ICML 2024

GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers

Guoguo Ai, Guansong Pang, Hezhe Qiao, Yuan Gao, Hui Yan

Main figure for GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers

Abstract

Graph Transformers (GTs) have demonstrated remarkable performance in graph representation learning over popular graph neural networks (GNNs). However, self--attention, the core module of GTs, preserves only low-frequency signals in graph features, leading to ineffectiveness in capturing other important signals like high-frequency ones. Some recent GT models help alleviate this issue, but their flexibility and expressiveness are still limited since the filters they learn are fixed on predefined graph spectrum or spectral order. To tackle this challenge, we propose a Graph Fourier Kolmogorov-Arnold Transformer (GrokFormer), a novel GT model that learns highly expressive spectral filters with adaptive graph spectrum and spectral order through a Fourier series modeling over learnable activation functions. We demonstrate theoretically and empirically that the proposed GrokFormer filter offers better expressiveness than other spectral methods. Comprehensive experiments on 10 real-world node classification datasets across various domains, scales, and graph properties, as well as 5 graph classification datasets, show that GrokFormer outperforms state-of-the-art GTs and GNNs. Our code is available at https://github.com/GGA23/GrokFormer

Proposed method: GrokFormer

Benchmark Results

Tested on 6 datasets 10 baseline values reported too low

Tables show presented results in global context (best 3 papers + GCN + MLP).

Classic

#ModelAccuracy ↑Paper
1
GraphTARIF
0.9703 ±0.0019
2
GAT
actual #2 vs paper #401 399 places worse
0.9669 ±0.0014
best reported
actual #2 vs paper #401 399 places worse
paper 0.9094 ±0.0068
3
GAT+T
0.9660 ±0.0007
7
SAGE
0.9643 ±0.0027
8
GCN
actual #8 vs paper #488 480 places worse
0.9632 ±0.0008
best reported
actual #8 vs paper #488 480 places worse
paper 0.8826 ±0.0073
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 ±0.0011
18
Specformer
actual #18 vs paper #33 15 places worse
0.9580 ±0.0026
best reported
actual #18 vs paper #33 15 places worse
paper 0.9548 ±0.0032

Difference within reported uncertainty; not counted as underperformance.

paper 0.9548 ±0.0032 Δ at pub 0.0032
29
SGFormer
actual #29 vs paper #84 55 places worse
0.9434 ±0.0023
actual #29 vs paper #84 55 places worse
paper 0.9434 ±0.0023

Improvement within reported uncertainty; not highlighted.

paper 0.9434 ±0.0023 Δ at pub 0.0121 Δ today 0.0124
31
GrokFormer
0.9552 ±0.0052
This paper
33
GPRGNN
actual #33 vs paper #111 78 places worse
0.9549 ±0.0014
best reported
actual #33 vs paper #111 78 places worse
paper 0.9385 ±0.0028
paper 0.9385 ±0.0028 Δ at pub 0.0164
34
H2GCN
actual #34 vs paper #34
0.9548 ±0.0043
best reported
actual #34 vs paper #34
paper 0.9545 ±0.0067

Difference within reported uncertainty; not counted as underperformance.

paper 0.9545 ±0.0067 Δ at pub 0.0003
35
JacobiConv
0.9543 ±0.0023
This paper
39
HiGCN
0.9533 ±0.0037
This paper
44
NodeFormer
0.9527 ±0.0022
This paper
57
GraphGPS
actual #57 vs paper #81 24 places worse
0.9506 ±0.0013
best reported
actual #57 vs paper #81 24 places worse
paper 0.9435 ±0.0025
paper 0.9435 ±0.0025 Δ at pub 0.0071 Δ today 0.0071
76
HopGNN
0.9449 ±0.0033
This paper
99
PolyFormer
0.9408 ±0.0137
This paper
118
ChebyNet
actual #118 vs paper #118
0.9377 ±0.0032
actual #118 vs paper #118
paper 0.9377 ±0.0032
paper 0.9377 ±0.0032 Δ at pub 0.0417
127
BernNet
actual #127 vs paper #129 2 places worse
0.9368 ±0.0028
best reported
actual #127 vs paper #129 2 places worse
paper 0.9363 ±0.0035

Difference within reported uncertainty; not counted as underperformance.

