Subgraph Networks Based Contrastive Learning

Jinhuan Wang, Jiafei Shao, Zeyu Wang, Shanqing Yu, Qi Xuan, Xiaoniu Yang

Main figure for 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.

Proposed method: SGNCL

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

#ModelAccuracy ↑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
actual #199 vs paper #707 508 places worse
0.8993 ±0.0616
best reported
actual #199 vs paper #707 508 places worse
paper 0.7540 ±0.0780
paper 0.7540 ±0.0780 Δ at pub 0.1453
215
ADGCL
actual #215 vs paper #294 79 places worse
0.8970 ±0.0100
best reported
actual #215 vs paper #294 79 places worse
paper 0.8874 ±0.0185

Difference within reported uncertainty; not counted as underperformance.

paper 0.8874 ±0.0185 Δ at pub 0.0096
257
InfoGraph
actual #257 vs paper #272 15 places worse
0.8930 ±0.0514
best reported
actual #257 vs paper #272 15 places worse
paper 0.8901 ±0.0113

Difference within reported uncertainty; not counted as underperformance.

paper 0.8901 ±0.0113 Δ at pub 0.0029
270
SGNCL
0.8913 ±0.0191
This paper
351
JOAO
actual #351 vs paper #370 19 places worse
0.8770 ±0.0080
best reported
actual #351 vs paper #370 19 places worse
paper 0.8735 ±0.0102

Difference within reported uncertainty; not counted as underperformance.

paper 0.8735 ±0.0102 Δ at pub 0.0035 Δ today 0.0035
354
GraphCL
actual #354 vs paper #396 42 places worse
0.8766 ±0.0103
best reported
actual #354 vs paper #396 42 places worse
paper 0.8680 ±0.0134

Difference within reported uncertainty; not counted as underperformance.

paper 0.8680 ±0.0134 Δ at pub 0.0086
355
RGCL
0.8766 ±0.0101
This paper
403
MLP
0.8660 ±0.0495
#ModelAccuracy ↑Paper
1
WL-MLP
0.9954
2
GIN
0.9934
3
GCN
0.9727
104
GraphCL
actual #104 vs paper #325 221 places worse
0.8250 ±0.0013
best reported
actual #104 vs paper #325 221 places worse
paper 0.7787 ±0.0041
paper 0.7787 ±0.0041 Δ at pub 0.0463
131
GraphSAGE
0.8200 ±0.0100
230
SGNCL
0.7984 ±0.0023
This paper
301
JOAO
actual #301 vs paper #317 16 places worse
0.7840 ±0.0050
best reported
actual #301 vs paper #317 16 places worse
paper 0.7807 ±0.0047

Difference within reported uncertainty; not counted as underperformance.

paper 0.7807 ±0.0047 Δ at pub 0.0033
315
RGCL
0.7814 ±0.0108
This paper
338
InfoGraph
actual #338 vs paper #386 48 places worse
0.7750 ±0.0074
best reported
actual #338 vs paper #386 48 places worse
paper 0.7620 ±0.0106

Difference within reported uncertainty; not counted as underperformance.

paper 0.7620 ±0.0106 Δ at pub 0.0130
356
MVGRL
actual #356 vs paper #409 53 places worse
0.7700 ±0.0080
best reported
actual #356 vs paper #409 53 places worse
paper 0.7517 ±0.0070
paper 0.7517 ±0.0070 Δ at pub 0.0183 Δ today 0.0183
440
ADGCL
actual #440 vs paper #440
0.7391 ±0.0077
actual #440 vs paper #440
paper 0.7391 ±0.0077
paper 0.7391 ±0.0077 Δ at pub 0.0421

MoleculeNet

#ModelROC-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
actual #36 vs paper #158 122 places worse
0.8870 ±0.0190
best reported
actual #36 vs paper #158 122 places worse
paper 0.6970 ±0.0070
paper 0.6970 ±0.0070 Δ at pub 0.1900
39
JOAO
actual #39 vs paper #140 101 places worse
0.8790 ±0.0200
best reported
actual #39 vs paper #140 101 places worse
paper 0.7020 ±0.0100
paper 0.7020 ±0.0100 Δ at pub 0.1770
40
ContextPred
actual #40 vs paper #201 161 places worse
0.8770 ±0.0260
best reported
actual #40 vs paper #201 161 places worse
paper 0.6800 ±0.0200
paper 0.6800 ±0.0200 Δ at pub 0.1970
44
EdgePred
actual #44 vs paper #225 181 places worse
0.8730 ±0.0160
best reported
actual #44 vs paper #225 181 places worse
paper 0.6730 ±0.0240
paper 0.6730 ±0.0240 Δ at pub 0.2000
111
SGNCL
0.7160 ±0.0080
This paper
117
RGCL
actual #117 vs paper #117
0.7142 ±0.0066
best reported
actual #117 vs paper #117
paper 0.7140 ±0.0070

Difference within reported uncertainty; not counted as underperformance.

