NeurIPS 2025

Relieving the Over-Aggregating Effect in Graph Transformers

Junshu Sun, Wanxing Chang, Chen Yang, Qingming Huang, Shuhui Wang

Main figure for Relieving the Over-Aggregating Effect in Graph Transformers

Abstract

Graph attention has demonstrated superior performance in graph learning tasks. However, learning from global interactions can be challenging due to the large number of nodes. In this paper, we discover a new phenomenon termed over-aggregating. Over-aggregating arises when a large volume of messages is aggregated into a single node with less discrimination, leading to the dilution of the key messages and potential information loss. To address this, we propose Wideformer, a plug-and-play method for graph attention. Wideformer divides the aggregation of all nodes into parallel processes and guides the model to focus on specific subsets of these processes. The division can limit the input volume per aggregation, avoiding message dilution and reducing information loss. The guiding step sorts and weights the aggregation outputs, prioritizing the informative messages. Evaluations show that Wideformer can effectively mitigate over-aggregating. As a result, the backbone methods can focus on the informative messages, achieving superior performance compared to baseline methods.

Benchmark Results

Tested on 6 datasets 12 baseline values reported too low Non-standard metric on 1 dataset

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

Classic

#ModelAccuracy ↑Paper
1
CNA
0.9575 ±0.0058
2
IS-GIB
0.9390 ±0.0187
3
EERM
0.9112 ±0.0145
35
GAT
actual #35 vs paper #446 411 places worse
0.8080 ±0.0026
best reported
actual #35 vs paper #446 411 places worse
paper 0.7210 ±0.0110
paper 0.7210 ±0.0110 Δ at pub 0.0870
44
GCN
actual #44 vs paper #496 452 places worse
0.8033 ±0.0088
best reported
actual #44 vs paper #496 452 places worse
paper 0.7160 ±0.0040
paper 0.7160 ±0.0040 Δ at pub 0.0873
61
GraphSAGE
actual #61 vs paper #461 400 places worse
0.7923 ±0.0053
best reported
actual #61 vs paper #461 400 places worse
paper 0.7193 ±0.0085
paper 0.7193 ±0.0085 Δ at pub 0.0730
74
GraphGPS + Wideformer
0.7861 ±0.0035
This paper
86
GraphGPS+Entropy Reg
0.7819 ±0.0039
This paper
89
SGFormer
actual #89 vs paper #624 535 places worse
0.7798 ±0.0091
best reported
actual #89 vs paper #624 535 places worse
paper 0.6993 ±0.0031
paper 0.6993 ±0.0031 Δ at pub 0.0805
91
GraphGPS
0.7796 ±0.0037
This paper
259
SAGE
0.7361 ±0.0190
344
Exphormer
actual #344 vs paper #494 150 places worse
0.7290 ±0.0040
best reported
actual #344 vs paper #494 150 places worse
paper 0.7163 ±0.0119

Difference within reported uncertainty; not counted as underperformance.

paper 0.7163 ±0.0119 Δ at pub 0.0127
350
MLP
0.7289 ±0.0010
584
SGFormer + Wideformer
0.7063 ±0.0078
This paper
615
SGFormer + Entropy Reg
0.7012 ±0.0041
This paper
683
Polynormer + Wideformer
0.6810 ±0.0042
This paper
713
Polynormer + Entropy Reg
0.6721 ±0.0035
This paper
734
Polynormer
0.6643 ±0.0150
This paper

Heterophily Benchmark

Roman-empire

Global leaderboard →
Non-default metric. This paper reports ROC-AUC; the dataset default is Accuracy. Values below use ROC-AUC only.

Sorted by ROC-AUC. Highlighted rows are from other papers.

#ModelROC-AUC ↑Paper
1
Polynormer + Wideformer
0.9216 ±0.0024
This paper
2
Polynormer
0.9183 ±0.0016
This paper
3
Exphormer
0.8903 ±0.0037
This paper
4
GAT
0.8875 ±0.0041
This paper
5
GraphSAGE
0.8574 ±0.0067
This paper
6
GraphGPS + Wideformer
0.8212 ±0.0039
This paper
7
GraphGPS
0.8146 ±0.0040
This paper
8
DIFFormer
0.7910 ±0.0032
This paper
9
SGFormer + Wideformer
0.7703 ±0.0038
This paper
10
SGFormer
0.7520 ±0.0089
This paper
11
NAGphormer
0.7434 ±0.0077
This paper
12
GCN
0.7369 ±0.0074
This paper
13
GOAT
0.7159 ±0.0125
This paper
14
GPRGNN
0.6485 ±0.0027
This paper
15
NodeFormer
0.6449 ±0.0073
This paper
#ModelAccuracy ↑Paper
1
UniGAP
0.6375 ±0.0110
2
H2GCN + HalfHop
0.5961 ±0.0100
3
GraphSAGE + HalfHop
0.5897 ±0.0150
12
SAGE
0.5569 ±0.0023
14
GAT
actual #14 vs paper #51 37 places worse
0.5270 ±0.0062
actual #14 vs paper #51 37 places worse
paper 0.5270 ±0.0062
paper 0.5270 ±0.0062 Δ at pub 0.0214 Δ today 0.0289
15
GraphSAGE
actual #15 vs paper #30 15 places worse
0.5540 ±0.0020
best reported
actual #15 vs paper #30 15 places worse
paper 0.5363 ±0.0039
17
Polynormer + Wideformer
0.5505 ±0.0008
This paper
18
Polynormer
actual #18 vs paper #20 2 places worse
0.5471 ±0.0017
actual #18 vs paper #20 2 places worse
paper 0.5471 ±0.0017

