Model-Driven Graph Contrastive Learning
Abstract
We propose MGCL, a model-driven graph contrastive learning (GCL) framework that leverages graphons (probabilistic generative models for graphs) to guide contrastive learning by accounting for the data's underlying generative process. GCL has emerged as a powerful self-supervised framework for learning expressive node or graph representations without relying on annotated labels, which are often scarce in real-world data. By contrasting augmented views of graph data, GCL has demonstrated strong performance across various downstream tasks, such as node and graph classification. However, existing methods typically rely on manually designed or heuristic augmentation strategies that are not tailored to the underlying data distribution and operate at the individual graph level, ignoring similarities among graphs generated from the same model. Conversely, in our proposed approach, MGCL first estimates the graphon associated with the observed data and then defines a graphon-informed augmentation process, enabling data-adaptive and principled augmentations. Additionally, for graph-level tasks, MGCL clusters the dataset and estimates a graphon per group, enabling contrastive pairs to reflect shared semantics and structure. Extensive experiments on benchmark datasets demonstrate that MGCL achieves state-of-the-art performance, highlighting the advantages of incorporating generative models into GCL.
Benchmark Results
Tested on 7 datasets 22 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 | |
| 8 | GCN | 0.9632
±0.0008 best reported | |
| 172 | BGRL | 0.9337
±0.0021 best reported | best at pub: Wiener Graph Deconvolutional Network Improves Graph Self-Supervised Learning (AAAI 2022) Difference within reported uncertainty; not counted as underperformance. |
| 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) Difference within reported uncertainty; not counted as underperformance. |
| 203 | GRACE | 0.9313
±0.0017 best reported | best at pub: Learn Beneficial Noise as Graph Augmentation (ICML 2025) |
| 206 | MVGRL | 0.9310
±0.0040 best reported | best at pub: Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-training Tasks (ICLR 2024) |
| 213 | DGI | 0.9309
±0.0008 best reported | |
| 235 | GBT | 0.9282
±0.0040 best reported | best at pub: Str-GCL: Structural Commonsense Driven Graph Contrastive Learning (WWW 2025) Difference within reported uncertainty; not counted as underperformance. |
| 246 | MGCL | 0.9278
±0.0023 | This paper |
| 320 | GraphCL | 0.9222
±0.0042 | prev best: PyG-SSL: A Graph Self-Supervised Learning Toolkit (2024) |
| 390 | MLP | 0.9128
±0.0063 | |
| 457 | Node2Vec | 0.8970
±0.0010 best reported | best at pub: Learning Graph Augmentations to Learn Graph Representations (2022) best today: Multiplex Graph Contrastive Learning with Soft Negatives (2024) Difference within reported uncertainty; not counted as underperformance. |
| 531 | Raw features | 0.7999
±0.0090 | prev best: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) |
| # | Model | Accuracy ↑ | 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 best reported | best at pub: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 17 | SAGE | 0.9739
±0.0018 | |
| 58 | MLP | 0.9597
±0.0007 | |
| 63 | GCA | 0.9590
±0.0020 best reported | best at pub: Unifying Graph Contrastive Learning with Flexible Contextual Scopes (2022) Difference within reported uncertainty; not counted as underperformance. |
| 73 | MGCL | 0.9580
±0.0008 | This paper |
| 72 | GraphCL | 0.9580
±0.0014 | This paper |
| 69 | BGRL | 0.9580
±0.0040 best reported | best at pub: Unifying Graph Contrastive Learning with Flexible Contextual Scopes (2022) Difference within reported uncertainty; not counted as underperformance. |
| 77 | GRACE | 0.9574
±0.0006 best reported | best at pub: Learn Beneficial Noise as Graph Augmentation (ICML 2025) |
| 125 | MVGRL | 0.9544
±0.0027 best reported | best at pub: HAT-GAE: Self-Supervised Graph Auto-encoders with Hierarchical Adaptive Masking and Trainable Corruption (2023) Difference within reported uncertainty; not counted as underperformance. |
| 149 | GBT | 0.9520
±0.0010 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. |
| 167 | DGI | 0.9489
±0.0009 best reported | best at pub: Balancing Graph Embedding Smoothness in Self-Supervised Learning via Information-Theoretic Decomposition (WWW 2025) Difference within reported uncertainty; not counted as underperformance. |
| 182 | Raw features | 0.9432
±0.0014 | prev best: Learning Graph Augmentations to Learn Graph Representations (2022) |
| 268 | Node2Vec | 0.9120
±0.0010 best reported | best at pub: Learning Graph Augmentations to Learn Graph Representations (2022) best today: Unifying Graph Contrastive Learning with Flexible Contextual Scopes (2022) Difference within reported uncertainty; not counted as underperformance. |
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 | |
| 159 | WL | 0.9040
±0.0570 best reported | best at pub: How Powerful are $K$-hop Message Passing Graph Neural Networks (NeurIPS 2022) |
| 199 | MVGRL | 0.8993
±0.0616 best reported | best at pub: Improving Expressivity of GNNs with Subgraph-specific Factor Embedded Normalization (KDD 2023) |
| 227 | MGCL | 0.8955
±0.0108 | 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. |
| 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 |
| 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) |
| 131 | GraphSAGE | 0.8200
±0.0100 | |
| 210 | DGK | 0.8031
±0.0046 | This paper |
| 283 | MGCL | 0.7866
±0.0034 | 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. |
| 406 | graph2vec | 0.7540
±0.0120 best reported | best at pub: InfoGCL: Information-Aware Graph Contrastive Learning (NeurIPS 2021) Difference within reported uncertainty; not counted as underperformance. |
| 557 | Sub2Vec | 0.5976
±0.0035 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) |
| 571 | Node2Vec | 0.5490
±0.0160 best reported | best at pub: InfoGCL: Information-Aware Graph Contrastive Learning (NeurIPS 2021) best today: 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 | MSH-GNN | 0.9410
±0.0330 | |
| 2 | GRDL | 0.8260
±0.0120 | |
| 3 | GMN | 0.8225 | |
| 32 | GIN | 0.7880
±0.0410 | |
| 149 | MLP | 0.7600
±0.0320 | |
| 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) |
| 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. |
| 269 | MGCL | 0.7485
±0.0071 | 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 |
| 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 | |
| 80 | GraphCL | 0.8108
±0.0017 best reported | best at pub: Label-invariant Augmentation for Semi-Supervised Graph Classification (NeurIPS 2022) |
| 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) |
| 289 | MGCL | 0.7144
±0.0071 | This paper |
| # | 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) |
| 35 | MGCL | 0.9025
±0.0039 | This paper |
| 46 | InfoGraph | 0.8939
±0.0181 best reported | best at pub: Graph Contrastive Learning with Cohesive Subgraph Awareness (WWW 2024) |
| 65 | MVGRL | 0.8450
±0.0060 best reported | best at pub: Graph Self-Supervised Learning: A Survey (2021) |
| 73 | DGK | 0.7804
±0.0039 | This paper |
| 75 | GL | 0.7734
±0.0018 | This paper |
| 80 | graph2vec | 0.7580
±0.0100 best reported | best at pub: Prototypical Graph Contrastive Learning (2021) best today: Self-Supervised Representation Learning via Latent Graph Prediction (ICML 2022) Difference within reported uncertainty; not counted as underperformance. |
| 83 | Sub2Vec | 0.7150
±0.0040 best reported | best at pub: Self-Supervised Representation Learning via Latent Graph Prediction (ICML 2022) Difference within reported uncertainty; not counted as underperformance. |
| 85 | WL | 0.6882
±0.0041 | This paper |
