation on the MIMIC-III and MIMIC-IV datasets demonstrates that our method achieves state-of-the-art performance. Compared to the next best baseline, our model improves accuracy by 1.8\% while maintaining the same level of DDI as the baseline.