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 \textit{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 \textit{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 this https URL.
View on arXiv@article{wang2025_2506.07553,
title={ GTR-CoT: Graph Traversal as Visual Chain of Thought for Molecular Structure Recognition },
author={ Jingchao Wang and Haote Yang and Jiang Wu and Yifan He and Xingjian Wei and Yinfan Wang and Chengjin Liu and Lingli Ge and Lijun Wu and Bin Wang and Dahua Lin and Conghui He },
journal={arXiv preprint arXiv:2506.07553},
year={ 2025 }
}