paper 0.9363 ±0.0035 Δ at pub 0.0005
390
MLP
0.9128 ±0.0063
463
Transformer
0.8958 ±0.0105
This paper
#ModelAccuracy ↑Paper
1
GrokFormer
0.9831 ±0.0018
This paper
2
PolyFormer
0.9808 ±0.0027
This paper
3
SGFormer
0.9796 ±0.0081
This paper
4
HopGNN
0.9786 ±0.0016
This paper
5
NAGphormer
actual #5 vs paper #5
0.9785 ±0.0026
actual #5 vs paper #5
paper 0.9785 ±0.0026
paper 0.9785 ±0.0026 Δ at pub 0.0051
6
GAT
actual #6 vs paper #6
0.9782 ±0.0028
actual #6 vs paper #6
paper 0.9782 ±0.0028
paper 0.9782 ±0.0028 Δ at pub 0.0119
7
GPRGNN
actual #7 vs paper #23 16 places worse
0.9777 ±0.0015
best reported
actual #7 vs paper #23 16 places worse
paper 0.9725 ±0.0013
paper 0.9725 ±0.0013 Δ at pub 0.0052
8
Specformer
0.9775 ±0.0053
This paper
9
GCN
actual #9 vs paper #9
0.9774 ±0.0035
actual #9 vs paper #9
paper 0.9774 ±0.0035
paper 0.9774 ±0.0035 Δ at pub 0.0124
10
HiGCN
0.9765 ±0.0035
This paper
11
H2GCN
actual #11 vs paper #27 16 places worse
0.9764 ±0.0050
best reported
actual #11 vs paper #27 16 places worse
paper 0.9719 ±0.0013

Difference within reported uncertainty; not counted as underperformance.

paper 0.9719 ±0.0013 Δ at pub 0.0045
13
GraphGPS
actual #13 vs paper #13
0.9760 ±0.0005
actual #13 vs paper #13
paper 0.9760 ±0.0005
paper 0.9760 ±0.0005 Δ at pub 0.0048
14
JacobiConv
0.9756 ±0.0028
This paper
17
SAGE
0.9739 ±0.0018
20
BernNet
0.9736 ±0.0030
This paper
24
ChebyNet
0.9725 ±0.0078
This paper
34
NodeFormer
actual #34 vs paper #45 11 places worse
0.9680 ±0.0063
best reported
actual #34 vs paper #45 11 places worse
paper 0.9645 ±0.0028

Difference within reported uncertainty; not counted as underperformance.

paper 0.9645 ±0.0028 Δ today 0.0035
58
MLP
0.9597 ±0.0007
#ModelAccuracy ↑Paper
1
GCN
actual #1 vs paper #60 59 places worse
0.9302 ±0.0011
best reported
actual #1 vs paper #60 59 places worse
paper 0.8232 ±0.0069
paper 0.8232 ±0.0069 Δ at pub 0.1070
2
RSE + RGCN (70b)
0.8852 ±0.0019
3
LEMP+T
0.8825
9
SAGE
0.8771
20
H2GCN
actual #20 vs paper #47 27 places worse
0.8345 ±0.0026
actual #20 vs paper #47 27 places worse
paper 0.8345 ±0.0026
29
GrokFormer
0.8557 ±0.0065
This paper
31
GAT
actual #31 vs paper #51 20 places worse
0.8322 ±0.0078
actual #31 vs paper #51 20 places worse
paper 0.8322 ±0.0078

Improvement within reported uncertainty; not highlighted.

paper 0.8322 ±0.0078 Δ at pub 0.0043 Δ today 0.0211
32
Specformer
0.8515 ±0.0063
This paper
33
HopGNN
0.8473 ±0.0059
This paper
39
JacobiConv
0.8413 ±0.0049
This paper
45
PolyFormer
0.8362 ±0.0017
This paper
46
BernNet
0.8356 ±0.0061
This paper
48
NAGphormer
actual #48 vs paper #48
0.8341 ±0.0034
actual #48 vs paper #48
paper 0.8341 ±0.0034
paper 0.8341 ±0.0034 Δ at pub 0.0625
52
HiGCN
0.8314 ±0.0078
This paper
55
ChebyNet
0.8295 ±0.0045
This paper
57
SGFormer
0.8271 ±0.0056
This paper
58
GPRGNN
actual #58 vs paper #58
0.8258 ±0.0089
actual #58 vs paper #58
paper 0.8258 ±0.0089
paper 0.8258 ±0.0089 Δ at pub 0.0446
66
Transformer
actual #66 vs paper #195 129 places worse
0.8188 ±0.0015
best reported
actual #66 vs paper #195 129 places worse
paper 0.7736 ±0.0125
74
NodeFormer
actual #74 vs paper #74
0.8103 ±0.0094
actual #74 vs paper #74
paper 0.8103 ±0.0094
paper 0.8103 ±0.0094 Δ at pub 0.0556
120
GraphGPS
actual #120 vs paper #120
0.7926 ±0.0057
actual #120 vs paper #120
paper 0.7926 ±0.0057

