WWW 2026

Frequency-Corrupt Based Graph Self-Supervised Learning

Haojie Li, Mengjiao Zhang, Guanfeng Liu, Qiang Hu, Yan Wang, Junwei Du

Main figure for Frequency-Corrupt Based Graph Self-Supervised Learning

Abstract

Graph self-supervised learning (GSSL) alleviates the graph data labeling bottleneck without supervision, enabling wide application in domains like recommendation systems and social network analysis. High-frequency signals are valuable in GSSL for capturing local structural preferences, thereby enriching graph representations and boosting model performance. However, in practical applications, two critical problems hinder the efficient and robust use of these signals. First, the locality of high-frequency signals limits their full utilization by the model. Second, over-reliance on specific high-frequency signals will affect the model's generalization. To address the above problems, we propose the Frequency-Corrupt Based Graph Self-Supervised Learning (FC-GSSL) algorithm. Specifically, we generate corrupted graphs biased toward high-frequency signals by corrupting nodes and edges according to their low-frequency contributions. These corrupted graphs are fed as input to an autoencoder, with low-frequency and general features serving as the supervision. This compels the model to effectively fuse high- and low-frequency signals, thereby integrating and utilizing more valuable high-frequency information. Additionally, we design multiple sampling strategies and form diverse corrupted graphs based on the intersections and union between the results obtained from these strategies. By aligning the node representations from these views, the model can identify valuable frequency combinations, which helps reduce the negative impact of specific high-frequency components and improve generalization. FC-GSSL optimizes the design of GSSL for web applications, significantly improving model performance on complex web-related graphs, such as social networks and citation networks. This work makes a direct contribution to advancing the "Graph Algorithms and Modeling for the Web" research track. Experimental results on 14 datasets across multiple tasks illustrate the superiority of the proposed approach.

Proposed method: FC-GSSL

Benchmark Results

Tested on 6 datasets 11 baseline values reported too low

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

Heterophilic Graphs

#ModelAccuracy ↑Paper
1
DiGGR
0.4535 ±0.0353
2
TRIGON
0.4402 ±0.0028
3
DoG
0.4320 ±0.0120
18
FC-GSSL
0.4194 ±0.0092
This paper
42
MLP
0.4026 ±0.0108
68
GraphSAGE
0.3899 ±0.0085
77
GraphPAE
0.3855 ±0.0135
This paper
242
Sp^2GCL
0.3470 ±0.0092
This paper
247
MVGRL
actual #247 vs paper #247
0.3464 ±0.0020
actual #247 vs paper #247
paper 0.3464 ±0.0020
paper 0.3464 ±0.0020 Δ at pub 0.0255
252
GraphMAE2
0.3448 ±0.0026
This paper
280
MaskGAE
actual #280 vs paper #280
0.3344 ±0.0034
actual #280 vs paper #280
paper 0.3344 ±0.0034
paper 0.3344 ±0.0034 Δ at pub 0.0712
283
AUG-MAE
actual #283 vs paper #283
0.3342 ±0.0038
actual #283 vs paper #283
paper 0.3342 ±0.0038
paper 0.3342 ±0.0038 Δ at pub 0.0706
299
GraphMAE
actual #299 vs paper #299
0.3215 ±0.0133
actual #299 vs paper #299
paper 0.3215 ±0.0133
paper 0.3215 ±0.0133 Δ at pub 0.0318
309
VGAE
actual #309 vs paper #309
0.3157 ±0.0075
actual #309 vs paper #309
paper 0.3157 ±0.0075
paper 0.3157 ±0.0075 Δ at pub 0.0314
335
DGI
actual #335 vs paper #397 62 places worse
0.3067 ±0.0063
best reported
actual #335 vs paper #397 62 places worse
paper 0.2798 ±0.0009
paper 0.2798 ±0.0009 Δ at pub 0.0269
356
BGRL
actual #356 vs paper #412 56 places worse
0.2986
best reported
actual #356 vs paper #412 56 places worse
paper 0.2661 ±0.0057
400
CCA-SSG
actual #400 vs paper #400
0.2782 ±0.0060
best reported
actual #400 vs paper #400
paper 0.2779 ±0.0058

Difference within reported uncertainty; not counted as underperformance.

