Subgraph Networks Based Contrastive Learning
Abstract
Graph contrastive learning (GCL), as a self-supervised learning method, can solve the problem of annotated data scarcity. It mines explicit features in unannotated graphs to generate favorable graph representations for downstream tasks. Most existing GCL methods focus on the design of graph augmentation strategies and mutual information estimation operations. Graph augmentation produces augmented views by graph perturbations. These views preserve a locally similar structure and exploit explicit features. However, these methods have not considered the interaction existing in subgraphs. To explore the impact of substructure interactions on graph representations, we propose a novel framework called subgraph network-based contrastive learning (SGNCL). SGNCL applies a subgraph network generation strategy to produce augmented views. This strategy converts the original graph into an Edge-to-Node mapping network with both topological and attribute features. The single-shot augmented view is a first-order subgraph network that mines the interaction between nodes, node-edge, and edges. In addition, we also investigate the impact of the second-order subgraph augmentation on mining graph structure interactions, and further, propose a contrastive objective that fuses the first-order and second-order subgraph information. We compare SGNCL with classical and state-of-the-art graph contrastive learning methods on multiple benchmark datasets of different domains. Extensive experiments show that SGNCL achieves competitive or better performance (top three) on all datasets in unsupervised learning settings. Furthermore, SGNCL achieves the best average gain of 6.9\ Finally, experiments also demonstrate that mining substructure interactions have positive implications for graph contrastive learning.
Benchmark Results
Tested on 6 datasets 17 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 | |
| 199 | MVGRL | 0.8993
±0.0616 best reported | best at pub: Improving Expressivity of GNNs with Subgraph-specific Factor Embedded Normalization (KDD 2023) |
| 215 | ADGCL | 0.8970
±0.0100 best reported | best at pub: Learning Graph Augmentations to Learn Graph Representations (2022) Difference within reported uncertainty; not counted as underperformance. |
| 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. |
| 270 | SGNCL | 0.8913
±0.0191 | 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. |
| 355 | RGCL | 0.8766
±0.0101 | This paper |
| 403 | MLP | 0.8660
±0.0495 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9954 | |
| 2 | GIN | 0.9934 | |
| 3 | GCN | 0.9727 | |
| 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 | |
| 230 | SGNCL | 0.7984
±0.0023 | 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. |
| 315 | RGCL | 0.7814
±0.0108 | 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. |
| 356 | MVGRL | 0.7700
±0.0080 best reported | best at pub: InfoGCL: Information-Aware Graph Contrastive Learning (NeurIPS 2021) best today: Graph Self-Supervised Learning with Learnable Structural and Positional Encodings (WWW 2025) |
| 440 | ADGCL | 0.7391
±0.0077 | prev best: Omni-Granular Ego-Semantic Propagation for Self-Supervised Graph Representation Learning (ICML 2022) |
MoleculeNet
| # | Model | ROC-AUC ↑ | Paper |
|---|---|---|---|
| 1 | MAGPrompt+ | 0.9432
±0.0238 | |
| 2 | CamS-LLaMA | 0.9420 | |
| 3 | SE(3)-I MPPH | 0.9400
±0.0210 | |
| 34 | GIN | 0.8875
±0.0049 | |
| 36 | GraphCL | 0.8870
±0.0190 best reported | best at pub: KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular Property Prediction (KDD 2022) |
| 39 | JOAO | 0.8790
±0.0200 best reported | best at pub: KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular Property Prediction (KDD 2022) |
| 40 | ContextPred | 0.8770
±0.0260 best reported | best at pub: KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular Property Prediction (KDD 2022) |
| 44 | EdgePred | 0.8730
±0.0160 best reported | best at pub: KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular Property Prediction (KDD 2022) |
| 111 | SGNCL | 0.7160
±0.0080 | This paper |
| 117 | RGCL | 0.7142
±0.0066 best reported | best today: Graph Self-Contrast Representation Learning (2023) Difference within reported uncertainty; not counted as underperformance. |
