SpeGCL: Self-supervised Graph Spectrum Contrastive Learning without Positive Samples

Yuntao Shou, Xiangyong Cao, Deyu Meng

Main figure for SpeGCL: Self-supervised Graph Spectrum Contrastive Learning without Positive Samples

Abstract

Graph Contrastive Learning (GCL) excels at managing noise and fluctuations in input data, making it popular in various fields (e.g., social networks, and knowledge graphs). Our study finds that the difference in high-frequency information between augmented graphs is greater than that in low-frequency information. However, most existing GCL methods focus mainly on the time domain (low-frequency information) for node feature representations and cannot make good use of high-frequency information to speed up model convergence. Furthermore, existing GCL paradigms optimize graph embedding representations by pulling the distance between positive sample pairs closer and pushing the distance between positive and negative sample pairs farther away, but our theoretical analysis shows that graph contrastive learning benefits from pushing negative pairs farther away rather than pulling positive pairs closer. To solve the above-mentioned problems, we propose a novel spectral GCL framework without positive samples, named SpeGCL. Specifically, to solve the problem that existing GCL methods cannot utilize high-frequency information, SpeGCL uses a Fourier transform to extract high-frequency and low-frequency information of node features, and constructs a contrastive learning mechanism in a Fourier space to obtain better node feature representation. Furthermore, SpeGCL relies entirely on negative samples to refine the graph embedding. We also provide a theoretical justification for the efficacy of using only negative samples in SpeGCL. Extensive experiments on un-supervised learning, transfer learning, and semi-supervised learning have validated the superiority of our SpeGCL framework over the state-of-the-art GCL methods.

Proposed method: SpeGCL

Benchmark Results

Tested on 11 datasets 14 baseline values reported too low Non-standard metric on 6 datasets

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

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
76
SpeGCL
0.9186 ±0.0274
This paper
129
LAMP-Soft
0.9089 ±0.0104
This paper
155
GCS
actual #155 vs paper #155
0.9045 ±0.0081
actual #155 vs paper #155
paper 0.9045 ±0.0081
paper 0.9045 ±0.0081 Δ at pub 0.0226
159
WL
actual #159 vs paper #596 437 places worse
0.9040 ±0.0570
best reported
actual #159 vs paper #596 437 places worse
paper 0.8072 ±0.0300
paper 0.8072 ±0.0300 Δ at pub 0.0968
179
SEGA
0.9021 ±0.0066
This paper
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
302
AutoGCL
0.8864 ±0.0108
This paper
354
GraphCL
actual #354 vs paper #396 42 places worse
0.8766 ±0.0103
best reported
actual #354 vs paper #396 42 places worse
paper 0.8680 ±0.0134

Difference within reported uncertainty; not counted as underperformance.

paper 0.8680 ±0.0134 Δ at pub 0.0086
365
DGK
0.8744 ±0.0272
This paper
403
MLP
0.8660 ±0.0495
407
graph2vec
actual #407 vs paper #517 110 places worse
0.8644 ±0.0125
best reported
actual #407 vs paper #517 110 places worse
paper 0.8315 ±0.0925

Difference within reported uncertainty; not counted as underperformance.

paper 0.8315 ±0.0925 Δ at pub 0.0329
444
GL
actual #444 vs paper #577 133 places worse
0.8520 ±0.0090
best reported
actual #444 vs paper #577 133 places worse
paper 0.8166 ±0.0211
paper 0.8166 ±0.0211 Δ at pub 0.0354
472
Sub2Vec
actual #472 vs paper #786 314 places worse
0.8447 ±0.0037
best reported
actual #472 vs paper #786 314 places worse
paper 0.6105 ±0.1580

Difference within reported uncertainty; not counted as underperformance.

paper 0.6105 ±0.1580 Δ at pub 0.2342
746
Node2Vec
0.7263 ±0.1020
This paper
#ModelAccuracy ↑Paper
1
WL-MLP
0.9954
2
GIN
0.9934
3
GCN
0.9727
12
WL
actual #12 vs paper #223 211 places worse
0.8590 ±0.0010
best reported
actual #12 vs paper #223 211 places worse
paper 0.8001 ±0.0050
best at pub: Propagation Kernels (2014)
paper 0.8001 ±0.0050 Δ at pub 0.0589
104
GraphCL
actual #104 vs paper #325 221 places worse
0.8250 ±0.0013
best reported
actual #104 vs paper #325 221 places worse
paper 0.7787 ±0.0041
paper 0.7787 ±0.0041 Δ at pub 0.0463
124
LAMP-Soft
0.8217 ±0.0048
This paper
125
SpeGCL
0.8214 ±0.0112
This paper
133
AutoGCL
0.8200 ±0.0029
This paper
131
GraphSAGE
0.8200 ±0.0100
210
DGK
0.8031 ±0.0046
This paper
264
SEGA
0.7900 ±0.0072
This paper
338
InfoGraph
actual #338 vs paper #386 48 places worse
0.7750 ±0.0074
best reported
actual #338 vs paper #386 48 places worse
paper 0.7620 ±0.0106

