A Fused Gromov-Wasserstein Approach to Subgraph Contrastive Learning
Abstract
Self-supervised learning has become a key method for training deep learning models when labeled data is scarce or unavailable. While graph machine learning holds great promise across various domains, the design of effective pretext tasks for self-supervised graph representation learning remains challenging. Contrastive learning, a popular approach in graph self-supervised learning, leverages positive and negative pairs to compute a contrastive loss function. However, current graph contrastive learning methods often struggle to fully use structural patterns and node similarities. To address these issues, we present a new method called Fused Gromov Wasserstein Subgraph Contrastive Learning (FOSSIL). Our model integrates node-level and subgraph-level contrastive learning, seamlessly combining a standard node-level contrastive loss with the Fused Gromov-Wasserstein distance. This combination helps our method capture both node features and graph structure together. Importantly, our approach works well with both homophilic and heterophilic graphs and can dynamically create views for generating positive and negative pairs. Through extensive experiments on benchmark graph datasets, we show that FOSSIL outperforms or achieves competitive performance compared to current state-of-the-art methods.
Benchmark Results
Tested on 2 datasets 7 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DoG | 0.9690
±0.0030 | |
| 2 | GWN-fa | 0.9667
±0.0026 | |
| 3 | GWN-sym | 0.9666
±0.0026 | |
| 6 | GraphSAGE | 0.9593
±0.0025 | |
| 13 | FOSSIL v2 | 0.9504
±0.0003 | This paper |
| 20 | FOSSIL | 0.9449
±0.0004 | This paper |
| 26 | SubG-Con | 0.9400
±0.0060 best reported | best at pub: Towards Graph Self-Supervised Learning with Contrastive Adjusted Zooming (2021) |
| 40 | BNLL | 0.9360
±0.0003 | This paper |
| 43 | DGI | 0.9350
±0.0030 best reported | best at pub: PyG-SSL: A Graph Self-Supervised Learning Toolkit (2024) |
| 53 | BGRL | 0.9331
±0.0013 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) |
| 69 | GRACE | 0.9301
±0.0003 | |
| 88 | MLP | 0.9280
±0.0020 | |
| 103 | FS-GCN | 0.9250
±0.0002 | This paper |
| 122 | FS-MLP | 0.9205
±0.0006 | This paper |
| 162 | GSC | 0.9016
±0.0006 | This paper |
| 169 | GSC+Cheb | 0.8920
±0.0014 | This paper |
| 175 | DSSL | 0.8773
±0.0008 | This paper |
| 206 | MUSE | 0.5432
±0.0176 | This paper |
Heterophilic Graphs
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DiGGR | 0.4535
±0.0353 | |
| 2 | TRIGON | 0.4402
±0.0028 | |
| 3 | DoG | 0.4320
±0.0120 | |
| 35 | PolyGCL | 0.4115
±0.0088 best reported | best at pub: Cross-Domain Graph Data Scaling: A Showcase with Diffusion Models (NeurIPS 2024) |
| 42 | MLP | 0.4026
±0.0108 | |
| 68 | GraphSAGE | 0.3899
±0.0085 | |
| 79 | MUSE | 0.3855
±0.0134 best reported | best at pub: Disentangled Generative Graph Representation Learning (2024) Difference within reported uncertainty; not counted as underperformance. |
| 207 | FOSSIL | 0.3561
±0.0015 | This paper |
| 216 | FOSSIL v2 | 0.3541
±0.0018 | This paper |
| 251 | GRACE | 0.3450
±0.0110 best reported | best at pub: Graph Contrastive Learning under Heterophily via Graph Filters (2023) |
| 295 | GSC+Cheb | 0.3246
±0.0013 | This paper |
| 335 | DGI | 0.3067
±0.0063 best reported | best at pub: Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating (AAAI 2022) best today: Toward General Digraph Contrastive Learning: A Dual Spatial Perspective (2025) |
| 350 | FS-MLP | 0.3008
±0.0020 | This paper |
| 356 | BGRL | 0.2986 best reported | best at pub: Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating (AAAI 2022) |
| 360 | FS-GCN | 0.2969
±0.0014 | This paper |
| 386 | GSC | 0.2843
±0.0016 | This paper |
| 393 | DSSL | 0.2815
±0.0031 best reported | best today: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) |
| 405 | SubG-Con | 0.2760
±0.0018 | This paper |
| 430 | BNLL | 0.2533
±0.0034 | This paper |
