Perfect Alignment May be Poisonous to Graph Contrastive Learning
Abstract
Graph Contrastive Learning (GCL) aims to learn node representations by aligning positive pairs and separating negative ones. However, few of researchers have focused on the inner law behind specific augmentations used in graph-based learning. What kind of augmentation will help downstream performance, how does contrastive learning actually influence downstream tasks, and why the magnitude of augmentation matters so much? This paper seeks to address these questions by establishing a connection between augmentation and downstream performance. Our findings reveal that GCL contributes to downstream tasks mainly by separating different classes rather than gathering nodes of the same class. So perfect alignment and augmentation overlap which draw all intra-class samples the same can not fully explain the success of contrastive learning. Therefore, in order to understand how augmentation aids the contrastive learning process, we conduct further investigations into the generalization, finding that perfect alignment that draw positive pair the same could help contrastive loss but is poisonous to generalization, as a result, perfect alignment may not lead to best downstream performance, so specifically designed augmentation is needed to achieve appropriate alignment performance and improve downstream accuracy. We further analyse the result by information theory and graph spectrum theory and propose two simple but effective methods to verify the theories. The two methods could be easily applied to various GCL algorithms and extensive experiments are conducted to prove its effectiveness. The code is available at https://github.com/somebodyhh1/GRACEIS
Benchmark Results
Tested on 3 datasets 5 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | 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 | |
| 184 | Supervised GCN | 0.9328
±0.0003 | This paper |
| 191 | GCA | 0.9320
±0.0060 best reported | best at pub: Unifying Graph Contrastive Learning with Flexible Contextual Scopes (2022) best today: Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-training Tasks (ICLR 2024) |
| 200 | Supervised GAT | 0.9317
±0.0005 | This paper |
| 203 | GRACE | 0.9313
±0.0017 best reported | best at pub: Learning Graph Augmentations to Learn Graph Representations (2022) best today: Learn Beneficial Noise as Graph Augmentation (ICML 2025) |
| 339 | GCA+S | 0.9202
±0.0034 | This paper |
| 344 | GRACE+S | 0.9199
±0.0035 | This paper |
| 345 | GCA+I | 0.9194
±0.0013 | This paper |
| 362 | AD GCL+I | 0.9171
±0.0078 | This paper |
| 365 | GRACE+I | 0.9164
±0.0021 | This paper |
| 370 | GRACE+SpCo | 0.9156
±0.0019 | This paper |
| 386 | AD GCL | 0.9134
±0.0033 | This paper |
| 390 | MLP | 0.9128
±0.0063 | |
| 442 | GCS | 0.9015
±0.0024 | This paper |
| # | Model | Accuracy ↑ | 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 | |
| 139 | GRACE | 0.8953
±0.0035 best reported | best at pub: Spectral Augmentation for Self-Supervised Learning on Graphs (ICLR 2022) best today: Adaptive Negative Scheduling for Graph Contrastive Learning (2026) |
| 160 | GCA | 0.8894
±0.0015 best reported | best at pub: Barlow Graph Auto-Encoder for Unsupervised Network Embedding (2021) best today: Adaptive Negative Scheduling for Graph Contrastive Learning (2026) |
| 205 | Supervised GCN | 0.8811
±0.0014 | This paper |
| 228 | GRACE+S | 0.8767
±0.0033 | This paper |
| 234 | GRACE+I | 0.8757
±0.0053 | This paper |
| 256 | GCA+S | 0.8697
±0.0040 | This paper |
| 259 | Supervised GAT | 0.8682
±0.0009 | This paper |
| 267 | GCA+I | 0.8660
±0.0029 | This paper |
| 269 | GCS | 0.8654
±0.0026 | This paper |
| 289 | AD GCL+I | 0.8602
±0.0053 | This paper |
| 317 | AD GCL | 0.8480
±0.0051 | This paper |
| 320 | MLP | 0.8463 | |
| 376 | GRACE+SpCo | 0.8337
±0.0038 | This paper |
Heterogeneous Graph Benchmarks
DBLP
Global leaderboard →Default metric is Micro-F1. The paper reports 9 values on Micro-F1 and 3 values on Accuracy .
| # | Model | Micro-F1 ↑ default | Accuracy ↑ | Paper |
|---|---|---|---|---|
| 1 | LMSPS | 0.9566
±
0.0020 | — | |
| 2 | PSHGCN | 0.9561
±
0.0012 | — | |
| 3 | RpHGNN | 0.9555
±
0.0029 | — | |
| 21 | GCN | 0.9460
±
0.0031 | — | |
| 74 | GRACE | 0.9128
±0.0007 best reported | — | Accuracy
— best at pub: Heterogeneous Graph Contrastive Multi-view Learning (2022) |
| 107 | GRACE+S | 0.8483
±
0.0018 | — | Accuracy
— |
| 108 | GRACE+I | 0.8480
±
0.0017 | — | Accuracy
— |
| 109 | GCA+I | —
| 0.8479
±
0.0028 | Accuracy
0.8479
±
0.0028 |
| 109 | AD GCL+I | —
| 0.8476
±
0.0009 | Accuracy
0.8476
±
0.0009 |
| 110 | GCA+S | —
| 0.8449
±
0.0024 | Accuracy
0.8449
±
0.0024 |
| 112 | GCA | 0.8399
±0.0021 | — | Accuracy
— prev best: Mixed Graph Contrastive Network for Semi-Supervised Node Classification (2022) |
| 113 | GRACE+SpCo | 0.8361
±
0.0014 | — | Accuracy
— |
| 114 | GCS | 0.8338
±
0.0037 | — | Accuracy
— |
| 115 | AD GCL | 0.8314
±
0.0016 | — | Accuracy
— |
| 122 | Supervised GAT | 0.8192
±
0.0003 | — | Accuracy
— |
| 125 | Supervised GCN | 0.8126
±
0.0001 | — | Accuracy
— |
| 176 | MLP | 0.6447
±
0.0136 | — |
