Organizations: University of Virginia · Capital One
Abstract
Graph Language Models (GLMs) have become a promising direction for adapting Large Language Models (LLMs) to graph learning tasks. By transforming graph topology and node information into graph tokens, GLMs allow LLMs to jointly process structured graph inputs and textual instructions. Yet, it remains unclear how LLMs internally interpret these graph tokens and whether graph tokens act as meaningful carriers of graph structure. In this work, we analyze how LLMs process graph information through graph-token behavior in representative GLM architectures. Findings. We find that the internal saliency of graph tokens in GLMs is not equivalent to graph information utilization. Graph sink tokens consistently emerge as activation-level outliers: they can be identified by massive activation values along a small set of hidden-state dimensions and are biased toward early graph-token positions. However, this activation-level saliency does not imply that these tokens are the main carriers of graph information. Unlike classical attention sinks in language and vision-language models, graph sink tokens do not necessarily attract the largest attention weights from query tokens. Through pruning, repositioning, and swapping interventions, we show that graph sink tokens are not the most important semantic or structural tokens for downstream prediction. Implications. Together, these results suggest that after current GLMs map graph structure into the LLM token space, the resulting graph-token representations do not naturally form a fully usable topology-aware internal representation; instead, they exhibit a decoupling between activation-level saliency and graph-semantic utility. This decoupling points to limitations in existing graph-token construction, placement, and alignment mechanisms.
The remarkable success of large language models (LLMs) has motivated researchers to adapt them as universal predictors for various graph tasks. As a widely recognized paradigm, Graph-Tokenizing LLMs (GTokenLLMs) compress complex graph data into graph tokens and treat them as prefix tokens for querying LLMs, leading many to believe that LLMs can understand graphs more effectively and efficiently. In this paper, we challenge this belief: \textit{Do GTokenLLMs fully understand graph tokens in the natural-language embedding space?} Motivated by this question, we formalize a unified framework for GTokenLLMs and propose an evaluation pipeline, \textbf{GTEval}, to assess graph-token understanding via instruction transformations at the format and content levels. We conduct extensive experiments on 6 representative GTokenLLMs with GTEval. The primary findings are as follows: (1) Existing GTokenLLMs do not fully understand graph tokens. They exhibit over-sensitivity or over-insensitivity to instruction changes, and rely heavily on text for reasoning; (2) Although graph tokens preserve task-relevant graph information and receive attention across LLM layers, their utilization varies across models and instruction variants; (3) Additional instruction tuning can improve performance on the original and seen instructions, but it does not fully address the challenge of graph-token understanding, calling for further improvement.
Large Language Models (LLMs) show remarkable semantic understanding but often struggle with structural understanding when processing graph topologies in a serialized format. Existing solutions rely on training external graph-based adapters or fine-tuning, which incur high costs and lost generalizability. In this work, we investigate the internal mechanisms of LLMs and present a critical finding: LLMs spontaneously reconstruct the graph's topology internally, evidenced by a distinct "sawtooth" pattern in their attention maps that structurally aligns with the "token-level adjacency matrix". However, this intrinsic structural understanding is diluted by the attention sink. We theoretically formalize this dilution as a representation bottleneck, stemming from a fundamental conflict: the model's anisotropic bias, essential for language tasks, suppresses the topology-aware local aggregation required for graph reasoning. To address this, we propose a training-free solution, named StructuraL Attention SHarpening (SLASH), which amplifies this internal structural understanding via a plug-and-play attention redistribution. Experiments on pure graph tasks and molecular prediction validate that SLASH delivers significant and consistent performance gains across diverse LLMs.
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.