Dual-perspective Cross Contrastive Learning in Graph Transformers
Abstract
Graph contrastive learning (GCL) is a popular method for leaning graph representations by maximizing the consistency of features across augmented views. Traditional GCL methods utilize single-perspective (i.e. data or model-perspective) augmentation to generate positive samples, restraining the diversity of positive samples. In addition, these positive samples may be unreliable due to uncontrollable augmentation strategies that potentially alter the semantic information. To address these challenges, this paper proposed a innovative framework termed dual-perspective cross graph contrastive learning (DC-GCL), which incorporates three modifications designed to enhance positive sample diversity and reliability: 1) We propose dual-perspective augmentation strategy that provide the model with more diverse training data, enabling the model effective learning of feature consistency across different views. 2) From the data perspective, we slightly perturb the original graphs using controllable data augmentation, effectively preserving their semantic information. 3) From the model perspective, we enhance the encoder by utilizing more powerful graph transformers instead of graph neural networks. Based on the model's architecture, we propose three pruning-based strategies to slightly perturb the encoder, providing more reliable positive samples. These modifications collectively form the DC-GCL's foundation and provide more diverse and reliable training inputs, offering significant improvements over traditional GCL methods. Extensive experiments on various benchmarks demonstrate that DC-GCL consistently outperforms different baselines on various datasets and tasks..
Benchmark Results
Tested on 9 datasets 24 baseline values reported too low
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 | |
| 154 | DC-GCL | 0.9050
±0.0155 | This paper |
| 159 | WL | 0.9040
±0.0570 best reported | best at pub: How Powerful are $K$-hop Message Passing Graph Neural Networks (NeurIPS 2022) |
| 211 | iGCL | 0.8980
±0.0120 | This paper |
| 222 | JOAOv2 | 0.8967
±0.0524 best reported | best at pub: Unifying Graph Contrastive Learning via Graph Message Augmentation (2024) Difference within reported uncertainty; not counted as underperformance. |
| 229 | DRGCL | 0.8950
±0.0060 | 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. |
| 272 | SimGRACE | 0.8910
±0.0140 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. |
| 310 | DualGCL | 0.8850
±0.0090 | This paper |
| 351 | JOAO | 0.8770
±0.0080 best reported | best at pub: Graph Self-Supervised Learning: A Survey (2021) best today: Learning Graph Augmentations to Learn Graph Representations (2022) Difference within reported uncertainty; not counted as underperformance. |
| 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 |
| 378 | GraphTrans | 0.8722
±0.0705 | prev best: SignGT: Signed Attention-based Graph Transformer for Graph Representation Learning (2023) Improvement within reported uncertainty; not highlighted. |
| 403 | MLP | 0.8660
±0.0495 | |
| 444 | GL | 0.8520
±0.0090 best reported | best at pub: On Valid Optimal Assignment Kernels and Applications to Graph Classification (NeurIPS 2016) |
| 448 | GraphGPS | 0.8500
±0.0316 | 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) |
| 35 | GraphGPS | 0.8421
±0.0225 | This paper |
| 97 | iGCL | 0.8270
±0.0040 | This paper |
| 100 | GraphTrans | 0.8260
