Adaptive Tokenization: On the Hop-Overpriority Problem in Tokenized Graph Learning Models
Abstract
Graph Transformers, leveraging the global attention to capture long-range dependencies in graph structures, have significantly advanced graph machine learning, but face prohibitive computational complexity. Tokenized Graph Learning Models (TGLMs) address this issue by converting graphs into ordered token lists for scalable processing. Besides, TGLMs also empower Large Language Models (LLMs) to handle text-attributed graphs more effectively, and thus are also employed in Graph LLMs. However, existing TGLMs rely on hand-designed token lists and their adaptability to diverse graph learning scenarios remains unexplored. In this paper, we first conduct extensive empirical and theoretical preliminary studies for hand-designed token lists. Surprisingly, we identify an unexplored ``hop-overpriority problem'': the common predefined token lists overemphasize nearby nodes and overwhelm the ability of TGLMs to balance local and global signals. This phenomenon is especially harmful for heterophilic graphs. To address this problem, we propose the Learnable Graph Token List (LGTL), a plug-and-play module to replace hand-designed token lists in TGLMs. Specifically, LGTL adaptively adjusts the weights across hops and prioritizes informative nodes within hops through a graph attention gate module and a selection module, respectively. In this way, contextually informative nodes can be adaptively emphasized for both homophilic and heterophilic graphs. Besides, we theoretically show that LGTL can address the hop-overpriority problem. Extensive experiments on benchmarks validate the efficacy of LGTL across both Graph Transformers and Graph LLM backbones.
Benchmark Results
Tested on 7 datasets 6 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphSAGE+CNA | 0.9418
±0.0033 | |
| 2 | GCN+CNA | 0.9366
±0.0048 | |
| 3 | TransformerConv | 0.9350
±0.0058 | |
| 21 | GCN | 0.9004 best reported | best at pub: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 35 | LGTL | 0.8930
±0.0009 | This paper |
| 37 | LLAGA-HO | 0.8922
±0.0010 | This paper |
| 39 | SAGE | 0.8911
±0.0012 | |
| 44 | GAT | 0.8897
±0.0014 | prev best: Learned Low Precision Graph Neural Networks (2020) Improvement within reported uncertainty; not highlighted. |
| 49 | LLAGA-ND | 0.8886
±0.0013 | This paper |
| 51 | H2GCN | 0.8882
±0.0011 | prev best: Feature Transportation Improves Graph Neural Networks (AAAI 2023) |
| 68 | NodeFormer | 0.8848
±0.0033 best reported | best at pub: Efficient Tuning and Inference for Large Language Models on Textual Graphs (IJCAI 2024) Difference within reported uncertainty; not counted as underperformance. |
| 724 | MLP | 0.7768 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | LGTL | 0.9518
±0.0011 | This paper |
| 2 | MixHop (LO) | 0.9513
±0.0038 | |
| 3 | GraphSAGE (LO) | 0.9511
±0.0036 | |
| 5 | LLAGA-HO | 0.9503
±0.0012 | This paper |
| 6 | LLAGA-ND | 0.9503
±0.0014 | This paper |
| 7 | NodeFormer | 0.9490
±0.0019 | |
| 16 | H2GCN | 0.9361
±0.0013 | prev best: Optimization-Induced Graph Implicit Nonlinear Diffusion (ICML 2022) |
| 18 | GCN | 0.9296
±0.0015 | prev best: Node Identifiers: Compact, Discrete Representations for Efficient Graph Learning (ICLR 2024) |
| 20 | GAT | 0.9233
±0.0018 | prev best: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 116 | SAGE | 0.8881
±0.0015 | |
| 210 | MLP | 0.8690
±0.0074 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9703
±0.0019 | |
| 2 | GAT | 0.9669
±0.0014 best reported | |
| 3 | GAT+T | 0.9660
±0.0007 | |
| 7 | SAGE | 0.9643
±0.0027 | |
| 8 | GCN | 0.9632
