Towards Improved Sentence Representations using Token Graphs

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 integration of Graph Neural Networks (GNNs) with Large Language Models (LLMs) has emerged as a promising paradigm for Graph Question Answering (GraphQA). However, effective methods for encoding complex structural information into the LLM's latent space remain an open challenge. Current state-of-the-art architectures, such as G-Retriever, typically rely on standard GNNs and aggressive mean pooling to compress entire graph substructures into a single token, creating a severe information bottleneck. This work mitigates this bottleneck by investigating two orthogonal strategies: (1) increasing the bandwidth of the graph-to-LLM interface via multi-token pooling, and (2) enhancing the semantic quality of the graph encoder via global attention mechanisms. We evaluate a suite of hierarchical pruning and clustering-based pooling operators including Top-k, SAGPool, DiffPool, MinCutPool, and Virtual Node Pooling (VNPool) to project graph data into multiple learnable tokens. Empirically, we demonstrate that while pooling introduces significant instability during soft prompt tuning, the application of Low-Rank Adaptation (LoRA) effectively stabilizes specific hierarchical projections (notably VNPool and pruning methods), though dense clustering operators remain challenging. This stabilization allows compressed representations to rival full-graph baselines (achieving ~73% Hit@1 on WebQSP). Conceptually, we demonstrate that a Graph Transformer with VNPool implementation functions structurally as a single-layer Perceiver IO encoder. Finally, we adapt the FandE (Features and Edges) Score to the generative GraphQA domain. Our analysis reveals that the GraphQA benchmark suffers from representational saturation, where target answers are often highly correlated with isolated node features. The implementation is available at https://github.com/Agrover112/G-Retriever/tree/all_good/

The remarkable success of large language models (LLMs) has motivated researchers to adapt them as universal predictors for various graph-related tasks, with the ultimate goal of developing a graph foundation model that generalizes diverse scenarios. The key challenge is to align graph data with language spaces so that LLMs can better comprehend graphs. As a popular paradigm, Graph-Tokenizing LLMs (GTokenLLMs) encode complex structures and lengthy texts into a graph token sequence, and then align them with text tokens via language instructions tuning. Despite their initial success, our information-theoretic analysis reveals that existing GTokenLLMs rely solely on text supervision from language instructions, which achieve only implicit graph-text alignment, resulting in a text-dominant bias that underutilizes graph context. To overcome this limitation, we first prove that the alignment objective is upper-bounded by the mutual information between the input graphs and their hidden representations in the LLM, which motivates us to improve this upper bound to achieve better alignment. To this end, we further propose a reconstructive graph instruction tuning pipeline, RGLM. Our key idea is to reconstruct the graph information from the LLM's graph token outputs, explicitly incorporating graph supervision to constrain the alignment process. Technically, we embody RGLM by exploring three distinct variants from two complementary perspectives: RGLM-Decoder from the input space; RGLM-Similarizer and RGLM-Denoiser from the latent space. Additionally, we theoretically analyze the alignment effectiveness of each variant. Extensive experiments on various benchmarks and task scenarios validate the effectiveness of the proposed RGLM, paving the way for new directions in GTokenLLMs' alignment research.