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.
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
| # | Model | Accuracy ↑ | 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 | 0.9045
±0.0081 | prev best: Community-Invariant Graph Contrastive Learning (ICML 2024) |
| 159 | WL | 0.9040
±0.0570 best reported | best at pub: How Powerful are $K$-hop Message Passing Graph Neural Networks (NeurIPS 2022) |
| 179 | SEGA | 0.9021
±0.0066 | This paper |
| 257 | InfoGraph | 0.8930
±0.0514 best reported | best at pub: Improving Expressivity of GNNs with Subgraph-specific Factor Embedded Normalization (KDD 2023) Difference within reported uncertainty; not counted as underperformance. |
| 302 | AutoGCL | 0.8864
±0.0108 | This paper |
| 354 | GraphCL | 0.8766
±0.0103 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) Difference within reported uncertainty; not counted as underperformance. |
| 365 | DGK | 0.8744
±0.0272 | This paper |
| 403 | MLP | 0.8660
±0.0495 | |
| 407 | graph2vec | 0.8644
±0.0125 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) Difference within reported uncertainty; not counted as underperformance. |
| 444 | GL | 0.8520
±0.0090 best reported | best at pub: On Valid Optimal Assignment Kernels and Applications to Graph Classification (NeurIPS 2016) |
| 472 | Sub2Vec | 0.8447
±0.0037 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) Difference within reported uncertainty; not counted as underperformance. |
| 746 | Node2Vec | 0.7263
±0.1020 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9954 | |
| 2 | GIN | 0.9934 | |
| 3 | GCN | 0.9727 | |
| 12 | WL | 0.8590
±0.0010 best reported | best at pub: Propagation Kernels (2014) |
| 104 | GraphCL | 0.8250
±0.0013 best reported | best at pub: Label-invariant Augmentation for Semi-Supervised Graph Classification (NeurIPS 2022) |
| 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 | 0.7750
±0.0074 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) Difference within reported uncertainty; not counted as underperformance. |
| 344 | GCS | 0.7737
±0.0030 | prev best: Community-Invariant Graph Contrastive Learning (ICML 2024) Improvement within reported uncertainty; not highlighted. |
| # | Model | Accuracy ↑ | 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 | 0.7580
±0.0036 | prev best: Automated Data Augmentations for Graph Classification (ICLR 2022) |
| 178 | DGK | 0.7568
±0.0054 best reported | best at pub: Graph Capsule Convolutional Neural Networks (ICML 2018) best today: Hierarchical Graph Capsule Network (AAAI 2020) |
| 190 | WL | 0.7560
±0.0040 best reported | best at pub: On Valid Optimal Assignment Kernels and Applications to Graph Classification (NeurIPS 2016) |
| 245 | GCS | 0.7502
±0.0081 | prev best: Community-Invariant Graph Contrastive Learning (ICML 2024) Improvement within reported uncertainty; not highlighted. |
| 265 | GraphCL | 0.7489
±0.0065 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) Difference within reported uncertainty; not counted as underperformance. |
| 294 | InfoGraph | 0.7444
±0.0031 | This paper |
| 309 | JOAOv2 | 0.7407
±0.0110 best reported | best at pub: Adversarial Graph Augmentation to Improve Graph Contrastive Learning (NeurIPS 2021) best today: Fractal Graph Contrastive Learning (2025) |
| 338 | AD-GCL | 0.7360
±0.0070 best reported | best at pub: GPS: graph contrastive learning via multi-scale augmented views from adversarial pooling (2024) Difference within reported uncertainty; not counted as underperformance. |
| 350 | graph2vec | 0.7330
±0.0205 | This paper |
| 474 | Sub2Vec | 0.6731
±0.0050 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) |
| 514 | Node2Vec | 0.5750
±0.0360 best reported | best at pub: GPS: graph contrastive learning via multi-scale augmented views from adversarial pooling (2024) Difference within reported uncertainty; not counted as underperformance. |
| # | Model | Accuracy ↑ | 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 | 0.8216
±0.0017 best reported | best at pub: Label-invariant Augmentation for Semi-Supervised Graph Classification (NeurIPS 2022) |
| 80 | GraphCL | 0.8108
±0.0017 best reported | best at pub: Label-invariant Augmentation for Semi-Supervised Graph Classification (NeurIPS 2022) |
| 151 | MLP | 0.7920
±0.0240 | |
| 204 | AutoGCL | 0.7716
±0.0148 best reported | best at pub: GIMM: InfoMin-Max for Automated Graph Contrastive Learning (2023) best today: Unifying Graph Contrastive Learning via Graph Message Augmentation (2024) |
| 231 | LAMP-Soft | 0.7596
±0.0067 | This paper |
| 233 | AD-GCL | 0.7582
±0.0026 best reported | best at pub: Graph Contrastive Learning with Personalized Augmentation (2022) best today: Unifying Graph Contrastive Learning via Graph Message Augmentation (2024) |
| 239 | GCS | 0.7556
±0.0041 | prev best: Community-Invariant Graph Contrastive Learning (ICML 2024) |
| 261 | SEGA | 0.7412
±0.0047 | This paper |
| # | Model | Accuracy ↑ | 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 | 0.5600
±0.0030 best reported | best at pub: GPS: graph contrastive learning via multi-scale augmented views from adversarial pooling (2024) Difference within reported uncertainty; not counted as underperformance. |
| 16 | AD-GCL | 0.5490
±0.0040 best reported | |
| 19 | InfoGraph | 0.5350
±0.0100 best reported | best at pub: GPS: graph contrastive learning via multi-scale augmented views from adversarial pooling (2024) Difference within reported uncertainty; not counted as underperformance. |
| 20 | JOAOv2 | 0.5271
±0.0028 best reported | best at pub: GIMM: InfoMin-Max for Automated Graph Contrastive Learning (2023) best today: Unifying Graph Contrastive Learning via Graph Message Augmentation (2024) |
| 23 | graph2vec | 0.4790
±0.0030 best reported | best at pub: GPS: graph contrastive learning via multi-scale augmented views from adversarial pooling (2024) Difference within reported uncertainty; not counted as underperformance. |
| 25 | WL | 0.4610
±0.0020 best reported | best at pub: GPS: graph contrastive learning via multi-scale augmented views from adversarial pooling (2024) Difference within reported uncertainty; not counted as underperformance. |
| 26 | GraphSAGE | 0.4380
±0.0320 | |
| 27 | DGK | 0.4127
±0.0018 | This paper |
| 28 | GL | 0.4101
±0.0017 | This paper |
| 31 | Sub2Vec | 0.3670
±0.0040 best reported | best at pub: GPS: graph contrastive learning via multi-scale augmented views from adversarial pooling (2024) Difference within reported uncertainty; not counted as underperformance. |
MoleculeNet
Tox21
Global leaderboard →Sorted by Accuracy. Highlighted rows are from other papers.
| # | Model | Accuracy ↑ | 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 →Sorted by Accuracy. Highlighted rows are from other papers.
| # | Model | Accuracy ↑ | 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 →Sorted by Accuracy. Highlighted rows are from other papers.
| # | Model | Accuracy ↑ | 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 →Sorted by Accuracy. Highlighted rows are from other papers.
| # | Model | Accuracy ↑ | 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 →Sorted by Accuracy. Highlighted rows are from other papers.
| # | Model | Accuracy ↑ | 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 →Sorted by Accuracy. Highlighted rows are from other papers.
| # | Model | Accuracy ↑ | 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 |
