Graphs are a fundamental data structure underlying many problems in the natural and social sciences. Over the past decade, Graph Neural Networks (GNNs) have dominated graph machine learning, supported by solid theoretical foundations. Yet scientists often understand graph structure through vision: chemists read molecular diagrams and social scientists inspect network visualizations. Despite decades of work on graph visualization, most graph learning pipelines still treat graphs purely as symbolic structures, rarely leveraging the visual form of graphs. We argue that this gap deserves renewed attention in the era of powerful vision and vision-language models. This survey provides a first systematic overview of the emerging area we term vision meets graphs, which treats visual depictions of graphs as first-class inputs for reasoning and learning. We organize existing work into three threads. Vision for Graph Reasoning studies how models can use visual depictions of graphs to understand structure and carry out multi-step reasoning. Vision for Graph Learning explores how visual features can complement or augment graph encoders beyond known limitations of message passing. Scientific Graphs examines domains where standardized depiction conventions support both reasoning and learning. Our goal is to clarify what current methods can and cannot do, and to outline a path toward foundation models that perceive and reason about graphs as scientists do.
Reasoning over text-attributed graphs (TAGs) requires large language models (LLMs) to combine a node's text with evidence distributed across its neighbourhood. Existing methods fix the set of accessible neighbours before generation, forcing reasoning to operate over a static context and preventing the model from acquiring missing evidence during inference. We argue that neighbour selection should itself be part of the reasoning process. To this end, we propose Call Neighbours Yourself (CNY), a framework that enables LLMs to proactively explore graph neighbourhoods through topology-constrained graph-walk actions. Instead of reasoning over a pre-selected neighbour set, CNY exposes lightweight neighbour previews and learns when to expand candidate neighbours for additional evidence. To address the delayed-credit challenge of neighbour exploration, we introduce destination-conditioned on-policy self-distillation, which retrospectively evaluates a selected neighbour after its content is revealed and converts the resulting change in action preference into an action-level training signal. Experiments on standard TAG reasoning benchmarks under a unified raw-text setting show that CNY consistently outperforms fixed-context post-training baselines. Furthermore, the learned exploration policy transfers to unseen graphs and to a graph-level task not encountered during training. Code is available at https://github.com/superallen13/CNY.
Despite their potential in standardized graph tasks, Large Language Models (LLMs) remain brittle to real-world shifts in node identifiers and task formulation. While deterministic graph tools are invariant to such shifts, extracting topological structures from noisy text is highly fragile for LLMs, which often overfit to surface patterns. Moreover, mitigating these parsing failures via multi-agent systems incurs prohibitive latency. To address this, we propose GRAIN, a single-agent framework optimized via reinforcement learning. GRAIN models reasoning as a semantic parsing and tool-execution pipeline, guided by a Structure Invariance Reward. By validating extracted intermediate graphs against ground-truth topologies, this reward forces the LLM to learn robust text-to-structure mappings rather than memorizing linguistic artifacts. We also introduce GRIT, a benchmark evaluating sensitivity to such linguistic shifts. GRAIN outperforms multi-agent baselines by 16.45\% in accuracy with approximately 24\% lower latency. Furthermore, it demonstrates superior structural generalization, halving the out-of-distribution (OOD) gap of SFT models (from 15.77\% to 7.80\%) and maintaining robustness on large-scale graphs beyond the training distribution.