Improvement within reported uncertainty; not highlighted.

paper 0.5471 ±0.0017 Δ at pub 0.0025
19
Polynormer +ENACT
0.5494
This paper
23
SGFormer
actual #23 vs paper #55 32 places worse
0.5414 ±0.0062
best reported
actual #23 vs paper #55 32 places worse
paper 0.5238 ±0.0022
24
GCN
actual #24 vs paper #111 87 places worse
0.5411 ±0.0034
best reported
actual #24 vs paper #111 87 places worse
paper 0.4870 ±0.0063
32
Exphormer
0.5351 ±0.0046
This paper
35
SGFormer + Wideformer
0.5347 ±0.0014
This paper
39
SGFormer +ENACT
0.5332
This paper
40
GraphGPS
actual #40 vs paper #97 57 places worse
0.5327 ±0.0066
best reported
actual #40 vs paper #97 57 places worse
paper 0.4973 ±0.0011
71
NAGphormer
0.5126 ±0.0072
This paper
84
MLP
0.5058
94
GraphGPS + Wideformer
0.4996 ±0.0041
This paper
115
GraphGPS +ENACT
0.4852
This paper
125
DIFFormer
0.4784 ±0.0065
This paper
149
GPRGNN
0.4488 ±0.0034
This paper
152
GOAT
0.4461 ±0.0050
This paper
160
NodeFormer
0.4386 ±0.0035
This paper
#ModelROC-AUC ↑Paper
1
BuNN
0.9899 ±0.0016
2
DC-GNN
0.9850 ±0.0021
3
Tango -GPS
0.9839 ±0.0054
6
Polynormer + Wideformer
0.9726 ±0.0001
This paper
7
Polynormer + Entropy Reg
0.9720 ±0.0032
This paper
8
Polynormer
actual #8 vs paper #8
0.9713 ±0.0017
actual #8 vs paper #8
paper 0.9713 ±0.0017

Improvement within reported uncertainty; not highlighted.

paper 0.9713 ±0.0017 Δ at pub 0.0017
36
GAT
actual #36 vs paper #36
0.9391 ±0.0035
actual #36 vs paper #36
paper 0.9391 ±0.0035
paper 0.9391 ±0.0035 Δ at pub 0.0153
42
GraphSAGE
actual #42 vs paper #45 3 places worse
0.9358 ±0.0005
best reported
actual #42 vs paper #45 3 places worse
paper 0.9351 ±0.0057

Difference within reported uncertainty; not counted as underperformance.

paper 0.9351 ±0.0057 Δ at pub 0.0007
45
GraphGPS + Wideformer
0.9352 ±0.0007
This paper
46
SAGE
0.9351 ±0.0057
48
GraphGPS+Entropy Reg
0.9335 ±0.0023
This paper
49
GraphGPS
actual #49 vs paper #49
0.9326 ±0.0010
actual #49 vs paper #49
paper 0.9326 ±0.0010
paper 0.9326 ±0.0010 Δ at pub 0.0263
59
Exphormer
actual #59 vs paper #112 53 places worse
0.9226 ±0.0056
best reported
actual #59 vs paper #112 53 places worse
paper 0.8419 ±0.0053
best at pub: Even Sparser Graph Transformers (NeurIPS 2024)
paper 0.8419 ±0.0053 Δ at pub 0.0807
68
GCN
actual #68 vs paper #88 20 places worse
0.9150 ±0.0006
best reported
actual #68 vs paper #88 20 places worse
paper 0.8975 ±0.0052
paper 0.8975 ±0.0052 Δ at pub 0.0175
75
DIFFormer
0.9089 ±0.0058
This paper
97
SGFormer + Wideformer
0.8902 ±0.0022
This paper
99
SGFormer + Entropy Reg
0.8887 ±0.0033
This paper
102
SGFormer
actual #102 vs paper #102
0.8860 ±0.0049
actual #102 vs paper #102
paper 0.8860 ±0.0049
108
NodeFormer
0.8671 ±0.0088
This paper
109
GPRGNN
actual #109 vs paper #109
0.8624 ±0.0061
actual #109 vs paper #109
paper 0.8624 ±0.0061
113
NAGphormer
0.8419 ±0.0066
This paper
118
GOAT
0.8109 ±0.0102
This paper
156
MLP
0.5099 ±0.0147
#ModelROC-AUC ↑Paper
1
Polynormer-r
0.8591 ±0.0074
2
DC-GNN
0.8588 ±0.0081
3
TANGO-GPS
0.8566 ±0.0101
7
Polynormer + Wideformer
0.8533 ±0.0023
This paper
8
Polynormer + Entropy Reg
0.8521 ±0.0033
This paper
12
Polynormer
actual #12 vs paper #12
0.8509 ±0.0021
actual #12 vs paper #12
paper 0.8509 ±0.0021