Difference within reported uncertainty; not counted as underperformance.

paper 0.7620 ±0.0106 Δ at pub 0.0130
344
GCS
actual #344 vs paper #344
0.7737 ±0.0030
actual #344 vs paper #344
paper 0.7737 ±0.0030

Improvement within reported uncertainty; not highlighted.

paper 0.7737 ±0.0030 Δ at pub 0.0019
#ModelAccuracy ↑Paper
1
MSH-GNN
0.9410 ±0.0330
2
GRDL
0.8260 ±0.0120
3
GMN
0.8225
32
GIN
0.7880 ±0.0410
48
SpeGCL
0.7805 ±0.0123
This paper
65
LAMP-Soft
0.7734 ±0.0053
This paper
146
SEGA
0.7601 ±0.0066
This paper
149
MLP
0.7600 ±0.0320
168
AutoGCL
actual #168 vs paper #168
0.7580 ±0.0036
actual #168 vs paper #168
paper 0.7580 ±0.0036
paper 0.7580 ±0.0036 Δ at pub 0.0740
178
DGK
actual #178 vs paper #349 171 places worse
0.7568 ±0.0054
best reported
actual #178 vs paper #349 171 places worse
paper 0.7330 ±0.0082
best today: Hierarchical Graph Capsule Network (AAAI 2020)
paper 0.7330 ±0.0082 Δ at pub 0.0238 Δ today 0.0238
190
WL
actual #190 vs paper #369 179 places worse
0.7560 ±0.0040
best reported
actual #190 vs paper #369 179 places worse
paper 0.7292 ±0.0056
paper 0.7292 ±0.0056 Δ at pub 0.0268
245
GCS
actual #245 vs paper #245
0.7502 ±0.0081
actual #245 vs paper #245
paper 0.7502 ±0.0081

Improvement within reported uncertainty; not highlighted.

paper 0.7502 ±0.0081 Δ at pub 0.0098
265
GraphCL
actual #265 vs paper #296 31 places worse
0.7489 ±0.0065
best reported
actual #265 vs paper #296 31 places worse
paper 0.7439 ±0.0045

Difference within reported uncertainty; not counted as underperformance.

paper 0.7439 ±0.0045 Δ at pub 0.0050
294
InfoGraph
0.7444 ±0.0031
This paper
309
JOAOv2
actual #309 vs paper #434 125 places worse
0.7407 ±0.0110
best reported
actual #309 vs paper #434 125 places worse
paper 0.7125 ±0.0085
paper 0.7125 ±0.0085 Δ at pub 0.0282 Δ today 0.0282
338
AD-GCL
actual #338 vs paper #339 1 place worse
0.7360 ±0.0070
best reported
actual #338 vs paper #339 1 place worse
paper 0.7359 ±0.0065

Difference within reported uncertainty; not counted as underperformance.

paper 0.7359 ±0.0065 Δ at pub 0.0001
350
graph2vec
0.7330 ±0.0205
This paper
474
Sub2Vec
actual #474 vs paper #517 43 places worse
0.6731 ±0.0050
best reported
actual #474 vs paper #517 43 places worse
paper 0.5303 ±0.0555
paper 0.5303 ±0.0555 Δ at pub 0.1428
514
Node2Vec
actual #514 vs paper #514
0.5750 ±0.0360
best reported
actual #514 vs paper #514
paper 0.5749 ±0.0357

Difference within reported uncertainty; not counted as underperformance.

