MolSight: A Graph-Aware Vision-Language Model for Unified Chemical Image Understanding

Abstract: Using molecular large language models (LLMs) as a unified framework for understanding molecular structures and functions is emerging as a new trend in tasks such as molecular design and drug discovery. However, these models struggle to fully capture the visual representation of molecular structures, limiting their potential. While existing molecular vision-language models (VLMs) show promise, they still face challenges in structural alignment and lack the necessary topological modeling for accurate molecular understanding. To address this, we propose MolSight, a graph-aware vision-language model framework designed to enhance the understanding of molecular images by VLMs. MolSight integrates a Molecular Topology Module to inject chemical-bond adjacency information into vision tokens, and a Molecular Grounding Module to align visual features with chemical symbolic semantics. Our experiments demonstrate that MolSight significantly outperforms existing VLMs, molecular LLMs, and specialized tools across multiple chemical visual understanding tasks, achieving a new level of molecular image reasoning.