This work introduces agentic graph token reasoning, which recasts graph tokenization as part of the reasoning process itself and pushes LLM-based graph analysis from static graph-token encoders towards a graph-native agent paradigm.
Abstract
Graphs model relational data throughout science and industry, from citation networks to product co-purchase graphs. Because the nodes of many such graphs carry rich text, a growing line of work applies large language models (LLMs) to graph analysis. The most graph-native of these methods use graph tokens: a graph encoder compresses a graph view, such as a node, its k-hop neighbourhood, or a cluster, into a short block of continuous tokens that jointly encodes node attributes and topology and is read directly by the model. Existing methods, however, use graph tokens in a static single-shot manner: they encode one predefined graph view before the model has even seen the target and never revise it, leaving the model's step-by-step reasoning ability unused. We introduce agentic graph token reasoning, which recasts graph tokenization as part of the reasoning process itself. At each step, the model chooses which graph view to encode and at what granularity; a graph encoder is invoked on demand to materialise the corresponding graph tokens; and the resulting block is spliced into the running context. The model thus reasons step by step in the graph token space, and the tokens it reads are trajectory-dependent. We realise this with a three-stage training pipeline: (i) self-supervised tasks that teach the model to read heterogeneous graph tokens, (ii) a token-robust trajectory stage with a graph-token consistency regulariser, and (iii) preference optimisation that rewards trajectories in which the graph-token evidence and the node-text evidence agree. Across evaluations spanning seven graph domains, our models outperform a broad set of baselines by a large margin and transfer zero-shot to unseen domains without any per-target fine-tuning. More broadly, this work pushes LLM-based graph analysis from static graph-token encoders towards a graph-native agent paradigm.
Tool-calling LLM agents navigate unfamiliar codebases with a handful of generic primitives for listing, reading and searching files (ls, cat, grep). A knowledge graph admits the same interface: listing neighbours, reading node content and searching descriptions are the same operations on a different substrate. Building on this correspondence, we present GRA, a Graph Reasoning Agent that explores hybrid knowledge graphs, whose nodes are either textual concepts or relational tables, with seven generic tools, discovering everything domain-specific at run time. On UFK-M (Unified Factory Knowledge Model), an industrial benchmark of 258 analytical questions whose gold answers are produced by executing validated SQL programs, GRA beats a full-context agent by 5.1 pp (88.4% vs. 83.3%), while reading under a third of its input tokens. A graph-free control shows the gain comes chiefly from selective agentic access rather than graph topology, and that the effect depends on a model able to drive tools reliably. Seeing less, the agent answers better: selective navigation over a structured substrate beats exhaustive context.
M. Dragić, Ruben Ifrah, Alexandre Rio· 0 citations
This work proposes AgentGFM, in which all node agents follow a shared end-to-end trainable policy rather than using independent models, and describes this capability as information-flow control, which is inspired by recent advances in agent technology.
Jingbo Cui, Jitao Zhao, Di Jin et al.· 0 citations
Text-attributed graphs (TAGs), where each node carries a natural language description, require models to jointly reason over text and graph topology. Existing approaches often handle the two modalities separately: graph neural networks operate on shallow text features, while hybrids of LLMs and graphs use the language model mainly as a text encoder and delegate structure learning to a separate graph module. We propose method that unifies textual reasoning and graph message passing within a masked diffusion language model, a language model with bidirectional attention and generative decoding. For each graph instance, method linearises a sampled local neighbourhood into a token sequence and injects graph structure through a topology attention mask, which realises message passing over the graph. Because the diffusion language model can both interpret and generate text, the method adapts to different tasks simply by changing the prompt, supporting node classification, link prediction, and cross-dataset transfer with no target-specific fine-tuning. Experiments show that method outperforms graph neural networks, graph transformers, and LLM-based baselines on all three TAG benchmarks across two tasks, improving over the strongest baseline by up to 3.9 points.