±0.0120 | prev best: Search to Capture Long-range Dependency with Stacking GNNs for Graph Classification (WWW 2023) Improvement within reported uncertainty; not highlighted. |
| 104 | GraphCL | 0.8250
±0.0013 best reported | best at pub: Label-invariant Augmentation for Semi-Supervised Graph Classification (NeurIPS 2022) |
| 131 | GraphSAGE | 0.8200
±0.0100 | |
| 141 | SimGRACE | 0.8180
±0.0015 best reported | best at pub: Label-invariant Augmentation for Semi-Supervised Graph Classification (NeurIPS 2022) |
| 146 | JOAOv2 | 0.8170
±0.0026 best reported | best at pub: Label-invariant Augmentation for Semi-Supervised Graph Classification (NeurIPS 2022) |
| 210 | DGK | 0.8031
±0.0046 | This paper |
| 235 | DualGCL | 0.7980
±0.0030 | This paper |
| 242 | DC-GCL | 0.7962
±0.0037 | This paper |
| 277 | DRGCL | 0.7870
±0.0040 | This paper |
| 301 | JOAO | 0.7840
±0.0050 best reported | best at pub: Omni-Granular Ego-Semantic Propagation for Self-Supervised Graph Representation Learning (ICML 2022) Difference within reported uncertainty; not counted as underperformance. |
| 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. |
| # | 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 | |
| 112 | DC-GCL | 0.7645
±0.0026 | This paper |
| 149 | MLP | 0.7600
±0.0320 | |
| 170 | GraphGPS | 0.7577
±0.0219 | This paper |
| 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) |
| 189 | DualGCL | 0.7560
±0.0050 | This paper |
| 190 | WL | 0.7560
±0.0040 best reported | best at pub: On Valid Optimal Assignment Kernels and Applications to Graph Classification (NeurIPS 2016) |
| 209 | SimGRACE | 0.7535
±0.0009 | This paper |
| 226 | DRGCL | 0.7520
±0.0060 | This paper |
| 231 | GraphTrans | 0.7518
±0.0336 | prev best: Search to Capture Long-range Dependency with Stacking GNNs for Graph Classification (WWW 2023) 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. |
| 275 | iGCL | 0.7480
±0.0050 | This paper |
| 283 | JOAO | 0.7460
±0.0040 best reported | best at pub: GPS: graph contrastive learning via multi-scale augmented views from adversarial pooling (2024) best today: Balancing Graph Embedding Smoothness in Self-Supervised Learning via Information-Theoretic Decomposition (WWW 2025) Difference within reported uncertainty; not counted as underperformance. |
| 294 | InfoGraph | 0.7444
±0.0031 | This paper |
| 309 | JOAOv2 | 0.7407
±0.0110 | This paper |
| # | 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) |
| 37 | SimGRACE | 0.8188
±0.0023 best reported | best at pub: Label-invariant Augmentation for Semi-Supervised Graph Classification (NeurIPS 2022) |
| 63 | GraphGPS | 0.8140
±0.0026 | This paper |
| 80 | GraphCL | 0.8108
±0.0017 best reported | best at pub: Label-invariant Augmentation for Semi-Supervised Graph Classification (NeurIPS 2022) |
| 130 | DC-GCL | 0.7983
±0.0043 | This paper |
| 131 | GraphTrans | 0.7981
±0.0084 | This paper |
| 146 | InfoGraph | 0.7940 best reported | best at pub: CogDL: A Comprehensive Library for Graph Deep Learning (WWW 2021) |
| 151 | MLP | 0.7920
±0.0240 | |
| 248 | JOAO | 0.7535
±0.0093 best reported | best at pub: Spectral Augmentation for Self-Supervised Learning on Graphs (ICLR 2022) |
| 249 | DualGCL | 0.7530
±0.0040 | This paper |
| 285 | iGCL | 0.7200
±0.0080 | This paper |
| 296 | DRGCL | 0.7060
±0.0080 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GC-GNN (GCN) | 0.9210
±0.0810 | |
| 2 | SUGAR | 0.8403
±0.0133 | |
| 3 | Ortho-g-U-Nets | 0.8387 | |
| 15 | SAGE | 0.8088
±0.0233 | |
