RxnMiner: A Multimodal Agent for Structured Reaction Data Extraction from Chemistry Figures

Jinbo Hu; Songren Zhang; Chuanxun Fu; Jinrui Huang; Zhen Hao Wong; Dongxu Cui; Haoran Fan; Muhao Ge; Zhen Jian; Jian Zhou; Chengxiang Luo; Han Lyu; Haoyi Tao; Chaozheng Huang; Hanzheng Li; ZiChen Wang; Hengtian Ma; Jinyang Dai; Nan Wang; Yanhui Hong; Xi Fang; Guolin Ke

arXiv · 2611.02826

RxnMiner: A Multimodal Agent for Structured Reaction Data Extraction from Chemistry Figures

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Abstract

Reaction data underpin machine learning for reaction prediction, condition recommendation, and retrosynthetic planning, yet extracting these data from literature figures still requires substantial manual effort. Many figures encode multiple experiments through shared templates, substituent tables, and product grids. Recovering concrete reaction records therefore requires molecular recognition, association of evidence with individual experimental entries, and reconstruction of indirectly specified participants. We present RxnMiner, a multimodal agent system that combines an expert-informed extraction procedure with a chemistry toolbox to coordinate these operations. The agent reads molecular structures, resolves shared and entry-specific evidence, and instantiates participants from templates to assemble source-linked reaction records. We also introduce ChemRxn-Bench, a benchmark of 603 reaction figures with 8,547 manually annotated and reviewed reaction records, evaluated under a common protocol for exact molecular identity and reactant-product pairing. On this benchmark, with Qwen3.8-Flash-Next as the backbone, RxnMiner raises stereochemistry-aware reaction macro-F1 from 21.0% under direct prediction to 71.0%, compared with 25.0% for the strongest existing extraction system. Across five backbones, it also outperforms the same base agent without the extraction procedure and chemistry toolbox by 9.4 to 25.5 points. Applied without human intervention to 10,107 literature figures, RxnMiner produces a silver corpus of 88,202 source-linked reaction records.

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Jinbo Hu, Songren Zhang, Chuanxun Fu, Jinrui Huang, Zhen Hao Wong, Dongxu Cui, Haoran Fan, Muhao Ge, Zhen Jian, Jian Zhou, Chengxiang Luo, Han Lyu, Haoyi Tao, Chaozheng Huang, Hanzheng Li, ZiChen Wang, Hengtian Ma, Jinyang Dai, Nan Wang, Yanhui Hong, Xi Fang, Guolin Ke. 2026-11-02. RxnMiner: A Multimodal Agent for Structured Reaction Data Extraction from Chemistry Figures. https://arxiv.org/abs/2611.02826

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