paper 0.5749 ±0.0357 Δ at pub 0.0001
#ModelAccuracy ↑Paper
1
WL-MLP
0.9792
2
MSH-GNN
0.9640 ±0.0070
3
CoCN
0.8722 ±0.0013
23
GCN
0.8260 ±0.0220
32
JOAOv2
actual #32 vs paper #298 266 places worse
0.8216 ±0.0017
best reported
actual #32 vs paper #298 266 places worse
paper 0.7040 ±0.0221
paper 0.7040 ±0.0221 Δ at pub 0.1176
80
GraphCL
actual #80 vs paper #290 210 places worse
0.8108 ±0.0017
best reported
actual #80 vs paper #290 210 places worse
paper 0.7136 ±0.0115
paper 0.7136 ±0.0115 Δ at pub 0.0972
151
MLP
0.7920 ±0.0240
204
AutoGCL
actual #204 vs paper #300 96 places worse
0.7716 ±0.0148
best reported
actual #204 vs paper #300 96 places worse
paper 0.7012 ±0.0068
paper 0.7012 ±0.0068 Δ at pub 0.0704 Δ today 0.0704
231
LAMP-Soft
0.7596 ±0.0067
This paper
233
AD-GCL
actual #233 vs paper #271 38 places worse
0.7582 ±0.0026
best reported
actual #233 vs paper #271 38 places worse
paper 0.7332 ±0.0061
paper 0.7332 ±0.0061 Δ at pub 0.0250 Δ today 0.0250
239
GCS
actual #239 vs paper #239
0.7556 ±0.0041
actual #239 vs paper #239
paper 0.7556 ±0.0041
paper 0.7556 ±0.0041 Δ at pub 0.0156
261
SEGA
0.7412 ±0.0047
This paper
#ModelAccuracy ↑Paper
1
SpeGCL
0.5944 ±0.0018
This paper
2
GIN
0.5760 ±0.0150
3
LAMP-Soft
0.5738 ±0.0041
This paper
4
GCS
0.5704 ±0.0049
This paper
6
AutoGCL
0.5675 ±0.0018
This paper
10
SEGA
0.5613 ±0.0030
This paper
11
GraphCL
actual #11 vs paper #11
0.5600 ±0.0030
best reported
actual #11 vs paper #11
paper 0.5599 ±0.0028

Difference within reported uncertainty; not counted as underperformance.

paper 0.5599 ±0.0028 Δ at pub 0.0001
16
AD-GCL
actual #16 vs paper #19 3 places worse
0.5490 ±0.0040
best reported
actual #16 vs paper #19 3 places worse
paper 0.5300 ±0.0082
19
InfoGraph
actual #19 vs paper #19
0.5350 ±0.0100
best reported
actual #19 vs paper #19
paper 0.5346 ±0.0103

Difference within reported uncertainty; not counted as underperformance.

paper 0.5346 ±0.0103 Δ at pub 0.0004
20
JOAOv2
actual #20 vs paper #25 5 places worse
0.5271 ±0.0028
best reported
actual #20 vs paper #25 5 places worse
paper 0.4557 ±0.0286
paper 0.4557 ±0.0286 Δ at pub 0.0714 Δ today 0.0714
23
graph2vec
actual #23 vs paper #23
0.4790 ±0.0030
best reported
actual #23 vs paper #23
paper 0.4786 ±0.0026

Difference within reported uncertainty; not counted as underperformance.

paper 0.4786 ±0.0026 Δ at pub 0.0004
25
WL
actual #25 vs paper #25
0.4610 ±0.0020
best reported
actual #25 vs paper #25
paper 0.4606 ±0.0021

Difference within reported uncertainty; not counted as underperformance.

paper 0.4606 ±0.0021 Δ at pub 0.0004
26
GraphSAGE
0.4380 ±0.0320
27
DGK
0.4127 ±0.0018
This paper
28
GL
0.4101 ±0.0017
This paper
31
Sub2Vec
actual #31 vs paper #31
0.3670 ±0.0040
best reported
actual #31 vs paper #31
paper 0.3668 ±0.0042

Difference within reported uncertainty; not counted as underperformance.

paper 0.3668 ±0.0042 Δ at pub 0.0002

MoleculeNet

Tox21

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

Sorted by Accuracy. Highlighted rows are from other papers.

#ModelAccuracy ↑Paper
1
GraphSNN
0.9224 ±0.0059
2
UnionSNN
0.9176 ±0.0085
3
GIN
0.9174 ±0.0095
14
GCN
0.9010 ±0.0077
26
SpeGCL
0.7831 ±0.0018
This paper
29
LAMP-Soft
0.7723 ±0.0041
This paper
30
SEGA
0.7672 ±0.0043
This paper
31
AttrMasking
0.7670 ±0.0040
This paper
32
AD-GCL
0.7654 ±0.0082
This paper
34
GCS
0.7616 ±0.0041
This paper
35
EdgePred
0.7600 ±0.0060
This paper
36
ContextPred
0.7570 ±0.0070
This paper
37
AutoGCL
0.7569 ±0.0029
This paper
38
Infomax
0.7530 ±0.0050
This paper
39
JOAOv2
0.7427 ±0.0062
This paper
40
No pretrain
0.7400 ±0.0080
This paper
41
GraphCL
0.7387 ±0.0066
This paper

BACE

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

Sorted by Accuracy. Highlighted rows are from other papers.

