GTR-CoT: Graph Traversal as Visual Chain of Thought for Molecular
  Structure Recognition
Authors: name: Jingchao Wang; name: Haote Yang; name: Jiang Wu; name: Yifan He; name: Xingjian Wei; name: Yinfan Wang; name: Chengjin Liu; name: Lingli Ge; name: Lijun Wu; name: Bin Wang; name: Dahua Lin; name: Conghui He
Published: 2025-06-09 08:47:10

Abstract: Optical Chemical Structure Recognition (OCSR) is crucial for digitizing
chemical knowledge by converting molecular images into machine-readable
formats. While recent vision-language models (VLMs) have shown potential in
this task, their image-captioning approach often struggles with complex
molecular structures and inconsistent annotations. To overcome these
challenges, we introduce GTR-Mol-VLM, a novel framework featuring two key
innovations: (1) the Graph Traversal as Visual Chain of Thought
mechanism that emulates human reasoning by incrementally parsing molecular
graphs through sequential atom-bond predictions, and (2) the data-centric
principle of Faithfully Recognize What You've Seen, which addresses
the mismatch between abbreviated structures in images and their expanded
annotations. To support model development, we constructed GTR-CoT-1.3M, a
large-scale instruction-tuning dataset with meticulously corrected annotations,
and introduced MolRec-Bench, the first benchmark designed for a fine-grained
evaluation of graph-parsing accuracy in OCSR. Comprehensive experiments
demonstrate that GTR-Mol-VLM achieves superior results compared to specialist
models, chemistry-domain VLMs, and commercial general-purpose VLMs. Notably, in
scenarios involving molecular images with functional group abbreviations,
GTR-Mol-VLM outperforms the second-best baseline by approximately 14 percentage
points, both in SMILES-based and graph-based metrics. We hope that this work
will drive OCSR technology to more effectively meet real-world needs, thereby
advancing the fields of cheminformatics and AI for Science. We will release
GTR-CoT at https://github.com/opendatalab/GTR-CoT.