Self-Supervised Graph Learning via Spectral Bootstrapping and Laplacian-Based Augmentations

Lorenzo Bini, Stéphane Marchand-Maillet

Main figure for Self-Supervised Graph Learning via Spectral Bootstrapping and Laplacian-Based Augmentations

Abstract

We present LaplaceGNN, a novel self-supervised graph learning framework that bypasses the need for negative sampling by leveraging spectral bootstrapping techniques. Our method integrates Laplacian-based signals into the learning process, allowing the model to effectively capture rich structural representations without relying on contrastive objectives or handcrafted augmentations. By focusing on positive alignment, LaplaceGNN achieves linear scaling while offering a simpler, more efficient, self-supervised alternative for graph neural networks, applicable across diverse domains. Our contributions are twofold: we precompute spectral augmentations through max-min centrality-guided optimization, enabling rich structural supervision without relying on handcrafted augmentations, then we integrate an adversarial bootstrapped training scheme that further strengthens feature learning and robustness. Our extensive experiments on different benchmark datasets show that LaplaceGNN achieves superior performance compared to state-of-the-art self-supervised graph methods, offering a promising direction for efficiently learning expressive graph representations.

Proposed method: LaplaceGNN

Benchmark Results

Tested on 8 datasets 13 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
0.9669 ±0.0014
3
GAT+T
0.9660 ±0.0007
7
SAGE
0.9643 ±0.0027
22
LaplaceGNN
0.9570 ±0.0015
This paper
164
GraphMAE
actual #164 vs paper #443 279 places worse
0.9341 ±0.0010
best reported
actual #164 vs paper #443 279 places worse
paper 0.9005 ±0.0008
paper 0.9005 ±0.0008 Δ at pub 0.0336
172
BGRL
actual #172 vs paper #198 26 places worse
0.9337 ±0.0021
best reported
actual #172 vs paper #198 26 places worse
paper 0.9317 ±0.0030

Difference within reported uncertainty; not counted as underperformance.

paper 0.9317 ±0.0030 Δ at pub 0.0020
184
Supervised GCN
actual #184 vs paper #292 108 places worse
0.9328 ±0.0003
best reported
actual #184 vs paper #292 108 places worse
paper 0.9242 ±0.0022
paper 0.9242 ±0.0022 Δ at pub 0.0086
189
Sp^2GCL
0.9323 ±0.0026
This paper
203
GRACE
actual #203 vs paper #244 41 places worse
0.9313 ±0.0017
best reported
actual #203 vs paper #244 41 places worse
paper 0.9278 ±0.0045

Difference within reported uncertainty; not counted as underperformance.

paper 0.9278 ±0.0045 Δ at pub 0.0035
269
SSGE
0.9261 ±0.0022
This paper
390
MLP
0.9128 ±0.0063
#ModelAccuracy ↑Paper
1
GraphTARIF
0.9461 ±0.0017
2
GCN
0.9412 ±0.0008
3
GAT
0.9398 ±0.0022
8
SAGE
0.9351 ±0.0006
19
LaplaceGNN
0.9230 ±0.0023
This paper
79
BGRL
0.9034 ±0.0019
This paper
96
Sp^2GCL
0.9009 ±0.0032
This paper
100
GraphMAE
actual #100 vs paper #277 177 places worse
0.9002 ±0.0024
best reported
actual #100 vs paper #277 177 places worse
paper 0.8628 ±0.0007
paper 0.8628 ±0.0007 Δ at pub 0.0374
139
GRACE
0.8953 ±0.0035
This paper
154
SSGE
0.8905 ±0.0058
This paper
205
Supervised GCN
actual #205 vs paper #269 64 places worse
0.8811 ±0.0014
best reported
actual #205 vs paper #269 64 places worse
paper 0.8651 ±0.0054
paper 0.8651 ±0.0054 Δ at pub 0.0160
320
MLP
0.8463
#ModelAccuracy ↑Paper
1
GrokFormer
0.9831 ±0.0018
2
PolyFormer
0.9808 ±0.0027
3
SGFormer
0.9796 ±0.0081
9
GCN
0.9774 ±0.0035
36
LaplaceGNN
0.9672 ±0.0011
This paper
58
MLP
0.9597 ±0.0007
69
BGRL
actual #69 vs paper #88 19 places worse
0.9580 ±0.0040
best reported
actual #69 vs paper #88 19 places worse
paper 0.9569 ±0.0005