#ModelAccuracy ↑Paper
1
GIN
0.9980 ±0.0040
2
ProtGNN
0.9960 ±0.0049
3
LAMP-Soft
0.8558 ±0.0143
This paper
4
SpeGCL
0.8477 ±0.0105
This paper
6
AutoGCL
0.8326 ±0.0113
This paper
7
EdgePred
0.7990 ±0.0090
This paper
8
ContextPred
0.7960 ±0.0120
This paper
9
AttrMasking
0.7930 ±0.0160
This paper
10
AD-GCL
0.7851 ±0.0080
This paper
11
GCS
0.7790 ±0.0026
This paper
12
SEGA
0.7707 ±0.0046
This paper
13
Infomax
0.7590 ±0.0160
This paper
14
JOAOv2
0.7549 ±0.0127
This paper
15
GraphCL
0.7538 ±0.0144
This paper
16
No pretrain
0.7010 ±0.0540
This paper
18
GCN
0.5220 ±0.0040

BBBP

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

Sorted by Accuracy. Highlighted rows are from other papers.

#ModelAccuracy ↑Paper
1
ProtGNN
0.8940 ±0.0410
2
GIN
0.8620 ±0.0110
3
GCN
0.8460 ±0.0340
5
SpeGCL
0.7603 ±0.0056
This paper
6
LAMP-Soft
0.7577 ±0.0076
This paper
7
AutoGCL
0.7336 ±0.0077
This paper
8
SEGA
0.7186 ±0.0106
This paper
9
GCS
0.7146 ±0.0046
This paper
10
JOAOv2
0.7139 ±0.0092
This paper
11
AD-GCL
0.7001 ±0.0107
This paper
12
GraphCL
0.6968 ±0.0067
This paper
13
Infomax
0.6880 ±0.0080
This paper
14
ContextPred
0.6800 ±0.0200
This paper
15
EdgePred
0.6730 ±0.0240
This paper
16
No pretrain
0.6580 ±0.0450
This paper
17
AttrMasking
0.6430 ±0.0280
This paper

ClinTox

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

Sorted by Accuracy. Highlighted rows are from other papers.

#ModelAccuracy ↑Paper
1
LAMP-Soft
0.8598 ±0.0127
This paper
2
SEGA
0.8499 ±0.0094
This paper
3
SpeGCL
0.8457 ±0.0201
This paper
4
GCS
0.8201 ±0.0190
This paper
5
AutoGCL
0.8099 ±0.0338
This paper
6
JOAOv2
0.8097 ±0.0164
This paper
7
AD-GCL
0.7978 ±0.0352
This paper
8
GraphCL
0.7599 ±0.0265
This paper
9
AttrMasking
0.7180 ±0.0410
This paper
10
Infomax
0.6990 ±0.0300
This paper
11
ContextPred
0.6590 ±0.0380
This paper
12
EdgePred
0.6410 ±0.0370
This paper
13
No pretrain
0.5800 ±0.0440
This paper

SIDER

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

Sorted by Accuracy. Highlighted rows are from other papers.

#ModelAccuracy ↑Paper
1
SpeGCL
0.6473 ±0.0042
This paper
2
LAMP-Soft
0.6424 ±0.0068
This paper
3
GCS
0.6420 ±0.0035
This paper
4
SEGA
0.6368 ±0.0034
This paper
5
AD-GCL
0.6328 ±0.0079
This paper
6
AutoGCL
0.6251 ±0.0063
This paper
7
AttrMasking
0.6100 ±0.0070
This paper
8
ContextPred
0.6090 ±0.0060
This paper
9
GraphCL
0.6053 ±0.0088
This paper
10
JOAOv2
0.6049 ±0.0074
This paper
11
EdgePred
0.6040 ±0.0070
This paper
12
Infomax
0.5840 ±0.0080
This paper
13
No pretrain
0.5730 ±0.0160
This paper

ToxCast

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

Sorted by Accuracy. Highlighted rows are from other papers.

#ModelAccuracy ↑Paper
1
GINE w/ VN
0.7490 ±0.0020
2
GINe+ K=1 w/ VN
0.7490 ±0.0080
3
GCN w/ VN
0.7430 ±0.0030
6
GCN
0.7350 ±0.0020
9
SpeGCL
0.6611 ±0.0026
This paper
10
LAMP-Soft
0.6587 ±0.0033
This paper
11
GCS
0.6535 ±0.0017
This paper
12
SEGA
0.6523 ±0.0091
This paper
13
AttrMasking
0.6420 ±0.0050
This paper
14
EdgePred
0.6410 ±0.0060
This paper
15
ContextPred
0.6390 ±0.0060
This paper
16
AutoGCL
0.6347 ±0.0038
This paper
17
No pretrain
0.6340 ±0.0060
This paper
18
JOAOv2
0.6316 ±0.0045
This paper
19
AD-GCL
0.6307 ±0.0072
This paper
20
Infomax
0.6270 ±0.0040
This paper
21
GraphCL
0.6240 ±0.0057
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