Graph Tokenization for Bridging Graphs and Transformers

Transformers have become a central architecture for graph learning, but their application to graphs requires first choosing a tokenization: a graph-to-token map that determines which structural information is exposed at the input. In this work, we show that this choice is a fundamental component of transformer expressivity. We examine three tokenizations that serve as building blocks for many existing graph tokenizations: spectral, random-walk, and adjacency tokenizations. We prove that different tokenizations induce distinct depth regimes: the same graph computation may be realizable by a shallow transformer under one tokenization, while requiring substantially larger depth under another. For example, we prove that random-walk tokenization is lossy for any walk length, making it impossible in general to recover the graph from it, and that while spectral tokenization is lossless, it is ill-conditioned for local tasks. We further show that although both random-walk and spectral tokenizations are derived from adjacency information, it is impossible for a limited-depth transformer to convert between tokenization families in general. In particular, we establish lower bounds and impossibility results showing that unfavorable tokenizations may preclude the efficient recovery of more suitable structural representations. Finally, we complement our theory with controlled experiments on synthetic and real-world tasks, validating the predicted separations and showing that different tasks favor different structural views, and combining complementary tokenizations allows the transformer to leverage distinct signals from each representation.

Foundation models are at the forefront of artificial intelligence. A tokenizer, converting the raw input into discrete representations that the model can understand, plays an important role to the success of foundation models. Unlike the text tokenizer that is well studied in large language models, graph tokenizer is still at its early stage, facing the challenges of tackling the non-Euclidean structures and capturing the structural semantics. How to design a graph tokenizer for structural knowledge transfer? To this end, we propose a Riemannian Graph Tokenizer (RGT) that bridges the structural knowledge and quantized representations to support cross-domain structural knowledge transfer. The connection is established by Riemannian geometry. Specifically, we first define the geometric vocabulary (trees, cycles and sequences), which captures fundamental structural patterns and reflects the intrinsic geometry of graph. Second, we construct a Riemannian quantizer with Riemannian Straight-Through Estimator to tokenise graph structures across multiple domains into discrete tokens. To ensure consistency and transferability across diverse geometric spaces, RGT further incorporates a geometry-aligned decoder that projects manifold-specific tokens into a unified tangent space. The theoretical analysis and geometric interpretations are provided to support the effectiveness of our proposed method. Extensive experiments across diverse datasets demonstrate that RGT significantly enhances structural knowledge transferability across graph domains.

Using Large Language Models (LLMs) to process graph-structured data is an active research area, yet current state-of-the-art approaches typically rely on multi-step pipelines with Graph Neural Network (GNN) encoders that compress rich textual attributes into solitary tokens, creating a significant semantic bottleneck. In this paper, we introduce the Graph Transformer Language Model (GTLM), a novel architecture that enables pretrained LLMs to natively process graph topologies while entirely eliminating this compressive bottleneck. GTLM is exceptionally parameter-efficient: by injecting graph-aware attention biases directly into the LLM's attention modules, it introduces only 0.015% additional parameters relative to the base model. We theoretically prove that our bidirectional attention prefix preserves node permutation equivariance while maintaining exact backward compatibility with the pretrained base model. Extensive evaluations demonstrate that a 1B-parameter GTLM matches or exceeds the performance of 7B-parameter state-of-the-art models on standard Text-Attributed Graph benchmarks, while significantly surpassing baselines on GraphQA. Finally, we demonstrate that GTLM attention heads implicitly learn to simulate message passing, explaining its superior performance on algorithmic tasks. This paradigm shift enables true algorithmic reasoning within LLMs and provides a scalable foundation for next-generation GraphRAG and relational deep learning.