ReactBench: A Benchmark for Topological Reasoning in MLLMs on Chemical Reaction Diagrams
Authors: Qiang Xu, Shengyuan Bai, Yu Wang, He Cao, Leqing Chen, Yuanyuan Liu, Bin Feng, Zijing Liu, +1 more
Organizations: International Digital Economy Academy, Shenzhen, China · University of Wisconsin–Madison
Abstract
Multimodal Large Language Models (MLLMs) excel at recognizing individual visual elements and reasoning over simple linear diagrams. However, when faced with complex topological structures involving branching paths, converging flows, and cyclic dependencies, their reasoning capabilities degrade sharply, even on tasks as basic as counting endpoints. Existing benchmarks fail to probe this gap, focusing on semantic comprehension rather than structural reasoning. We introduce ReactBench, a benchmark that reveals fundamental limitations in structural reasoning through chemical reaction diagrams. These real-world scientific diagrams offer an ideal testbed because they naturally span diverse structures from linear chains to cyclic graphs, while requiring both precise local recognition and coherent global reasoning. Our benchmark comprises 1,618 expert-annotated QA pairs across four hierarchical task dimensions. Extensive evaluation across 24 MLLMs reveals a significant performance gap exceeding 30% between anchor-based tasks and holistic structural reasoning tasks. Controlled ablations confirm this bottleneck lies in reasoning, not perception. These findings expose a fundamental deficit in structural understanding and establish directions for advancing visual reasoning.
While Large Language Models (LLMs) have revolutionized scientific text processing, they exhibit a significant capability gap when interpreting chemical reaction diagrams. We identify two fundamental bottlenecks restricting current systems: a Visual Deficit, where generic vision encoders struggle to resolve the strict topological connectivity of dense molecular graphs, and a Semantic Disconnect, where standard linear strings, such as SMILES, fail to effectively activate the model's latent chemical reasoning. To bridge these gaps, we propose the Chemical Visual Activation (ChemVA) framework, which employs a Visual Anchor mechanism to ground functional groups via hybrid-granularity detection, followed by a semantic alignment approach that translates visual features into entity names to maximize knowledge activation in LLMs. We evaluate our approach on OCRD-Bench, a newly constructed dataset featuring dense visual-semantic contexts and comprehensive reaction coverage to evaluate the full spectrum from recognition to reasoning. Extensive experiments on OCRD-Bench demonstrate that ChemVA achieves 92.0% structural recognition accuracy. By bridging visual and semantic bottlenecks, our framework delivers a consistent performance gain of approximately 20 percentage points across 9 diverse LLMs, enabling open-weight models to rival proprietary SOTA systems in complex chemical reasoning tasks.
Parsing chemical reaction diagrams from scientific literature is challenging due to heterogeneous layouts, intertwined visual elements, and the difficulty of integrating recognition and reasoning. Existing vision-language models advance multimodal understanding but still fail on complex diagrams, struggling to maintain spatial coherence and to integrate multidimensional information during reasoning. To address these issues, we propose MACReD, a hierarchical multi-agent framework that coordinates specialized agents for molecular perception, arrow understanding, text extraction, and reaction reconstruction within a unified VLM-guided architecture. The planning and perception layers use flexible, fine-grained detection to handle visual complexity, while the reasoning layer uses a multigraph fusion mechanism to integrate heterogeneous cues and enforce chemically consistent global reasoning. Experiments on the RxnScribe benchmark show that MACReD achieves state-of-the-art performance, with F1 scores of 75.2% and 84.6% under hard and soft match criteria, outperforming the RxnScribe baseline, which obtains 69.1% and 80.0%, respectively. These results demonstrate the robustness of MACReD across diverse diagram layouts, including multi-step and tree-structured reactions.
Reaction mechanisms consist of the step-by-step sequences of elementary reactions that explain chemical transformations. Learning the mechanism logic is therefore essential for enhancing the fundamental chemical intelligence of large language models (LLMs). The stepwise deduction of reaction mechanism aligns naturally with the reasoning paradigms of reasoning LLMs. However, current chemical LLMs primarily emphasize coarse-grained name reactions for product prediction and retrosynthesis, often leading to physical inconsistencies and hallucinations. In contrast, specialized small-scale generative models for mechanism inference typically suffer from restricted generalization capacity across diverse chemical spaces. To overcome these limitations, we built a novel, large-scale reasoning dataset of reaction mechanisms. Furthermore, we established the FukuyamaBench, a difficult benchmark derived from Fukuyama's Advanced Organic Reaction Mechanism book, to rigorously evaluate model performance on hierarchical mechanism reasoning. Our fine-tuned Qwen3-30B-A3B achieves 8.3% exact pathway match on FukuyamaBench Set~A, surpassing the specialized FlowER model (5.1%), demonstrating that mechanism-aware training substantially enhances chemical reasoning in language models.