Adaptive Tokenization: On the Hop-Overpriority Problem in Tokenized Graph Learning Models

Zhibiao Wang, Yunlong Zhou, Ziwei Zhang, Mengmei Zhang, Shirui Pan, Chunming Hu, Xiao Wang

Main figure for 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

#ModelAccuracy ↑Paper
1
GraphSAGE+CNA
0.9418 ±0.0033
2
GCN+CNA
0.9366 ±0.0048
3
TransformerConv
0.9350 ±0.0058
21
GCN
actual #21 vs paper #44 23 places worse
0.9004
best reported
actual #21 vs paper #44 23 places worse
paper 0.8893 ±0.0012
paper 0.8893 ±0.0012 Δ at pub 0.0111
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
actual #44 vs paper #44
0.8897 ±0.0014
actual #44 vs paper #44
paper 0.8897 ±0.0014

Improvement within reported uncertainty; not highlighted.

paper 0.8897 ±0.0014 Δ at pub 0.0007
49
LLAGA-ND
0.8886 ±0.0013
This paper
51
H2GCN
actual #51 vs paper #51
0.8882 ±0.0011
actual #51 vs paper #51
paper 0.8882 ±0.0011
paper 0.8882 ±0.0011 Δ at pub 0.0095
68
NodeFormer
actual #68 vs paper #80 12 places worse
0.8848 ±0.0033
best reported
actual #68 vs paper #80 12 places worse
paper 0.8823 ±0.0017

Difference within reported uncertainty; not counted as underperformance.

paper 0.8823 ±0.0017 Δ at pub 0.0025
724
MLP
0.7768
#ModelAccuracy ↑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
actual #7 vs paper #7
0.9490 ±0.0019
actual #7 vs paper #7
paper 0.9490 ±0.0019
paper 0.9490 ±0.0019 Δ at pub 0.0663
16
H2GCN
actual #16 vs paper #16
0.9361 ±0.0013
actual #16 vs paper #16
paper 0.9361 ±0.0013
paper 0.9361 ±0.0013 Δ at pub 0.0412
18
GCN
actual #18 vs paper #18
0.9296 ±0.0015
actual #18 vs paper #18
paper 0.9296 ±0.0015
paper 0.9296 ±0.0015 Δ at pub 0.0292
20
GAT
actual #20 vs paper #20
0.9233 ±0.0018
actual #20 vs paper #20
paper 0.9233 ±0.0018
paper 0.9233 ±0.0018 Δ at pub 0.0263
116
SAGE
0.8881 ±0.0015
210
MLP
0.8690 ±0.0074
#ModelAccuracy ↑Paper
1
GraphTARIF
0.9703 ±0.0019
2
GAT
actual #2 vs paper #111 109 places worse
0.9669 ±0.0014
best reported
actual #2 vs paper #111 109 places worse
paper 0.9387 ±0.0029
3
GAT+T
0.9660 ±0.0007
7
SAGE
0.9643 ±0.0027
8
GCN
actual #8 vs paper #254 246 places worse
0.9632 ±0.0008
best reported
actual #8 vs paper #254 246 places worse
paper 0.9270 ±0.0027
11
NAGphormer
actual #11 vs paper #32 21 places worse
0.9614 ±0.0016
best reported
actual #11 vs paper #32 21 places worse
paper 0.9549 ±0.0024
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
actual #34 vs paper #61 27 places worse
0.9548 ±0.0043
best reported
actual #34 vs paper #61 27 places worse
paper 0.9495 ±0.0025

Difference within reported uncertainty; not counted as underperformance.

paper 0.9495 ±0.0025 Δ at pub 0.0053
44
NodeFormer
actual #44 vs paper #58 14 places worse
0.9527 ±0.0022
best reported
actual #44 vs paper #58 14 places worse
paper 0.9502 ±0.0026

Difference within reported uncertainty; not counted as underperformance.

