TopoAgent: A Structure-Aware Perception-to-Reasoning Framework for Diagram-to-Graph Topology Extraction with Large Vision-Language Models

Structural diagrams are widely used to represent complex systems and relational information across scientific, engineering, procedural, and spatial domains. Recent vision-language models (VLMs) have become increasingly capable of recognizing diagram elements and reasoning about their content, while complete diagram topology extraction remains comparatively underexplored. In this paper, we study diagram-to-graph topology extraction: extracting all diagram entities and the complete relations among them. To enable large-scale supervised training and systematic evaluation of this task, we introduce Knossos, a benchmark of 19,200 diagrams across six diverse domains, with 245,179 nodes and 439,740 edges. Its symbolic generation process provides exact alignment between rendered diagrams and annotations of complete topology, relation types, and connector geometry. To address the modeling challenge of complete topology extraction, we also present Ariadne, a structured framework that decomposes the task into node inventory extraction and source-conditioned edge prediction. Extensive experiments show that training on Knossos substantially improves complete topology extraction in smaller open-source VLMs. Ariadne further improves over one-step extraction under matched supervision, demonstrating the additional benefit of structured decomposition. It achieves the highest average Edge F1 among the evaluated methods on Knossos, while both backbone variants also improve over their unadapted counterparts on the real-world external benchmark. Code and benchmark are available at https://github.com/bangwayne/knossos_Ariadne_Public.

Can structured text replace vision for diagram reasoning? A wrong answer after textualization can arise because the representation omits information the question needs, or because the solver fails to use information that is present. We introduce a diagnostic protocol to distinguish these explanations. Using the same solver model and generation settings, we compare three input conditions: the original image, question-blind structure extracted by a vision-language model, or gold structure derived from the diagram source. Validity-triggered recovery tests truncation and schema failure, question-relevant fidelity measures preservation of answer-critical structure, and matched edge interventions test the effect of error location. On a reserved holdout of 240 public FlowGen diagrams, evaluated under a frozen protocol, gold structure reaches 87% accuracy while direct vision and learned text both remain below 30%. The aggregate comparison includes source-derived relation labels that may not be printed in the image and uses different learned and gold graph encodings, so it does not isolate extraction error alone. Retrying only invalid extractions makes nearly every public representation schema-valid yet leaves accuracy essentially unchanged. The public learned-text deficit relative to gold more than doubles with structural difficulty. Question-relevant topology predicts correctness better than whole-graph topology. In an exposed intervention study, a single answer-relevant edge edit reduces the primary solver's original-answer accuracy to near zero, while matched irrelevant edits largely preserve it. Supplied structure requires fewer solving tokens than vision, but learned acquisition removes this advantage at single use. These comparisons motivate evaluating acquired text by the answer-relevant evidence it preserves and by the solver's ability to use that representation.

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.