| 35 | DC-GCL | 0.7943
±0.0063 | This paper |
| 58 | GraphCL | 0.7862
±0.0040 | This paper |
| 65 | DRGCL | 0.7840
±0.0070 | This paper |
| 93 | SimGRACE | 0.7744
±0.0111 | This paper |
| 94 | JOAOv2 | 0.7740
±0.0115 | This paper |
| 98 | JOAO | 0.7732
±0.0054 | This paper |
| 119 | GraphGPS | 0.7598
±0.0153 | This paper |
| 134 | GraphTrans | 0.7524
±0.0483 | This paper |
| 148 | InfoGraph | 0.7424
±0.0086 best reported | best at pub: Contrastive Self-supervised Learning for Graph Classification (AAAI 2020) Difference within reported uncertainty; not counted as underperformance. |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | OEPG | 0.9630
±0.0090 | |
| 2 | MSH-GNN | 0.9580
±0.0090 | |
| 3 | GNN-AK+ | 0.9480
±0.0080 | |
| 13 | GIN | 0.9240
±0.0250 | |
| 23 | GraphCL | 0.9169
±0.0070 best reported | best at pub: Graph Contrastive Learning with Cohesive Subgraph Awareness (WWW 2024) |
| 24 | JOAO | 0.9166
±0.0059 best reported | best at pub: Graph Contrastive Learning with Cohesive Subgraph Awareness (WWW 2024) |
| 29 | DC-GCL | 0.9104
±0.0045 | This paper |
| 31 | DRGCL | 0.9080
±0.0030 | This paper |
| 44 | SimGRACE | 0.8951
±0.0089 | This paper |
| 46 | InfoGraph | 0.8939
±0.0181 best reported | best at pub: Graph Contrastive Learning with Cohesive Subgraph Awareness (WWW 2024) |
| 49 | JOAOv2 | 0.8879
±0.0065 best reported | best at pub: Graph Contrastive Learning with Personalized Augmentation (2022) |
| 50 | GraphTrans | 0.8858
±0.0130 | This paper |
| 51 | GraphGPS | 0.8840
±0.0115 | This paper |
| 73 | DGK | 0.7804
±0.0039 | This paper |
| 75 | GL | 0.7734
±0.0018 | This paper |
| 85 | WL | 0.6882
±0.0041 | This paper |
MoleculeNet
| # | Model | ROC-AUC ↑ | Paper |
|---|---|---|---|
| 1 | ProtoMol | 0.9140
±0.0030 | |
| 2 | MMSG | 0.9080
±0.0050 | |
| 3 | MemGNN | 0.9070 | |
| 43 | GIN | 0.8646
±0.0081 | |
| 100 | JOAO | 0.8340
±0.0330 best reported | best at pub: KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular Property Prediction (KDD 2022) |
| 178 | DC-GCL | 0.7990
±0.0170 | This paper |
| 186 | ContextPred | 0.7960
±0.0120 | This paper |
| 191 | AttrMasking | 0.7930
±0.0160 | This paper |
| 213 | GraphCL | 0.7820
±0.0120 best reported | best at pub: Omni-Granular Ego-Semantic Propagation for Self-Supervised Graph Representation Learning (ICML 2022) |
| 214 | DRGCL | 0.7820
±0.0100 | This paper |
| 225 | Infomax | 0.7780
±0.0046 best reported | best at pub: UGMAE: A Unified Framework for Graph Masked Autoencoders (2024) best today: Pre-training Graph Neural Networks on Molecules by Using Subgraph-Conditioned Graph Information Bottleneck (AAAI 2024) Difference within reported uncertainty; not counted as underperformance. |
| 231 | No-pretrain | 0.7700
±0.0210 | prev best: GraphMAE: Self-Supervised Masked Graph Autoencoders (KDD 2022) |
| 242 | RGCL | 0.7603
±0.0077 best reported | best at pub: Let Invariant Rationale Discovery Inspire Graph Contrastive Learning (ICML 2022) best today: Graph Self-Contrast Representation Learning (2023) Difference within reported uncertainty; not counted as underperformance. |
| 244 | SimGRACE | 0.7580
±0.0040 best reported | best at pub: Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-training Tasks (ICLR 2024) Difference within reported uncertainty; not counted as underperformance. |
| 255 | ADGCL | 0.7400
±0.0220 | This paper |
| # | Model | ROC-AUC ↑ | Paper |
|---|---|---|---|
| 1 | SE(3)-I MPPH | 0.9930
±0.0040 | |
| 2 | KA-GCN | 0.9920
±0.0050 | |
| 3 | KA-GAT | 0.9910