Improvement within reported uncertainty; not highlighted.

paper 0.7926 ±0.0057 Δ at pub 0.0060
237
MLP
0.7469 ±0.0085

Heterophilic Graphs

#ModelAccuracy ↑Paper
1
P^2GNN
0.9672 ±0.0147
2
DoG
0.9660 ±0.0210
3
GPF-plus
0.9583 ±0.0419
8
GrokFormer
0.9459 ±0.0208
This paper
21
JacobiConv
0.9344 ±0.0213
This paper
22
BernNet
actual #22 vs paper #25 3 places worse
0.9328 ±0.0148
best reported
actual #22 vs paper #25 3 places worse
paper 0.9312 ±0.0065

Difference within reported uncertainty; not counted as underperformance.

paper 0.9312 ±0.0065 Δ at pub 0.0016
28
GPRGNN
actual #28 vs paper #28
0.9295 ±0.0131
actual #28 vs paper #28
paper 0.9295 ±0.0131

Improvement within reported uncertainty; not highlighted.

paper 0.9295 ±0.0131 Δ at pub 0.0003
32
SGFormer
0.9246 ±0.0148
This paper
34
MLP
0.9230 ±0.0070
37
HiGCN
0.9215 ±0.0073
This paper
40
H2GCN
actual #40 vs paper #40
0.9189 ±0.0393
actual #40 vs paper #40
paper 0.9189 ±0.0393

Improvement within reported uncertainty; not highlighted.

paper 0.9189 ±0.0393 Δ at pub 0.0424
43
NAGphormer
0.9180 ±0.0185
This paper
53
GraphSAGE
0.9000 ±0.0365
72
HopGNN
actual #72 vs paper #72
0.8915 ±0.0404
actual #72 vs paper #72
paper 0.8915 ±0.0404

Improvement within reported uncertainty; not highlighted.

paper 0.8915 ±0.0404 Δ at pub 0.0618
73
PolyFormer
0.8902 ±0.0544
This paper
78
Transformer
0.8875 ±0.0630
This paper
87
Specformer
0.8823 ±0.0038
This paper
113
ChebyNet
actual #113 vs paper #113
0.8622 ±0.0245
actual #113 vs paper #113
paper 0.8622 ±0.0245

Improvement within reported uncertainty; not highlighted.

paper 0.8622 ±0.0245 Δ at pub 0.0321
155
NodeFormer
0.8463 ±0.0347
This paper
173
GraphGPS
0.8371 ±0.0585
This paper
211
GAT
actual #211 vs paper #229 18 places worse
0.8082 ±0.0213
actual #211 vs paper #229 18 places worse
paper 0.8082 ±0.0213

Improvement within reported uncertainty; not highlighted.

paper 0.8082 ±0.0213 Δ at pub 0.0082
257
GCN
actual #257 vs paper #282 25 places worse
0.7933 ±0.0447
best reported
actual #257 vs paper #282 25 places worse
paper 0.7738 ±0.0328
best today: Graph Wave Networks (WWW 2025)

Difference within reported uncertainty; not counted as underperformance.

paper 0.7738 ±0.0328 Δ at pub 0.0102 Δ today 0.0195
#ModelAccuracy ↑Paper
1
DiGGR
0.4535 ±0.0353
2
TRIGON
0.4402 ±0.0028
3
DoG
0.4320 ±0.0120
7
GrokFormer
0.4298 ±0.0148
This paper
19
Specformer
actual #19 vs paper #19
0.4193 ±0.0104
actual #19 vs paper #19
paper 0.4193 ±0.0104
paper 0.4193 ±0.0104 Δ at pub 0.0367
20
HiGCN
0.4181 ±0.0052
This paper
21
BernNet
0.4179 ±0.0101
This paper
23
SGFormer
actual #23 vs paper #23
0.4169 ±0.0063
actual #23 vs paper #23
paper 0.4169 ±0.0063
paper 0.4169 ±0.0063 Δ at pub 0.0379
28
PolyFormer
0.4151 ±0.0071
This paper
34
JacobiConv
0.4117 ±0.0064
This paper
42
MLP
0.4026 ±0.0108
49
NAGphormer
actual #49 vs paper #49
0.4008 ±0.0150
actual #49 vs paper #49
paper 0.4008 ±0.0150
paper 0.4008 ±0.0150 Δ at pub 0.0584
51
Transformer
actual #51 vs paper #51
0.3995 ±0.0064
actual #51 vs paper #51
paper 0.3995 ±0.0064
paper 0.3995 ±0.0064 Δ at pub 0.0334
52
GPRGNN
0.3992 ±0.0067
This paper
61
HopGNN
actual #61 vs paper #61
0.3933 ±0.0279
actual #61 vs paper #61
paper 0.3933 ±0.0279