We introduce ClosureBench, a constructive benchmark for compositional graph-relational reasoning with programmatically verified ground truth. Unlike fixed-test-set benchmarks vulnerable to data contamination, ClosureBench generates instances on demand: each task's reference answer is computed by executing a program in the Ein tensor-logic language, ensuring machine-verified correctness. The benchmark spans 26 task categories at three compositional levels (L1-L3), with difficulty controlled along three independent axes: graph size, edge density, and query depth. We evaluate models from 1.5B open weights to frontier systems (o3, GPT-4.1, Gemini 2.5, Claude Sonnet 4) and report three findings. First, because the benchmark can always supply fresh instances, it measures memorisation directly: a model fine-tuned on a fixed test set shows a 19.3 percentage-point gap between its accuracy on seen and on fresh instances, which a static test set cannot reveal. We scope this to supervised fine-tuning on answer pairs, not pretraining contamination. Second, accuracy falls as graph size and query depth increase, and the two interact: models misread the graph from its natural-language description and then reason correctly over the wrong graph, so even the strongest frontier model degrades from atomic to compositional queries. This bottleneck is a property of the reasoning rather than the input format: it persists when the graph is given as a JSON edge list or an adjacency matrix instead of prose. Third, a 4B model fine-tuned to emit executable programs rather than answers stays nearly flat across compositional levels and approaches frontier accuracy (94.3% on held-out instances) at a fraction of the token cost. This holds for two program targets, Ein and Python+NetworkX, so it is a property of verified program synthesis rather than of one language.
Open-vocabulary referring segmentation in 3D Gaussian Splatting (3DGS) requires a neural model to select Gaussian primitives according to free-form language expressions. Existing 3DGS-based methods usually rely on global text-region similarity, which is weak for queries involving attributes, reference objects, spatial relations, and fine-grained parts. This often causes target-reference confusion, granularity mismatch, part-whole leakage, and relation violations. We propose QAGaussian, a query-adaptive neural reasoning framework for language-guided Gaussian primitive selection. QAGaussian first learns query-conditioned multi-scale Gaussian slots as differentiable candidates whose receptive fields are shaped by the input expression. It then builds a relation-aware slot graph with language-conditioned edge weighting to propagate target-reference, attribute, part-whole, and contextual evidence. A granularity-adaptive router softly combines region-level, object-level, part-level, attribute-aware, and relation-aware mask branches, followed by relation-constrained refinement for spatial, part-whole, attribute, and geometric consistency. QAGaussian is pretrained only on Mosaic3D-5.6M for Gaussian-text alignment and evaluated on independent benchmarks without target-dataset fine-tuning. It achieves 47.2 Avg. mIoU and 63.2 Avg. F1, outperforming the strongest 3DGS referring baseline by 2.7 mIoU points and 2.9 F1 points. It also improves Part-mIoU from 38.6 to 43.4, Rel-mIoU from 44.4 to 50.8, and reduces target-reference confusion from 10.8 to 7.4. These results demonstrate that query-conditioned slot learning, relation-aware graph reasoning, and adaptive routing provide an effective neural modeling strategy for open-vocabulary referring segmentation in 3DGS. The code is available at https://github.com/zqeslwyz/QAGaussian.
Fali Wang, Ali Al-Lawati, Iliyas Bektas +5cs.CL cs.AI cs.LG
Graph reasoning provides a promising testbed for evaluating the reasoning ability of large language models (LLMs), as graph instances can be programmatically generated, structurally controlled, and naturally scaled to long-input settings. However, existing graph reasoning benchmarks have limited coverage of data complexity, rely heavily on manual construction, and lack unified evaluation across text-based and code-based reasoning modes. To address these limitations, we propose {\dataset}, a five-stage \textit{semi-automatic} framework for constructing complex graph reasoning benchmarks. It expands benchmark coverage along five dimensions: \textit{Graph Size}, \textit{Task Complexity}, \textit{Task Description}, \textit{Graph Loading}, and \textit{Task Source}. The framework uses an LLM-based data generator to automatically produce task descriptions, graph data, reference solutions, graph-loading scripts, question forms, and evaluation scripts, while retaining human validation at key quality-control stages. Based on it, we construct a benchmark with $202$ tasks and evaluate LLMs under text-based, code-based, and augmented reasoning settings. Experiments show that the complexity dimensions reveal model limitations that are less visible in existing benchmarks; existing fine-tuned models struggle to generalize to GraphGym, whereas retrieval-augmented methods show scenario-dependent adaptability, improving textual reasoning but not consistently improving coding reasoning. These findings suggest that ours serves as a challenging and diagnostic benchmark for graph reasoning and provides empirical guidance for future enhancement methods. Code and dataset will be published soon.