| 129 | ADGCL | 0.7050
±0.0180 best reported | best today: Rethinking Tokenizer and Decoder in Masked Graph Modeling for Molecules (NeurIPS 2023) Difference within reported uncertainty; not counted as underperformance. |
| 173 | InfoGraph | 0.6920
±0.0080 best reported | best at pub: 16 Pre-training Molecular Graph Representation with 3D Geometry (ICLR 2021) best today: Graph Generative Pre-trained Transformer (ICML 2025) Difference within reported uncertainty; not counted as underperformance. |
| 230 | AttrMasking | 0.6712
±0.0045 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. |
| 257 | No Pre-train | 0.6580
±0.0450 | 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 | 0.8340
±0.0090 | prev best: Let Invariant Rationale Discovery Inspire Graph Contrastive Learning (ICML 2022) best today: Rethinking Tokenizer and Decoder in Masked Graph Modeling for Molecules (NeurIPS 2023) Improvement within reported uncertainty; not highlighted. |
| 61 | SGNCL | 0.8430
±0.0270 | This paper |
| 79 | JOAO | 0.8132
±0.0249 best reported | best at pub: GraphMAE: Self-Supervised Masked Graph Autoencoders (KDD 2022) best today: Graph Self-Contrast Representation Learning (2023) Difference within reported uncertainty; not counted as underperformance. |
| 93 | ADGCL | 0.7980
±0.0350 | This paper |
| 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. |
| 106 | InfoGraph | 0.7810 best reported | best at pub: GeomGCL: Geometric Graph Contrastive Learning for Molecular Property Prediction (AAAI 2021) |
| 115 | ContextPred | 0.7720
±0.0088 best reported | |
| 162 | AttrMasking | 0.7180
±0.0410 | This paper |
| 192 | EdgePred | 0.6410
±0.0370 | prev best: 16 Pre-training Molecular Graph Representation with 3D Geometry (ICLR 2021) Improvement within reported uncertainty; not highlighted. |
| 232 | No Pre-train | 0.5800
±0.0440 | This paper |
| # | 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 | This paper |
| 103 | ContextPred | 0.6220
±0.0059 best reported | |
| 114 | GraphCL | 0.6183
±0.0060 best reported | best at pub: Omni-Granular Ego-Semantic Propagation for Self-Supervised Graph Representation Learning (ICML 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. |
| 128 | RGCL | 0.6140
±0.0060 | prev best: Let Invariant Rationale Discovery Inspire Graph Contrastive Learning (ICML 2022) Improvement within reported uncertainty; not highlighted. |
| 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. |
| 135 | SGNCL | 0.6120
±0.0110 | This paper |
| 162 | InfoGraph | 0.6054
±0.0090 best reported | best at pub: A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining (ICML 2023) best today: Community-Invariant Graph Contrastive Learning (ICML 2024) |
| 170 | EdgePred | 0.6040
±0.0070 | prev best: KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular Property Prediction (KDD 2022) Improvement within reported uncertainty; not highlighted. |
| 222 | No Pre-train | 0.5730
±0.0160 | This paper |
| # | Model | ROC-AUC ↑ | Paper |
|---|---|---|---|
| 1 | GeomGCL | 0.7630 | |
| 2 | LiGhT DeepGPT | 0.7570
±0.0110 | |
| 3 | CoMPT | 0.7550 | |
| 14 | GCN | 0.7350
±0.0020 | |
| 28 | ContextPred | 0.7140
±0.0180 best reported | best at pub: KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular Property Prediction (KDD 2022) |
| 30 | EdgePred | 0.7120
±0.0110 best reported | best at pub: KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular Property Prediction (KDD 2022) |
| 31 | JOAO | 0.7110
±0.0140 best reported | best at pub: KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular Property Prediction (KDD 2022) |
| 35 | InfoGraph | 0.7050 best reported | best at pub: GeomGCL: Geometric Graph Contrastive Learning for Molecular Property Prediction (AAAI 2021) |
| 42 | GraphCL | 0.6960
±0.0230 best reported | best at pub: KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular Property Prediction (KDD 2022) |
| 126 | AttrMasking | 0.6420
±0.0050 | This paper |
| 132 | SGNCL | 0.6390
±0.0040 | This paper |
| 142 | No Pre-train | 0.6340
±0.0060 | This paper |
| 148 | RGCL | 0.6333
±0.0017 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. |
| 160 | ADGCL | 0.6310
±0.0070 | This paper |