Improvement within reported uncertainty; not highlighted.

paper 0.3933 ±0.0279 Δ at pub 0.0224
64
ChebyNet
actual #64 vs paper #111 47 places worse
0.3917 ±0.0143
best reported
actual #64 vs paper #111 47 places worse
paper 0.3761 ±0.0089

Difference within reported uncertainty; not counted as underperformance.

paper 0.3761 ±0.0089 Δ at pub 0.0156
68
GraphSAGE
0.3899 ±0.0085
71
H2GCN
actual #71 vs paper #171 100 places worse
0.3885 ±0.0117
best reported
actual #71 vs paper #171 100 places worse
paper 0.3631 ±0.0258

Difference within reported uncertainty; not counted as underperformance.

paper 0.3631 ±0.0258 Δ at pub 0.0209 Δ today 0.0254
110
GraphGPS
actual #110 vs paper #110
0.3768 ±0.0094
actual #110 vs paper #110
paper 0.3768 ±0.0094
prev best: Even Sparser Graph Transformers (NeurIPS 2024)

Improvement within reported uncertainty; not highlighted.

paper 0.3768 ±0.0094 Δ at pub 0.0058
135
GCN
actual #135 vs paper #284 149 places worse
0.3690
best reported
actual #135 vs paper #284 149 places worse
paper 0.3323 ±0.0116
paper 0.3323 ±0.0116 Δ at pub 0.0367
136
NodeFormer
actual #136 vs paper #247 111 places worse
0.3690 ±0.0100
best reported
actual #136 vs paper #247 111 places worse
paper 0.3462 ±0.0182
best at pub: Even Sparser Graph Transformers (NeurIPS 2024)

Difference within reported uncertainty; not counted as underperformance.

paper 0.3462 ±0.0182 Δ at pub 0.0228
182
GAT
actual #182 vs paper #270 88 places worse
0.3605 ±0.0035
best reported
actual #182 vs paper #270 88 places worse
paper 0.3393 ±0.0247

Difference within reported uncertainty; not counted as underperformance.

paper 0.3393 ±0.0247 Δ at pub 0.0212

LINKX Benchmarks

#ModelAccuracy ↑Paper
1
DC-GNN
0.8669 ±0.0022
2
M2M-GNN
0.8594 ±0.0040
3
GloGNN
0.8574 ±0.0042
13
GPRGNN
actual #13 vs paper #37 24 places worse
0.8455 ±0.0054
best reported
actual #13 vs paper #37 24 places worse
paper 0.8138 ±0.0016
paper 0.8138 ±0.0016 Δ at pub 0.0317
14
Specformer
0.8432 ±0.0032
This paper
18
GrokFormer
0.8359 ±0.0026
This paper
22
JacobiConv
0.8335 ±0.0011
This paper
23
BernNet
actual #23 vs paper #30 7 places worse
0.8326 ±0.0029
best reported
actual #23 vs paper #30 7 places worse
paper 0.8247 ±0.0021
paper 0.8247 ±0.0021 Δ at pub 0.0079 Δ today 0.0079
24
H2GCN
actual #24 vs paper #37 13 places worse
0.8320 ±0.0055
best reported
actual #24 vs paper #37 13 places worse
paper 0.8131 ±0.0060
paper 0.8131 ±0.0060 Δ at pub 0.0189
29
GIN
0.8268 ±0.0032
31
GCN
0.8247 ±0.0027
This paper
36
GAT
0.8153 ±0.0055
This paper
39
ChebyNet
0.8109 ±0.0033
This paper
43
PolyFormer
0.7927 ±0.0026
This paper
49
SGFormer
0.7665 ±0.0049
This paper
51
MLP
0.7534 ±0.0064
55
NAGphormer
0.7398 ±0.0053
This paper
62
NodeFormer
0.6966 ±0.0083
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 Improved at pub — later paper surpassed this result Best today — OK at publication; today's leaderboard best is elsewhere