±0.0050 | |
| 19 | GCN | 0.9130
±0.0170 | |
| 57 | RGCL | 0.8500
±0.0080 best reported | best at pub: Rethinking Tokenizer and Decoder in Masked Graph Modeling for Molecules (NeurIPS 2023) |
| 64 | DC-GCL | 0.8270
±0.0360 | This paper |
| 79 | JOAO | 0.8132
±0.0249 best reported | best at pub: Graph Self-Contrast Representation Learning (2023) Difference within reported uncertainty; not counted as underperformance. |
| 93 | ADGCL | 0.7980
±0.0350 best reported | best at pub: Subgraph Networks Based Contrastive Learning (2023) Difference within reported uncertainty; not counted as underperformance. |
| 97 | GraphCL | 0.7890
±0.0420 best reported | best at pub: 16 Pre-training Molecular Graph Representation with 3D Geometry (ICLR 2021) best today: Improving Molecular Pretraining with Complementary Featurizations (2022) Difference within reported uncertainty; not counted as underperformance. |
| 105 | DRGCL | 0.7820
±0.0150 | This paper |
| 115 | ContextPred | 0.7720
±0.0088 best reported | |
| 123 | SimGRACE | 0.7560
±0.0300 | prev best: Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-training Tasks (ICLR 2024) |
| 151 | Infomax | 0.7300
±0.0320 best reported | best at pub: Motif-based Graph Self-Supervised Learning for Molecular Property Prediction (NeurIPS 2021) Difference within reported uncertainty; not counted as underperformance. |
| 162 | AttrMasking | 0.7180
±0.0410 | This paper |
| 205 | No-pretrain | 0.6440
±0.0420 | prev best: GraphMAE: Self-Supervised Masked Graph Autoencoders (KDD 2022) Improvement within reported uncertainty; not highlighted. |
| # | Model | ROC-AUC ↑ | Paper |
|---|---|---|---|
| 1 | KA-GAT | 0.8470
±0.0020 | |
| 2 | KA-GCN | 0.8420
±0.0010 | |
| 3 | GraphKAN | 0.8370
±0.0010 | |
| 66 | GIN | 0.6403
±0.0104 | |
| 68 | JOAO | 0.6400
±0.0100 best reported | best at pub: KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular Property Prediction (KDD 2022) |
| 80 | ADGCL | 0.6330
±0.0080 best reported | best at pub: Subgraph Networks Based Contrastive Learning (2023) |
| 103 | ContextPred | 0.6220
±0.0059 best reported | |
| 114 | GraphCL | 0.6183
±0.0060 best reported | best at pub: Community-Invariant Graph Contrastive Learning (ICML 2024) best today: Pre-training Graph Neural Networks on Molecules by Using Subgraph-Conditioned Graph Information Bottleneck (AAAI 2024) Difference within reported uncertainty; not counted as underperformance. |
| 120 | Infomax | 0.6160
±0.0240 best reported | best at pub: KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular Property Prediction (KDD 2022) Difference within reported uncertainty; not counted as underperformance. |
| 128 | RGCL | 0.6140
±0.0060 | This paper |
| 133 | AttrMasking | 0.6121
±0.0065 best reported | best at pub: GraphMAE: Self-Supervised Masked Graph Autoencoders (KDD 2022) best today: Pre-training Graph Neural Networks on Molecules by Using Subgraph-Conditioned Graph Information Bottleneck (AAAI 2024) Difference within reported uncertainty; not counted as underperformance. |
| 140 | DRGCL | 0.6110
±0.0080 | This paper |
| 161 | DC-GCL | 0.6060
±0.0060 | This paper |
| 156 | SimGRACE | 0.6060
±0.0100 | prev best: Graph Self-supervised Learning with Accurate Discrepancy Learning (NeurIPS 2022) Improvement within reported uncertainty; not highlighted. |
| 213 | No-pretrain | 0.5810
±0.0100 | prev best: UGMAE: A Unified Framework for Graph Masked Autoencoders (2024) Improvement within reported uncertainty; not highlighted. |