paper 0.2779 ±0.0058 Δ at pub 0.0003
420
S2GAE
0.2617 ±0.0038
This paper
#ModelAccuracy ↑Paper
1
Hetero-S (GAT 8-layer)
0.8693
2
Dir-GNN+CNA
0.8586 ±0.0180
3
GAT
0.8560
5
FC-GSSL
0.8231 ±0.0051
This paper
6
GraphPAE
0.8051 ±0.0125
This paper
16
GraphMAE
actual #16 vs paper #16
0.7950 ±0.0057
actual #16 vs paper #16
paper 0.7950 ±0.0057
paper 0.7950 ±0.0057 Δ at pub 0.1083
20
GraphMAE2
0.7913 ±0.0019
This paper
22
Sp^2GCL
0.7888 ±0.0104
This paper
27
CCA-SSG
actual #27 vs paper #27
0.7500 ±0.0075
actual #27 vs paper #27
paper 0.7500 ±0.0075
paper 0.7500 ±0.0075 Δ at pub 0.1259
30
MaskGAE
actual #30 vs paper #30
0.7450 ±0.0087
actual #30 vs paper #30
paper 0.7450 ±0.0087
paper 0.7450 ±0.0087 Δ at pub 0.1314
34
MVGRL
actual #34 vs paper #34
0.7319 ±0.0042
actual #34 vs paper #34
paper 0.7319 ±0.0042
paper 0.7319 ±0.0042 Δ at pub 0.1938
37
AUG-MAE
actual #37 vs paper #54 17 places worse
0.7219 ±0.0155
best reported
actual #37 vs paper #54 17 places worse
paper 0.7010 ±0.0188

Difference within reported uncertainty; not counted as underperformance.

paper 0.7010 ±0.0188 Δ at pub 0.0209
52
GCN
0.7033
95
BGRL
actual #95 vs paper #118 23 places worse
0.6486 ±0.0063
best reported
actual #95 vs paper #118 23 places worse
paper 0.6124 ±0.0107
paper 0.6124 ±0.0107 Δ at pub 0.0362 Δ today 0.0362
114
VGAE
actual #114 vs paper #114
0.6232 ±0.0190
actual #114 vs paper #114
paper 0.6232 ±0.0190
paper 0.6232 ±0.0190 Δ at pub 0.1967
134
DGI
actual #134 vs paper #230 96 places worse
0.6027 ±0.0070
best reported
actual #134 vs paper #230 96 places worse
paper 0.4383 ±0.0014
paper 0.4383 ±0.0014 Δ at pub 0.1644 Δ today 0.1644
135
S2GAE
0.6024 ±0.0037
This paper
169
MLP
0.5429
#ModelAccuracy ↑Paper
1
IBG-NN
0.7763 ±0.0179
2
Dir-GNN+CNA
0.7747 ±0.0128
3
DHGNN
0.7684 ±0.0161
12
FC-GSSL
0.7403 ±0.0084
This paper
17
GraphPAE
0.7205 ±0.0140
This paper
20
GraphMAE2
0.7027 ±0.0088
This paper
22
S2GAE
0.6860 ±0.0056
This paper
23
MaskGAE
actual #23 vs paper #23
0.6853 ±0.0044
actual #23 vs paper #23
paper 0.6853 ±0.0044
paper 0.6853 ±0.0044 Δ at pub 0.1813
37
Sp^2GCL
0.6261 ±0.0087
This paper
38
AUG-MAE
actual #38 vs paper #38
0.6257 ±0.0067
actual #38 vs paper #38
paper 0.6257 ±0.0067
paper 0.6257 ±0.0067 Δ at pub 0.0934
42
CCA-SSG
actual #42 vs paper #42
0.6158 ±0.0198
actual #42 vs paper #42
paper 0.6158 ±0.0198
paper 0.6158 ±0.0198 Δ at pub 0.1482
44
GraphMAE
actual #44 vs paper #44
0.6113 ±0.0060
actual #44 vs paper #44
paper 0.6113 ±0.0060
paper 0.6113 ±0.0060 Δ at pub 0.1622
46
GCN
0.6067
50
MVGRL
actual #50 vs paper #50
0.6009 ±0.0044
actual #50 vs paper #50
paper 0.6009 ±0.0044
paper 0.6009 ±0.0044 Δ at pub 0.2134
108
BGRL
actual #108 vs paper #130 22 places worse
0.4624 ±0.0070
best reported
actual #108 vs paper #130 22 places worse
paper 0.4324 ±0.0052
141
VGAE
actual #141 vs paper #141
0.4250 ±0.0135
actual #141 vs paper #141
paper 0.4250 ±0.0135
paper 0.4250 ±0.0135 Δ at pub 0.0739
144
DGI
actual #144 vs paper #225 81 places worse
0.4222 ±0.0063
best reported
actual #144 vs paper #225 81 places worse
paper 0.3456 ±0.0010
172
MLP
0.3930 ±0.0079

