MOL-Mamba: Enhancing Molecular Representation with Structural & Electronic Insights

Jingjing Hu, Dan Guo, Zhan Si, Deguang Liu, Yunfeng Diao, Jing Zhang, Jinxing Zhou, Meng Wang

Abstract: Molecular representation learning plays a crucial role in various downstream tasks, such as molecular property prediction and drug design. To accurately represent molecules, Graph Neural Networks (GNNs) and Graph Transformers (GTs) have shown potential in the realm of self supervised pre-training. However, existing approaches often overlook the relationship between molecular structure and electronic information, as well as the internal semantic reasoning within molecules. This omission of fundamental chemical knowledge in graph semantics leads to incomplete molecular representations, missing the integration of structural and electronic data. To address these issues, we introduce MOL-Mamba, a framework that enhances molecular representation by combining structural and electronic insights. MOL-Mamba consists of an **Atom & Fragment Mamba-Graph (MG)** for hierarchical structural reasoning and a **Mamba-Transformer (MT) fuser** for integrating molecular structure and electronic correlation learning. Additionally, we propose a **Structural Distribution Collaborative Training** and **E-semantic Fusion Training** framework to further enhance molecular representation learning. Extensive experiments demonstrate that MOL-Mamba outperforms state-of-the-art baselines across eight molecular datasets. Visualization experiments also provide insights into what MOL-Mamba has learned. We will release the code after the anonymous review process.