Structure-Token Evidence-Anchored Reasoning for Scientific Chart Understanding

Charts are ubiquitous in scientific and financial literature for presenting structured data. However, chart reasoning remains challenging for multimodal large language models (MLLMs) due to the lack of high-quality training data, as well as the need for fine-grained visual grounding and precise numerical computation. To address these challenges, we first propose DuoChart, a scalable dual-source data pipeline that combines synthesized charts with real-world charts to construct diverse, high-quality chart training data. We then introduce CharTool, which equips MLLMs with external tools, including image cropping for localized visual perception and code-based computation for accurate numerical reasoning. Through agentic reinforcement learning on DuoChart, CharTool learns tool-integrated reasoning grounded in chart content. Extensive experiments on six chart benchmarks show that our method consistently improves over strong MLLM baselines across model scales. Notably, CharTool-7B outperforms the base model by +8.0% on CharXiv (Reasoning) and +9.78% on ChartQAPro, while achieving competitive performance with substantially larger or proprietary models. Moreover, CharTool demonstrates positive generalization to out-of-domain visual math reasoning benchmarks.

Chart question-answering (QA) benchmarks aim to pose questions that require visual reasoning to correctly answer, but models can often reach solutions through shortcuts or prior familiarity with a chart based on their own background knowledge. To strictly evaluate visual reasoning, we propose counterfactual charts where the chart-question task remains fixed, but underlying chart and the corresponding answer are varied. We introduce Chartographer, a framework to reverse engineer charts into executable code, validate reconstruction fidelity, generate seed-controlled counterfactual variants, and derive new answers from executable QA logic. We apply this framework to existing chart QA datasets and evaluate proprietary and open-source vision-language models (VLMs), measuring variation sensitivity and generalizability. Counterfactual charts reveal failures hidden by single-chart performance: VLMs often fail to generalize after answering the original chart correctly. We find failures are most prevalent when updated charts require novel visual reasoning pathways.

Advanced chart question answering requires both precise perception of small visual elements and multi-step reasoning across several subplots. While existing MLLMs are strong at understanding single plots, they often struggle with multi-step reasoning across multiple subplots. We propose HierVA, a hierarchical visual agent framework for chart reasoning that iteratively constructs and updates a working context in a joint image--text space. A high-level manager generates plans and maintains a compact context containing only key information, while specialized workers perform reasoning, gather evidence, and return results. In particular, the agent maintains separate visual and textual contexts, using a zoom-in tool to restrict the visual context. Experiments on the CharXiv reasoning subset demonstrate consistent improvements over strong multimodal baselines, and ablation studies verify that hierarchical architecture, scoped visual context, and distilled context contribute complementary gains.