MoleculeNet

#ModelRMSE ↓Paper
1
SE(3)-I MPPH
0.3540 ±0.0530
2
ECFP-4 + RF
0.5600 ±0.0660
3
GPSE + GPS
0.6820
52
GraphPAE
actual #52 vs paper #69 17 places worse
2.0580 ±0.1900
best reported
actual #52 vs paper #69 17 places worse
paper 2.3480 ±0.2150

Difference within reported uncertainty; not counted as underperformance.

paper 2.3480 ±0.2150 Δ at pub 0.2900
56
InfoGraph
actual #56 vs paper #128 72 places worse
2.1040
best reported
actual #56 vs paper #128 72 places worse
paper 10.0050 ±8.1470

Difference within reported uncertainty; not counted as underperformance.

paper 10.0050 ±8.1470 Δ at pub 7.9010
66
FC-GSSL
2.2790 ±0.2330
This paper
69
GIN
2.3460 ±0.1220
70
AUG-MAE
2.3950 ±0.1580
This paper
76
StructMAE
2.5680 ±0.2620
This paper
83
GraphMAE
2.7400 ±0.2330
This paper
92
GraphMAE2
2.9130 ±0.2930
This paper
101
GraphCL
actual #101 vs paper #125 24 places worse
3.1660 ±0.0270
best reported
actual #101 vs paper #125 24 places worse
paper 7.6790 ±2.7480
104
JOAO
actual #104 vs paper #123 19 places worse
3.2820 ±0.0020
best reported
actual #104 vs paper #123 19 places worse
paper 5.1310 ±0.7820
117
Sp^2GCL
4.1440 ±0.5730
This paper
128
MVGRL
9.0240 ±1.9820
This paper

LINKX Benchmarks

#ModelAccuracy ↑Paper
1
DC-GNN
0.8669 ±0.0022
2
M2M-GNN
0.8594 ±0.0040
3
GloGNN
0.8574 ±0.0042
29
GIN
0.8268 ±0.0032
51
MLP
0.7534 ±0.0064
58
FC-GSSL
0.7350 ±0.0040
This paper
59
GraphPAE
0.7179 ±0.0037
This paper
60
S2GAE
0.7024 ±0.0009
This paper
61
AUG-MAE
0.6990 ±0.0043
This paper
63
Sp^2GCL
0.6880 ±0.0045
This paper
64
GraphMAE
0.6797 ±0.0021
This paper
65
GraphMAE2
0.6786 ±0.0042
This paper
66
MaskGAE
0.6384 ±0.0003
This paper
67
CCA-SSG
actual #67 vs paper #68 1 place worse
0.6346 ±0.0036
best reported
actual #67 vs paper #68 1 place worse
paper 0.6263 ±0.0020
paper 0.6263 ±0.0020 Δ at pub 0.0083
68
BGRL
actual #68 vs paper #68
0.6331 ±0.0049
actual #68 vs paper #68
paper 0.6331 ±0.0049
paper 0.6331 ±0.0049 Δ at pub 0.0433
72
VGAE
actual #72 vs paper #76 4 places worse
0.5829 ±0.0021
best reported
actual #72 vs paper #76 4 places worse
paper 0.5531 ±0.0028
paper 0.5531 ±0.0028 Δ at pub 0.0298
#ModelAccuracy ↑Paper
1
LargeScaleNet
0.6582 ±0.0036
2
S² DirGCN
0.6495 ±0.0033
3
FaberNet
0.6462 ±0.0101
31
GCN
0.4602 ±0.0026
38
BGRL
actual #38 vs paper #42 4 places worse
0.4302 ±0.0062
best reported
actual #38 vs paper #42 4 places worse
paper 0.4143 ±0.0004
paper 0.4143 ±0.0004 Δ at pub 0.0159
41
FC-GSSL
0.4200 ±0.0011
This paper
42
GraphPAE
0.4185 ±0.0004
This paper
43
CCA-SSG
actual #43 vs paper #43
0.4078 ±0.0001
actual #43 vs paper #43
paper 0.4078 ±0.0001
paper 0.4078 ±0.0001 Δ at pub 0.0127
45
MaskGAE
0.4059 ±0.0004
This paper
46
S2GAE
0.4032 ±0.0012
This paper
47
GraphMAE
0.4030 ±0.0004
This paper
50
Sp^2GCL
0.3909 ±0.0002
This paper
51
GraphMAE2
0.3897 ±0.0003
This paper
55
AUG-MAE
0.3710 ±0.0013
This paper
56
MLP
0.3670 ±0.0021
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