Difference within reported uncertainty; not counted as underperformance.

paper 0.9569 ±0.0005 Δ at pub 0.0011
91
Supervised GCN
0.9565 ±0.0016
This paper
117
GraphMAE
actual #117 vs paper #161 44 places worse
0.9550 ±0.0010
best reported
actual #117 vs paper #161 44 places worse
paper 0.9490 ±0.0009
paper 0.9490 ±0.0009 Δ at pub 0.0050 Δ today 0.0060
193
SSGE
0.9410 ±0.0021
This paper
206
Sp^2GCL
0.9377 ±0.0025
This paper
#ModelAccuracy ↑Paper
1
GCN
0.9302 ±0.0011
2
RSE + RGCN (70b)
0.8852 ±0.0019
3
LEMP+T
0.8825
9
SAGE
0.8771
60
LaplaceGNN
0.8234 ±0.0038
This paper
84
GraphMAE
actual #84 vs paper #264 180 places worse
0.8052 ±0.0032
best reported
actual #84 vs paper #264 180 places worse
paper 0.7060 ±0.0090
paper 0.7060 ±0.0090 Δ at pub 0.0992
94
GRACE
0.8014 ±0.0048
This paper
100
BGRL
actual #100 vs paper #100
0.8000 ±0.0010
best reported
actual #100 vs paper #100
paper 0.7998 ±0.0010

Difference within reported uncertainty; not counted as underperformance.

paper 0.7998 ±0.0010 Δ at pub 0.0002 Δ today 0.0002
114
Sp^2GCL
0.7942 ±0.0019
This paper
128
SSGE
actual #128 vs paper #128
0.7919 ±0.0057
actual #128 vs paper #128
paper 0.7919 ±0.0057

Improvement within reported uncertainty; not highlighted.

paper 0.7919 ±0.0057 Δ at pub 0.0001
203
Supervised GCN
0.7719 ±0.0012
This paper
237
MLP
0.7469 ±0.0085
#ModelAccuracy ↑Paper
1
DoG
0.9690 ±0.0030
2
GWN-fa
0.9667 ±0.0026
3
GWN-sym
0.9666 ±0.0026
6
GraphSAGE
0.9593 ±0.0025
15
LaplaceGNN
0.9486 ±0.0016
This paper
45
SSGE
actual #45 vs paper #66 21 places worse
0.9346 ±0.0045
best reported
actual #45 vs paper #66 21 places worse
paper 0.9306 ±0.0041

Difference within reported uncertainty; not counted as underperformance.

paper 0.9306 ±0.0041 Δ at pub 0.0040
53
BGRL
0.9331 ±0.0013
This paper
63
GraphMAE
actual #63 vs paper #175 112 places worse
0.9313 ±0.0015
best reported
actual #63 vs paper #175 112 places worse
paper 0.8770 ±0.0004
paper 0.8770 ±0.0004 Δ at pub 0.0543
68
Supervised GCN
0.9303 ±0.0031
This paper
69
GRACE
actual #69 vs paper #148 79 places worse
0.9301 ±0.0003
best reported
actual #69 vs paper #148 79 places worse
paper 0.9112 ±0.0020
paper 0.9112 ±0.0020 Δ at pub 0.0189
88
MLP
0.9280 ±0.0020
100
Sp^2GCL
0.9261 ±0.0024
This paper

TU Dortmund

#ModelAccuracy ↑Paper
1
MSH-GNN
0.9910 ±0.0030
2
ID-GNN+BEC
0.9830 ±0.0360
3
SupCosine
0.9830 ±0.0250
39
GIN
0.9330 ±0.0290
47
LaplaceGNN
0.9285 ±0.0074
This paper
105
InfoGCL
actual #105 vs paper #137 32 places worse
0.9120 ±0.0130
best reported
actual #105 vs paper #137 32 places worse
paper 0.9062 ±0.0132

Difference within reported uncertainty; not counted as underperformance.