±0.0008 best reported | |
| 11 | NAGphormer | 0.9614
±0.0016 best reported | |
| 14 | NAGphormer-LGTL | 0.9601
±0.0015 | This paper |
| 17 | VCR-Graphormer-LGTL | 0.9582
±0.0017 | This paper |
| 30 | VCR-Graphormer | 0.9553
±0.0023 | This paper |
| 34 | H2GCN | 0.9548
±0.0043 best reported | best at pub: Clarify Confused Nodes via Separated Learning (2023) Difference within reported uncertainty; not counted as underperformance. |
| 44 | NodeFormer | 0.9527
±0.0022 best reported | best at pub: SignGT: Signed Attention-based Graph Transformer for Graph Representation Learning (2023) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) Difference within reported uncertainty; not counted as underperformance. |
| 390 | MLP | 0.9128
±0.0063 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9461
±0.0017 | |
| 2 | GCN | 0.9412
±0.0008 best reported | best at pub: Diss-l-ECT: Dissecting Graph Data with local Euler Characteristic Transforms (ICML 2024) |
| 3 | GAT | 0.9398
±0.0022 best reported | best at pub: Diss-l-ECT: Dissecting Graph Data with local Euler Characteristic Transforms (ICML 2024) |
| 8 | SAGE | 0.9351
±0.0006 | |
| 35 | NAGphormer-LGTL | 0.9178
±0.0012 | This paper |
| 38 | NAGphormer | 0.9169
±0.0030 best reported | best at pub: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) |
| 47 | VCR-Graphormer-LGTL | 0.9113
±0.0014 | This paper |
| 48 | NodeFormer | 0.9112
±0.0043 best reported | best at pub: SignGT: Signed Attention-based Graph Transformer for Graph Representation Learning (2023) Difference within reported uncertainty; not counted as underperformance. |
| 71 | VCR-Graphormer | 0.9051
±0.0020 | This paper |
| 114 | H2GCN | 0.8986
±0.0022 | prev best: Clarify Confused Nodes via Separated Learning (2023) Improvement within reported uncertainty; not highlighted. |
| 320 | MLP | 0.8463 |
Heterophilic Graphs
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9672
±0.0147 | |
| 2 | DoG | 0.9660
±0.0210 | |
| 3 | GPF-plus | 0.9583
±0.0419 | |
| 34 | MLP | 0.9230
±0.0070 | |
| 40 | H2GCN | 0.9189
±0.0393 best reported | best at pub: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 51 | LGTL | 0.9032
±0.0068 | This paper |
| 53 | GraphSAGE | 0.9000
±0.0365 | |
| 155 | NodeFormer | 0.8463
±0.0347 best reported | best at pub: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) Difference within reported uncertainty; not counted as underperformance. |
| 211 | GAT | 0.8162
±0.0645 best reported | best at pub: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) best today: Equivariance Everywhere All At Once: A Recipe for Graph Foundation Models (2025) |
| 257 | GCN | 0.7933
±0.0447 best reported | best at pub: Graph Wave Networks (WWW 2025) Difference within reported uncertainty; not counted as underperformance. |
| 338 | LLAGA-ND | 0.7419
±0.0191 | This paper |
| 377 | LLAGA-HO | 0.7140
±0.0192 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9541
±0.0272 | |
| 2 | ACM-GCN | 0.9480
±0.0380 | |
| 3 | RF-GCN | 0.9429 | |
| 24 | MLP | 0.9136
±0.0070 | |
| 138 | SAGE | 0.8269 | |
| 519 | LLAGA-ND | 0.4667
±0.0438 | This paper |
| 545 | LLAGA-HO | 0.4267
±0.0438 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DMD++ | 0.9190
±0.0260 | |
| 2 | F-GREAD-BS | 0.9059
±0.0380 | |
| 3 | APPNP | 0.9010
±0.0350 | |
| 22 | H2GCN | 0.8790
±0.0420 best reported | best at pub: When Graph Neural Networks Meet Dynamic Mode Decomposition (ICLR 2024) |
| 37 | MLP | 0.8629
±0.0450 | |
| 63 | GCN | 0.8310
±0.0320 | |
| 95 | LGTL | 0.7708
±0.0079 | This paper |
| 146 | NodeFormer | 0.6583
±0.0262 | This paper |
| 207 | LLAGA-ND | 0.5083
±0.0360 | This paper |
| 212 | LLAGA-HO | 0.4958
±0.0374 | This paper |