Improvement within reported uncertainty; not highlighted.

paper 0.8509 ±0.0021 Δ at pub 0.0026
24
GraphGPS + Wideformer
0.8467 ±0.0066
This paper
28
GAT
actual #28 vs paper #40 12 places worse
0.8443 ±0.0100
best reported
actual #28 vs paper #40 12 places worse
paper 0.8378 ±0.0043

Difference within reported uncertainty; not counted as underperformance.

paper 0.8378 ±0.0043 Δ at pub 0.0065
35
GraphGPS+Entropy Reg
0.8423 ±0.0051
This paper
39
GraphGPS
actual #39 vs paper #39
0.8395 ±0.0081
actual #39 vs paper #39
paper 0.8395 ±0.0081

Improvement within reported uncertainty; not highlighted.

paper 0.8395 ±0.0081 Δ at pub 0.0024
42
Exphormer
0.8377 ±0.0078
This paper
50
GCN
0.8364 ±0.0067
This paper
51
DIFFormer
0.8357 ±0.0068
This paper
59
SGFormer
actual #59 vs paper #79 20 places worse
0.8333 ±0.0068
best reported
actual #59 vs paper #79 20 places worse
paper 0.8224 ±0.0013
paper 0.8224 ±0.0013 Δ at pub 0.0109
62
GOAT
0.8311 ±0.0104
This paper
72
SGFormer + Wideformer
0.8255 ±0.0003
This paper
77
GraphSAGE
0.8243 ±0.0044
This paper
76
SAGE
0.8243 ±0.0044
78
SGFormer + Entropy Reg
0.8239 ±0.0019
This paper
110
NAGphormer
0.7832 ±0.0095
This paper
117
NodeFormer
0.7810 ±0.0103
This paper
139
MLP
0.7362 ±0.0020
144
GPRGNN
0.7294 ±0.0097
This paper
#ModelROC-AUC ↑Paper
1
NID_GAT
0.9703 ±0.0002
2
NID_GCN
0.9685 ±0.0010
3
UniGAP
0.8421 ±0.0080
16
GCN
actual #16 vs paper #62 46 places worse
0.7902 ±0.0060
best reported
actual #16 vs paper #62 46 places worse
paper 0.7609 ±0.0127
17
Polynormer + Wideformer
0.7900 ±0.0020
This paper
23
Polynormer + Entropy Reg
0.7869 ±0.0024
This paper
24
Polynormer
actual #24 vs paper #24
0.7866 ±0.0050
actual #24 vs paper #24
paper 0.7866 ±0.0050

Improvement within reported uncertainty; not highlighted.

paper 0.7866 ±0.0050 Δ at pub 0.0071
26
GAT
actual #26 vs paper #53 27 places worse
0.7835 ±0.0116
best reported
actual #26 vs paper #53 27 places worse
paper 0.7679 ±0.0071
paper 0.7679 ±0.0071 Δ at pub 0.0156
46
GraphSAGE
actual #46 vs paper #57 11 places worse
0.7721 ±0.0130
best reported
actual #46 vs paper #57 11 places worse
paper 0.7644 ±0.0062

Difference within reported uncertainty; not counted as underperformance.

paper 0.7644 ±0.0062 Δ at pub 0.0077
50
SGFormer + Wideformer
0.7694 ±0.0005
This paper
52
SGFormer + Entropy Reg
0.7683 ±0.0018
This paper
53
SGFormer
actual #53 vs paper #53
0.7681 ±0.0009
actual #53 vs paper #53
paper 0.7681 ±0.0009
paper 0.7681 ±0.0009 Δ at pub 0.0376
58
SAGE
0.7644 ±0.0062
66
GOAT
0.7576 ±0.0166
This paper
68
GraphGPS + Wideformer
0.7569 ±0.0117
This paper
73
GraphGPS
actual #73 vs paper #73
0.7548 ±0.0066
actual #73 vs paper #73
paper 0.7548 ±0.0066
paper 0.7548 ±0.0066 Δ at pub 0.0333
82
NodeFormer
0.7427 ±0.0146
This paper
83
Exphormer
0.7394 ±0.0106
This paper
89
DIFFormer
0.7215 ±0.0131
This paper
96
MLP
0.7082 ±0.0010
116
NAGphormer
0.6817 ±0.0153
This paper
150
GPRGNN
0.5548 ±0.0091
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