This paper introduces a novel task, graph textual summarization, which aims to generate natural language descriptions that capture both the semantic content and structural characteristics of graph data based on large language models (LLMs). Unlike traditional summarization tasks for text, images, or videos, summarizing graph data presents unique challenges due to its abstract and non-intuitive nature. We develop a comprehensive benchmark construction framework and construct three diverse benchmark datasets, including text-attributed graphs (TAGs), knowledge graphs (KGs), and heterogeneous attributed graphs (HAGs). To facilitate empirical studies, we deliver three representative benchmark datasets: SurveyGraphSum, consisting of 7835 citation graphs from survey papers across 10 major domains and 56 subdomains; BookGraphSum, containing 6175 knowledge graphs extracted from 186 books; and E-comGraphSum, with 912 heterogeneous graphs from real-world e-commerce networks, each representing a fraud group with 14 node types, 19 relation types, and 9 numerical attributes related to user behavior and interactions. In addition, we propose a unified evaluation framework that assesses both linguistic quality and factual consistency, providing a comprehensive approach to evaluating generated summaries for content fidelity and accuracy. By formalizing the task, releasing benchmark datasets, and proposing an evaluation framework, we aim to advance research in graph textual summarization and promote methods that produce accurate, informative, and human-readable summaries for complex graphs.
Xiaoxuan Gou, Weiguo Zheng, Hanqing Guo et al.· Proceedings of the 32nd ACM...· 0 citations
Large language model (LLM) agents are increasingly capable of planning, using tools, and interacting with external environments. They are typically supported by harnesses, which manage state and coordinate multi-step execution. Graph analysis provides a promising setting for evaluating their agentic capabilities, because it requires agents to access data and execute operations in a graph environment. However, existing graph benchmarks for LLMs provide limited coverage of graph tasks and graph types, making it difficult to comprehensively evaluate LLM agents. Moreover, they typically formulate graph analysis as text-based question answering, where graph information is directly provided in the prompt, limiting the evaluation of end-to-end agentic capabilities. To address these limitations, we introduce GABench, a comprehensive benchmark for agentic graph analysis. GABench spans three graph types and covers four graph analysis task categories: graph retrieval, graph theory, graph machine learning, and graph open-ended question answering. GABench also provides 84 executable tools for accessing graph data and performing diverse graph operations. Building on these tools, we develop an agentic graph analysis task generation pipeline and construct 10,400 tasks with verifiable ground truth.Using GABench, we evaluate a range of frontier LLMs and agent harnesses. Our experiments reveal three key findings: (1) Existing LLM agents still struggle with complex graph analysis tasks. (2) Harness choice significantly affects performance, yet existing harnesses remain limited on complex graph tasks. (3) Graph analysis depends more on tool-call quality than quantity. Our findings provide practical insights into the development and evaluation of LLM agents for graph analysis.
Jiarui Tan, Zhongjian Zhang, YaBo Guo et al.· 0 citations
Graph retrieval-augmented generation (GraphRAG) enhances large language models with structured knowledge, yet existing systems construct knowledge graphs in a single extraction pass, producing noisy entities and brittle retrieval. RAGU, an open-source modular GraphRAG engine, addresses this by separating extraction from consolidation: entities and relations pass through two-stage typed extraction, DBSCAN-backed deduplication, LLM summarization, and Leiden community detection. A key insight motivates a compact extractor: the skills an in-pipeline LLM needs - comprehension, extraction, reasoning over context - are language skills that grow only weakly with model size, unlike factual world knowledge. Accordingly, we train Meno-Lite-0.1, a 7B model optimized for language skills, which outperforms Qwen2.5-32B on knowledge-graph construction (+12.5% relative harmonic mean) and matches it on English GraphRAG tasks. On GraphRAG-Bench (Medical), RAGU retrieves the most complete context at every factoid level (evidence recall up to 0.84 vs. $\leq$0.76) and overtakes HippoRAG2 on synthesis tasks; on multi-hop factoid QA, the apparent HippoRAG2 advantage is shown to be largely an answer-format artifact. RAGU is installable via $\texttt{pip install graph_ragu}$, runs on a single GPU, and is released under MIT. The source code is publicly available at https://github.com/RaguTeam/RAGU, and the Meno-Lite-0.1 model can be obtained from https://huggingface.co/bond005/meno-lite-0.1.
Mikhail Komarov, Ivan Bondarenko, Stanislav Shtuka et al.· 0 citations