KnowMol: Advancing Molecular Large Language Models with Multi-Level Chemical Knowledge

Hong Chang (Institute of Computing Technology, Chinese Academy of Sciences) · RuiBing Hou (Chinese Academy of Sciences) · Shiguang Shan (Chinese Academy of Sciences) · Xilin Chen (Institute of Computing Technology, Chinese Academy of Sciences) · Zaifei Yang (Hong Kong University of Science and Technology)
ai-driven molecular analysischemically-informative representationdataset constructionfine-grained molecular annotationsknowmol-100kmolecular applicationsmolecular generationmolecular large language modelsmolecular representation strategiesmolecular understandingmulti-modalperformance evaluationpretrainingtextual descriptions

The molecular large language models have garnered widespread attention due to their promising potential on molecular applications. However, current molecular large language models face significant limitations in understanding molecules due to inadequate textual descriptions and suboptimal molecular representation strategies during pretraining. To address these challenges, we introduce KnowMol-100K, a large-scale dataset with 100K fine-grained molecular annotations across multiple levels, bridging the gap between molecules and textual descriptions. Additionally, we propose chemically-informative molecular representation, effectively addressing limitations in existing molecular representation strategies. Building upon these innovations, we develop KnowMol, a state-of-the-art multi-modal molecular large language model. Extensive experiments demonstrate that KnowMol achieves superior performance across molecular understanding and generation tasks.