paper 0.9502 ±0.0026 Δ at pub 0.0025 Δ today 0.0025
390
MLP
0.9128 ±0.0063
#ModelAccuracy ↑Paper
1
GraphTARIF
0.9461 ±0.0017
2
GCN
actual #2 vs paper #128 126 places worse
0.9412 ±0.0008
best reported
actual #2 vs paper #128 126 places worse
paper 0.8965 ±0.0024
3
GAT
actual #3 vs paper #60 57 places worse
0.9398 ±0.0022
best reported
actual #3 vs paper #60 57 places worse
paper 0.9078 ±0.0026
8
SAGE
0.9351 ±0.0006
35
NAGphormer-LGTL
0.9178 ±0.0012
This paper
38
NAGphormer
actual #38 vs paper #44 6 places worse
0.9169 ±0.0030
best reported
actual #38 vs paper #44 6 places worse
paper 0.9122 ±0.0021
47
VCR-Graphormer-LGTL
0.9113 ±0.0014
This paper
48
NodeFormer
actual #48 vs paper #56 8 places worse
0.9112 ±0.0043
best reported
actual #48 vs paper #56 8 places worse
paper 0.9096 ±0.0023

Difference within reported uncertainty; not counted as underperformance.

paper 0.9096 ±0.0023 Δ at pub 0.0016
71
VCR-Graphormer
0.9051 ±0.0020
This paper
114
H2GCN
actual #114 vs paper #114
0.8986 ±0.0022
actual #114 vs paper #114
paper 0.8986 ±0.0022

Improvement within reported uncertainty; not highlighted.

paper 0.8986 ±0.0022 Δ at pub 0.0018
320
MLP
0.8463

Heterophilic Graphs

#ModelAccuracy ↑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
actual #40 vs paper #191 151 places worse
0.9189 ±0.0393
best reported
actual #40 vs paper #191 151 places worse
paper 0.8258 ±0.0079
paper 0.8258 ±0.0079 Δ at pub 0.0931
51
LGTL
0.9032 ±0.0068
This paper
53
GraphSAGE
0.9000 ±0.0365
155
NodeFormer
actual #155 vs paper #221 66 places worse
0.8463 ±0.0347
best reported
actual #155 vs paper #221 66 places worse
paper 0.8129 ±0.0125

Difference within reported uncertainty; not counted as underperformance.

paper 0.8129 ±0.0125 Δ at pub 0.0334
211
GAT
actual #211 vs paper #400 189 places worse
0.8162 ±0.0645
best reported
actual #211 vs paper #400 189 places worse
paper 0.6920 ±0.0186
paper 0.6920 ±0.0186 Δ at pub 0.1162 Δ today 0.1242
257
GCN
actual #257 vs paper #340 83 places worse
0.7933 ±0.0447
best reported
actual #257 vs paper #340 83 places worse
paper 0.7400 ±0.0178
best at pub: Graph Wave Networks (WWW 2025)

Difference within reported uncertainty; not counted as underperformance.

paper 0.7400 ±0.0178 Δ at pub 0.0533
338
LLAGA-ND
0.7419 ±0.0191
This paper
377
LLAGA-HO
0.7140 ±0.0192
This paper
#ModelAccuracy ↑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
#ModelAccuracy ↑Paper
1
DMD++
0.9190 ±0.0260
2
F-GREAD-BS
0.9059 ±0.0380
3
APPNP
0.9010 ±0.0350
22
H2GCN
actual #22 vs paper #130 108 places worse
0.8790 ±0.0420
best reported
actual #22 vs paper #130 108 places worse
paper 0.6958 ±0.0195
paper 0.6958 ±0.0195 Δ at pub 0.1832
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
SOTA performance (not significantly different from the best) Proposed method (this paper) Baseline / comparison (this paper) Global context (other papers) Best at pub — reported result worse than the best known when published (best reported in green) Best at pub — reported value improved over the best known when published Best today — OK at publication; today's leaderboard best is elsewhere