Multi-entity compositional questions pose significant challenges to existing retrieval-augmented language models. Conventional methods fall into a dilemma: standard RAG lacks dynamic reasoning, traditional Graph-RAG is limited by structural sparsity, and LLM-constructed Graph-RAG incurs prohibitive costs. We propose \textbf{\fwa}, a unified framework that embeds unstructured text into structured knowledge graphs, creating a heterogeneous network for flexible evidence retrieval. Reasoning is formulated as adaptive structure induction, learned via a robust two-stage process: (1) imitation learning distills heuristic expert signals, and (2) reinforcement learning refines the policy using LLM-driven preference rewards. Experiments demonstrate that {\fwa} effectively merges textual richness with structural knowledge, outperforming SOTA baselines in answer accuracy and reasoning fidelity while maintaining extremely low token costs and near real-time inference((code available at https://github.com/wjywjy123/HyGRL) .
Writing a literature review requires a deep understanding of the relationships among cited papers: how they build on, challenge, or offer alternative perspectives to one another. We present Graph-Reasoning Aided Survey Planning (GRASP), a framework combining LLM planning for related work generation with graph algorithms to extract key relationships among cited papers. Our two-layer graph structure consists of a Graph of Thoughts and an Argument-Counterargument Planning Network, representing the cited papers at different levels of granularity, and we apply topology-aware pruning via a Steiner tree to identify the core inter-paper relationships captured in our graph. Our citation analysis-based evaluation shows that GRASP generates related work sections (RWS) that closely match human-written targets in terms of the discourse roles, intents, and grouping of citations.
Vision-language models (VLMs) are increasingly used to read maps for logistics, delivery, and accessible navigation, where the output is an actionable decision (a route, a pin, a parking choice) that must respect the road network. Yet most map benchmarks grade free text or multiple-choice answers that cannot be verified against the underlying graph. We present MapReason-OSM, a benchmark and evaluation harness for graph-verifiable mobility decisions on self-rendered OpenStreetMap panels. We render fixed-style maps for ten U.S. downtowns at two aligned zoom scales, overlay a consistent marker grammar, and pair each panel with a hidden street graph and exact oracles, yielding 6,000 instances (12,000 panels across the two zooms) over 12 routing, facility-location, and visual disambiguation tasks. Models return structured decisions that we snap back to the graph and score for validity, legality, optimality, and constraint satisfaction, plus cross-zoom consistency. Across seven VLMs, models read maps and route simply but fail at graph cost reasoning (single-facility pin placement is near chance even for frontier reasoning models), and are frequently scale-inconsistent. We release the benchmark, harness, and deterministic generator. Code and data: https://github.com/Vi-Sri/mapreason-osm
Table Question Answering (TableQA) aims to reason over tables to answer user queries. Existing research treats all questions uniformly and evaluates solely through overall accuracy, obscuring a critical reality that LLMs excel at simple lookups yet struggle with complex operations like aggregation and arithmetic. To reveal this disparity, we introduce a novel \emph{Operation-wise TableQA} task with a fine-grained question taxonomy and release two datasets named WikiTQ-ow and TabFact-ow for evaluation. As for modeling bottlenecks, existing methods flatten tables into linearized texts, disrupting inherent structures and inducing the ``lost-in-the-middle'' issue, which poses a primary barrier to complex cross-row reasoning. Moreover, they typically reason from scratch, neglecting reusable patterns shared across similar operations. To address these limitations, we propose a Skill-augmented Table Graph Reasoning (SkillTGR) framework for self-evolving structured reasoning. Specifically, SkillTGR represents tables as attributed graphs with explicit row-column-cell structures, where LLMs plan and execute dynamic chains to retrieve evidence subgraphs for graph traversal reasoning. Based on this, SkillTGR builds a hierarchical SkillBank to distill reason trajectories into abstract skills under cognitive heuristics, then hybrid retrieves both successful and failed skills for contrastive augmented table graph reasoning, thereby enabling the continual self-evolution. Extensive experiments demonstrate that SkillTGR achieves superior performance with an average of 5.91\% overall and 6.03\% operation-wise improvement, also reducing 19.76\% token consumption and 27.64\% inference latency. Our codes and data will be released upon publication.
