TMLR 2025

A Fused Gromov-Wasserstein Approach to Subgraph Contrastive Learning

Amadou S. Sangare, Nicolas Dunou, Jhony H. Giraldo, Fragkiskos D. Malliaros

Main figure for 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

#ModelAccuracy ↑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
actual #26 vs paper #190 164 places worse
0.9400 ±0.0060
best reported
actual #26 vs paper #190 164 places worse
paper 0.8229 ±0.0054
paper 0.8229 ±0.0054 Δ at pub 0.1171
40
BNLL
0.9360 ±0.0003
This paper
43
DGI
actual #43 vs paper #178 135 places worse
0.9350 ±0.0030
best reported
actual #43 vs paper #178 135 places worse
paper 0.8738 ±0.0006
paper 0.8738 ±0.0006 Δ at pub 0.0612
53
BGRL
actual #53 vs paper #131 78 places worse
0.9331 ±0.0013
best reported
actual #53 vs paper #131 78 places worse
paper 0.9181 ±0.0022
paper 0.9181 ±0.0022 Δ at pub 0.0150 Δ today 0.0150
69
GRACE
actual #69 vs paper #69
0.9301 ±0.0003
actual #69 vs paper #69
paper 0.9301 ±0.0003
paper 0.9301 ±0.0003 Δ at pub 0.0006
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

#ModelAccuracy ↑Paper
1
DiGGR
0.4535 ±0.0353
2
TRIGON
0.4402 ±0.0028
3
DoG
0.4320 ±0.0120
35
PolyGCL
actual #35 vs paper #415 380 places worse
0.4115 ±0.0088
best reported
actual #35 vs paper #415 380 places worse
paper 0.2652 ±0.0007
paper 0.2652 ±0.0007 Δ at pub 0.1463
42
MLP
0.4026 ±0.0108
68
GraphSAGE
0.3899 ±0.0085
79
MUSE
actual #79 vs paper #155 76 places worse
0.3855 ±0.0134
best reported
actual #79 vs paper #155 76 places worse
paper 0.3661 ±0.0015

Difference within reported uncertainty; not counted as underperformance.

paper 0.3661 ±0.0015 Δ at pub 0.0194
207
FOSSIL
0.3561 ±0.0015
This paper
216
FOSSIL v2
0.3541 ±0.0018
This paper
251
GRACE
actual #251 vs paper #376 125 places worse
0.3450 ±0.0110
best reported
actual #251 vs paper #376 125 places worse
paper 0.2891 ±0.0018
paper 0.2891 ±0.0018 Δ at pub 0.0559
295
GSC+Cheb
0.3246 ±0.0013
This paper
335
DGI
actual #335 vs paper #370 35 places worse
0.3067 ±0.0063
best reported
actual #335 vs paper #370 35 places worse
paper 0.2911 ±0.0014
350
FS-MLP
0.3008 ±0.0020
This paper
356
BGRL
actual #356 vs paper #398 42 places worse
0.2986
best reported
actual #356 vs paper #398 42 places worse
paper 0.2793 ±0.0017
360
FS-GCN
0.2969 ±0.0014
This paper
386
GSC
0.2843 ±0.0016
This paper
393
DSSL
actual #393 vs paper #412 19 places worse
0.2815 ±0.0031
best reported
actual #393 vs paper #412 19 places worse
paper 0.2660 ±0.0014
paper 0.2660 ±0.0014 Δ today 0.0155
405
SubG-Con
0.2760 ±0.0018
This paper
430
BNLL
0.2533 ±0.0034
This paper
SOTA performance (not significantly different from the best) Proposed method (this paper) Baseline / comparison (this paper) Global context (other papers) Best at pub — reported result worse than the best known when published (best reported in green) Best at pub — reported value improved over the best known when published Best today — OK at publication; today's leaderboard best is elsewhere