xmubiocode/MMPCS: MMPCS

- MMPCS: Multi-view Molecular Pretraining Based on Consistency Information and Specific Information Chenyang Xie1, +, Yingying Song1, +, Song He2, *, Xiaochen Bo2, *, Zhongnan Zhang1, * The goal of molecular representation learning is to automate the extraction of molecular features, a critical task in cheminformatics and drug discovery. While pretraining models using multiple views like SMILES, two-dimensional graphs, and three-dimensional conformations have advanced the field, integrating them effectively to produce superior representations remains a challenge. To bridge this gap, we propose a novel multi-view molecular pretraining method termed MMPCS, which explicitly factorizes representations into consistency and specific information. Our approach utilizes the Graph Isomorphism Network and the RoBERTa model to encode two-dimensional molecular topological graphs and SMILES sequences, respectively. Each resulting molecular embedding is decomposed into a shared consistency component and a view-specific remainder. An autoencoder then aligns the consistency information across views. The combined consistency and view-specific representations serve as input for downstream tasks, enabling precise and task-aware predictions. When benchmarked against 16 state-of-the-art molecular pretraining methods, MMPCS achieved the highest average performance across both classification and regression tasks for molecular property prediction. It also delivered outstanding results in predicting drug-target binding affinity and cancer drug response, demonstrating its robustness and broad applicability. Additionally, a case study on the SARS-CoV-2 Omicron variant highlights the potential of MMPCS in facilitating drug repurposing efforts.