RxnExBench is a multimodal benchmark designed to evaluate vision‑language models on the task of extracting structured chemical reaction data from dense figures in synthetic chemistry literature. The dataset, compiled from high‑impact journals, contains 3,565 expert‑annotated reactions and 2,361 molecular structures, organized under a unified schema of 15 reaction roles and 26 core fields. It also introduces a difficulty taxonomy, a modular annotation pipeline, and the Oracle‑MolRec protocol to separate molecular recognition from higher‑level reasoning, and shows that current state‑of‑the‑art models struggle as schema complexity and reasoning demands increase.
By Jiaxing Sun, Junyuan Gao, Ruikang Zhang, Hao Zheng, Lingli Ge, Xiao An, Jiang Wu, Huazheng Zeng, Jiahe Song, Chen Zhu, Haote Yang, Jingchao Wang, Lu Chen, Yuanyuan Cao, Ruijie Zhang, Shengxin Lu, Weijia Li, Lijun Wu, Conghui He
arXiv:2610.17183v1 Announce Type: new
Abstract: Current chemistry benchmarks primarily evaluate outcome prediction or reaction pathway generation, but rarely test whether a model can explain why an o...
By Aotian Chen, Frazier N. Baker, Reza Averly, Shan Zhang, Tianao Chen, Daniel Adu-Ampratwum, Xia Ning, Yuan Xue
The paper introduces MFP, a reaction yield prediction method that uses role-aware Morgan fingerprints. It computes count-based circular fingerprints for each reaction component, aggregates them by chemical role, and combines them with transformation-sensitive difference features into a fixed-length descriptor for a feed-forward neural regressor. On the Suzuki‑Miyaura and Buchwald‑Hartwig benchmarks, MFP achieves R² scores of 0.878 and 0.969 respectively, while training an order of magnitude faster than graph or Transformer-based alternatives.
By Chinmay Mirji, Prashant Shekhar, Foram Madiyar, Hao Peng
arXiv:2608. 16111v1 Announce Type: cross Abstract: Retrosynthesis is a cornerstone of drug discovery and organic synthesis.
By Mianzhi Liu, Fan Xiao, Zhiliang Yu, Huayang Huang, Yuke Li, Yi Yang, Wenbo Liu, Yu Wu
arXiv:2507.17448v2 Announce Type: replace-cross
Abstract: Retrosynthetic planning is a cornerstone of organic synthesis and drug discovery. Yet existing AI methods often rely on pattern matching rath...
By Situo Zhang, Hanqi Li, Lu Chen, Zihan Zhao, Xuanze Lin, Zichen Zhu, Danyu Luo, Bo Chen, Xin Chen, Kai Yu
arXiv:2607. 12771v1 Announce Type: new Abstract: Reaction mechanisms consist of the step-by-step sequences of elementary reactions that explain chemical transformations.
By Xingyu Dang, Haocheng Tang, Junmei Wang, Yanjun Li
The paper introduces VenusRX-Bench, a unified benchmark that evaluates forward reaction prediction, single‑step retrosynthesis, and EC‑number prediction for enzymatic reactions, integrating data from multiple biochemical databases with standardized curation and leakage‑controlled splits. It also presents VenusRX, a T5‑style sequence‑to‑sequence model that jointly learns these tasks, leveraging two‑stage training on millions of template‑expanded reactions and real biochemical data, with optional EC conditioning and molecule‑library‑constrained decoding to improve complex biomolecule generation. Across benchmark tasks and challenging generalization splits, VenusRX outperforms or matches existing chemical and enzymatic baselines, demonstrating that incorporating EC information and learned reaction representations yields a bidirectional relationship between reaction structure and catalytic function.
By Yutong Hu, Tianming Huang, Yanbo Zhao, Qiongyu Zhang, Shixiang Tang, Lei Bai, Ziyi Zhou, Liang Hong, Pan Tan
arXiv:2608. 03525v3 Announce Type: replace Abstract: In organic chemistry papers and patents, molecular structures, reaction schemes, and experimental conditions are often presented as molecular structure depictions, reaction diagrams, and complex tables or figures.
By Haote Yang, Jiang Wu, Jingchao Wang, Xingjian Wei, Lixin Ma, Linye Li, Chen Zhu, Xiaolong Wu, Yuheng Lu, Ziran Zhu, Junyuan Gao, Lingli Ge, Yuan Xu, Huijie Ao, QianQian Wu, Dechen Lin, Huaiyu Gu, Lu Chen, Shengxin Lu, ShaSha Wang, Yuanyuan Cao, Zhejia Yu, Ruijie Zhang, Zimai Tian, Jiaxing Sun, Yinfan Wang, Jiahe Song, Chuang Wang, Yubin Wang, Rui Nie, Hao Zheng, Bowen Jiang, Hongbin Lai, Yifan He, Chengjin Liu, Tingting Zhang, Liqun Wei, Lijun Wu, Bin Wang, Yuqiang Li, Guangyu Wang, Wei Li, Bowen Zhou, Dahua Lin, Conghui He
arXiv:2608. 06259v1 Announce Type: new Abstract: Reaction yield prediction remains challenging because labeled data are scarce and reaction space is both combinatorially large and sparsely populated, limiting the generalization of existing reaction representations.
By Yiting Zheng, Cheng Fang, Anthony Donofrio, Haote Li
R-GroundBench is a new diagnostic benchmark for evaluating AI models on R‑group grounding in Markush molecular editing, derived from real pharmaceutical patents. It includes a Multiple‑Choice VQA track with varying difficulty and modality splits, as well as an open‑ended Generation track. Experiments show a large performance gap: models score over 90% on easy VQA but drop to 56–66% on hard VQA, and generation exact match stays below 20% (and under 8% with visual input).
By Xin Wang, Zichuan Ying, Xinna Lin, Junqi Zhang, Hanyi Xiong, Tianyu Gao, Hairong Zhang, Qixiang Hua, Botian Shi, Zhenhailong Wang, Kaicheng Yu
arXiv:2603. 12666v2 Announce Type: replace-cross Abstract: Retrosynthesis prediction aims to identify reactants that can synthesize a given product molecule.
By Hanbum Ko, Chanhui Lee, Ye Rin Kim, Rodrigo Hormazabal, Sehui Han, Sungbin Lim, Sungwoong Kim
The paper introduces Align-React, a chemical reaction representation learning framework that incorporates atomic correspondence between reactants and products, an adapter for embedding reaction conditions, and a Reaction-Center-Aware attention mechanism. These components enable the model to capture precise molecular transformations and focus on critical functional groups, leading to improved performance across a variety of organic reaction tasks. The framework outperforms existing architectures on most benchmark datasets.
By Kaipeng Zeng, Xianbin Liu, Yu Zhang, Xiaokang Yang, Yaohui Jin, Yanyan Xu