paper 0.9062 ±0.0132 Δ at pub 0.0058 Δ today 0.0058
199
MVGRL
actual #199 vs paper #212 13 places worse
0.8993 ±0.0616
best reported
actual #199 vs paper #212 13 places worse
paper 0.8972 ±0.0113

Difference within reported uncertainty; not counted as underperformance.

paper 0.8972 ±0.0113 Δ at pub 0.0021
257
InfoGraph
actual #257 vs paper #272 15 places worse
0.8930 ±0.0514
best reported
actual #257 vs paper #272 15 places worse
paper 0.8901 ±0.0113

Difference within reported uncertainty; not counted as underperformance.

paper 0.8901 ±0.0113 Δ at pub 0.0029
258
GraphMAE
actual #258 vs paper #326 68 places worse
0.8930 ±0.0110
best reported
actual #258 vs paper #326 68 places worse
paper 0.8812 ±0.0132

Difference within reported uncertainty; not counted as underperformance.

paper 0.8812 ±0.0132 Δ at pub 0.0118
325
AugMAE
0.8821 ±0.0102
This paper
403
MLP
0.8660 ±0.0495
432
Supervised GCN
0.8563 ±0.0584
This paper
#ModelAccuracy ↑Paper
1
WL-MLP
0.9954
2
GIN
0.9934
3
GCN
0.9727
120
LaplaceGNN
0.8221 ±0.0042
This paper
131
GraphSAGE
0.8200 ±0.0100
200
GraphMAE
actual #200 vs paper #200
0.8042 ±0.0035
actual #200 vs paper #200
paper 0.8042 ±0.0035

Improvement within reported uncertainty; not highlighted.

paper 0.8042 ±0.0035 Δ at pub 0.0002
214
Supervised GCN
0.8021 ±0.0202
This paper
215
InfoGCL
actual #215 vs paper #230 15 places worse
0.8020 ±0.0060
best reported
actual #215 vs paper #230 15 places worse
paper 0.7981 ±0.0046

Difference within reported uncertainty; not counted as underperformance.

paper 0.7981 ±0.0046 Δ at pub 0.0039 Δ today 0.0039
220
AugMAE
0.8011 ±0.0043
This paper
338
InfoGraph
actual #338 vs paper #440 102 places worse
0.7750 ±0.0074
best reported
actual #338 vs paper #440 102 places worse
paper 0.7382 ±0.0071
paper 0.7382 ±0.0071 Δ at pub 0.0368
356
MVGRL
actual #356 vs paper #410 54 places worse
0.7700 ±0.0080
best reported
actual #356 vs paper #410 54 places worse
paper 0.7502 ±0.0072
paper 0.7502 ±0.0072 Δ at pub 0.0198 Δ today 0.0198
#ModelAccuracy ↑Paper
1
WL-MLP
0.9792
2
MSH-GNN
0.9640 ±0.0070
3
CoCN
0.8722 ±0.0013
22
GraphMAE
actual #22 vs paper #109 87 places worse
0.8270 ±0.0100
best reported
actual #22 vs paper #109 87 places worse
paper 0.8033 ±0.0063
paper 0.8033 ±0.0063 Δ at pub 0.0237
23
GCN
0.8260 ±0.0220
25
LaplaceGNN
0.8241 ±0.0042
This paper
104
MVGRL
actual #104 vs paper #290 186 places worse
0.8048 ±0.0029
best reported
actual #104 vs paper #290 186 places worse
paper 0.7131 ±0.0121
paper 0.7131 ±0.0121 Δ at pub 0.0917
108
AugMAE
0.8040 ±0.0052
This paper
126
InfoGCL
actual #126 vs paper #126
0.8001 ±0.0132
actual #126 vs paper #126
paper 0.8001 ±0.0132

Improvement within reported uncertainty; not highlighted.

paper 0.8001 ±0.0132 Δ at pub 0.0001
146
InfoGraph
actual #146 vs paper #295 149 places worse
0.7940
best reported
actual #146 vs paper #295 149 places worse
paper 0.7062 ±0.0112
paper 0.7062 ±0.0112 Δ at pub 0.0878
151
MLP
0.7920 ±0.0240
156
Supervised GCN
0.7901 ±0.0181
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)