Donald Loveland, Puja Trivedi, Ari Weinstein +2cs.LG
Large Language Models (LLMs) have shown promise for reasoning over Text-Attributed Graphs (TAGs). However, applying LLMs to graphs requires linearizing their structure into sequences, introducing distortion rooted in the graph bandwidth problem. While this distortion has been shown to degrade performance, it is often attributed to prompt design or model scale, leaving the underlying mechanism unclear. In this work, we show \textit{how} rotary positional embeddings turn graph linearization into bandwidth-dependent attention decay, suppressing attention between graph-adjacent nodes that are forced far apart in the serialized sequence. This shifts the focus of LLM-based graph reasoning from prompt engineering and scaling toward correcting attention misalignment. Motivated by this analysis, we propose \textbf{G}raph-\textbf{a}ligned \textbf{L}anguage \textbf{A}ttention (\textbf{GaLA}), a lightweight, inference-time modification for LLMs. GaLA biases attention toward graph-adjacent nodes while preserving the LLM's sequential inductive biases. Across TAG benchmarks, GaLA improves performance with negligible overhead, demonstrating that distortion is a correctable bottleneck in LLM-based graph reasoning.
Large-scale web-harvested datasets have fueled the progress of cross-modal retrieval but inevitably suffer from noisy correspondence, which severely degrades model generalization. Existing methods primarily address this by filtering out noise or seeking a substitute label, yet they predominantly remain bound by a "Discrete Selection" paradigm. We argue that relying on a single discrete proxy induces Single-Point Fragility and Discretization Error. To overcome these limitations, we propose a novel framework, Intra-modal Neighbor-aware Noise Rectification (IN2R), which shifts the paradigm from searching for a substitute to synthesizing a reliable supervision target. Leveraging the intrinsic geometric stability of intra-modal data, IN2R employs a Graph Refiner to perform relational reasoning over neighbors retrieved from a dynamic Cross-Model Memory. Instead of propagating discrete labels, our method synthesizes a continuous, soft prototype that reflects the consensus of the local semantic neighborhood, effectively rectifying inter-modal misalignment. Extensive experiments on Flickr30K, MS-COCO, and CC152K demonstrate that IN2R significantly outperforms state-of-the-art methods. Our code and pre-trained models are publicly available at https://github.com/liuyyy111/IN2R.
Grounding radiology report descriptions to 3D CT volumes is essential for verifiable clinical interpretation, yet remains challenging due to the semantic-spatial gap between free-text narratives and volumetric anatomy. Existing report-assisted and vision-language grounding methods typically rely on phrase-level alignment or dense pixel supervision, resulting in limited lesion-wise correspondence and suboptimal localization accuracy. We propose GLeVE, a graph-guided lesion grounding framework with anatomical prior verification and octree-based autoregressive refinement. GLeVE treats each lesion description as an atomic semantic unit and encodes organ attribution, attributes, and inter-lesion relations through relation-aware graph reasoning to produce discriminative lesion-wise queries. Anatomy-aware proposal generation with region-level verification enforces one-to-one text-lesion alignment, while hierarchical octree refinement progressively improves boundary delineation. Experiments on AbdomenAtlas 3.0 demonstrate consistent gains over classical multimodal foundation models and report-supervised baselines in both segmentation accuracy and lesion-level localization.