Daily Papers

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.

Learning a precise dynamics model can be crucial for offline reinforcement learning, which, unfortunately, has been found to be quite challenging. Dynamics models that are learned by fitting historical transitions often struggle to generalize to unseen transitions. In this study, we identify a hidden but pivotal factor termed dynamics reward that remains consistent across transitions, offering a pathway to better generalization. Therefore, we propose the idea of reward-consistent dynamics models: any trajectory generated by the dynamics model should maximize the dynamics reward derived from the data. We implement this idea as the MOREC (Model-based Offline reinforcement learning with Reward Consistency) method, which can be seamlessly integrated into previous offline model-based reinforcement learning (MBRL) methods. MOREC learns a generalizable dynamics reward function from offline data, which is subsequently employed as a transition filter in any offline MBRL method: when generating transitions, the dynamics model generates a batch of transitions and selects the one with the highest dynamics reward value. On a synthetic task, we visualize that MOREC has a strong generalization ability and can surprisingly recover some distant unseen transitions. On 21 offline tasks in D4RL and NeoRL benchmarks, MOREC improves the previous state-of-the-art performance by a significant margin, i.e., 4.6% on D4RL tasks and 25.9% on NeoRL tasks. Notably, MOREC is the first method that can achieve above 95% online RL performance in 6 out of 12 D4RL tasks and 3 out of 9 NeoRL tasks.

Optical Chemical Structure Recognition (OCSR) aims to translate molecular diagrams in scientific literature into machine-readable formats, but current systems remain unreliable on real-world images due to substantial visual and chemical complexity. We introduce MOSAIC, a dual-dimensional difficulty framework with 37 fine-grained labels that jointly characterize visual interference and chemical semantic challenges in molecular diagrams. Based on this framework, we construct MolRecBench-Wild, a benchmark of 5,029 structures from 820 recent chemistry papers, covering the full difficulty spectrum observed in real publications. To enable faithful semantic evaluation beyond SMILES and MolFile, we propose CARBON, a representation language capable of expressing valence variations, icon-based groups, and other non-standard chemical semantics. We further adopt a dual-track evaluation protocol supporting both CARBON and SMILES outputs for broad model compatibility. Comprehensive experiments over 18 OCSR-capable models reveal severe performance degradation on MolRecBench-Wild, exposing a large gap between previous patent benchmarks and real-world academic scenarios.

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. Such information is difficult for general-purpose document parsing systems to directly convert into machine-readable data. This limits data production for organic chemistry knowledge base construction and for AI for Chemistry tasks such as reaction prediction, retrosynthesis, condition recommendation, molecular property prediction, and drug molecule design. This report introduces MinerU-Chem, a document parsing system for organic chemistry literature integrated into the MinerU online platform. Built on top of MinerU's general document parsing pipeline, MinerU-Chem adds five chemistry-specific modules: chemistry relevance filtering, molecular structure detection, molecule identifier extraction, molecular structure recognition, and reaction scheme parsing. Together, these modules convert organic-chemistry-related image regions in documents into a Molecule Summary List and a Reaction Summary List. For molecular structure recognition, MinerU-Chem uses CARBON (Complex Atomic Representation and Bonding Object Notation) as its core representation. CARBON enables recognition results to preserve both the visual layout of the original image and complex chemical semantics, while supporting the export of standard downstream formats such as MolFile and SMILES. On the SMILES-evaluable subset of MolRecBench-Wild (N=2,392), MinerU-Chem's molecular structure recognition module achieves a SMILES exact-match accuracy of 93.02%, outperforming the best evaluated comparison system, GPT-5.6-Sol (74.87%), by 18.15 percentage points. The system has been integrated into the MinerU online platform and is available at https://mineru.net/OpenSourceTools/Extractor .