paper 0.7140 ±0.0070 Δ today 0.0002
129
ADGCL
actual #129 vs paper #150 21 places worse
0.7050 ±0.0180
best reported
actual #129 vs paper #150 21 places worse
paper 0.7000 ±0.0110

Difference within reported uncertainty; not counted as underperformance.

paper 0.7000 ±0.0110 Δ today 0.0050
173
InfoGraph
actual #173 vs paper #183 10 places worse
0.6920 ±0.0080
best reported
actual #173 vs paper #183 10 places worse
paper 0.6880 ±0.0080

Difference within reported uncertainty; not counted as underperformance.

paper 0.6880 ±0.0080 Δ at pub 0.0040 Δ today 0.0040
230
AttrMasking
actual #230 vs paper #279 49 places worse
0.6712 ±0.0045
best reported
actual #230 vs paper #279 49 places worse
paper 0.6430 ±0.0280

Difference within reported uncertainty; not counted as underperformance.

paper 0.6430 ±0.0280 Δ today 0.0282
257
No Pre-train
0.6580 ±0.0450
This paper
#ModelROC-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
actual #57 vs paper #63 6 places worse
0.8340 ±0.0090
actual #57 vs paper #63 6 places worse
paper 0.8340 ±0.0090

Improvement within reported uncertainty; not highlighted.

paper 0.8340 ±0.0090 Δ at pub 0.0002 Δ today 0.0160
61
SGNCL
0.8430 ±0.0270
This paper
79
JOAO
actual #79 vs paper #79
0.8132 ±0.0249
best reported
actual #79 vs paper #79
paper 0.8130 ±0.0250

Difference within reported uncertainty; not counted as underperformance.

paper 0.8130 ±0.0250 Δ today 0.0002
93
ADGCL
0.7980 ±0.0350
This paper
97
GraphCL
actual #97 vs paper #120 23 places worse
0.7890 ±0.0420
best reported
actual #97 vs paper #120 23 places worse
paper 0.7600 ±0.0270

Difference within reported uncertainty; not counted as underperformance.

paper 0.7600 ±0.0270 Δ at pub 0.0290 Δ today 0.0290
106
InfoGraph
actual #106 vs paper #174 68 places worse
0.7810
best reported
actual #106 vs paper #174 68 places worse
paper 0.6990 ±0.0300
paper 0.6990 ±0.0300 Δ at pub 0.0820
115
ContextPred
actual #115 vs paper #197 82 places worse
0.7720 ±0.0088
best reported
actual #115 vs paper #197 82 places worse
paper 0.6590 ±0.0380
162
AttrMasking
0.7180 ±0.0410
This paper
192
EdgePred
actual #192 vs paper #207 15 places worse
0.6410 ±0.0370
actual #192 vs paper #207 15 places worse
paper 0.6410 ±0.0370

Improvement within reported uncertainty; not highlighted.

paper 0.6410 ±0.0370 Δ at pub 0.0830
232
No Pre-train
0.5800 ±0.0440
This paper
#ModelROC-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
actual #68 vs paper #182 114 places worse
0.6400 ±0.0100
best reported
actual #68 vs paper #182 114 places worse
paper 0.6000 ±0.0080
paper 0.6000 ±0.0080 Δ at pub 0.0400
80
ADGCL
0.6330 ±0.0080
This paper
103
ContextPred
actual #103 vs paper #144 41 places worse
0.6220 ±0.0059
best reported
actual #103 vs paper #144 41 places worse
paper 0.6090 ±0.0060
114
GraphCL
actual #114 vs paper #162 48 places worse
0.6183 ±0.0060
best reported
actual #114 vs paper #162 48 places worse
paper 0.6050 ±0.0090

Difference within reported uncertainty; not counted as underperformance.

paper 0.6050 ±0.0090 Δ at pub 0.0030 Δ today 0.0133
128
RGCL
actual #128 vs paper #128
0.6140 ±0.0060
actual #128 vs paper #128
paper 0.6140 ±0.0060

Improvement within reported uncertainty; not highlighted.

paper 0.6140 ±0.0060 Δ at pub 0.0002
133
AttrMasking
actual #133 vs paper #141 8 places worse
0.6121 ±0.0065
best reported
actual #133 vs paper #141 8 places worse
paper 0.6100 ±0.0070

Difference within reported uncertainty; not counted as underperformance.

paper 0.6100 ±0.0070 Δ today 0.0021
135
SGNCL
0.6120 ±0.0110
This paper
162
InfoGraph
actual #162 vs paper #206 44 places worse
0.6054 ±0.0090
best reported
actual #162 vs paper #206 44 places worse
paper 0.5840 ±0.0080
paper 0.5840 ±0.0080 Δ at pub 0.0150 Δ today 0.0214
170
EdgePred
actual #170 vs paper #170
0.6040 ±0.0070
actual #170 vs paper #170
paper 0.6040 ±0.0070

Improvement within reported uncertainty; not highlighted.

paper 0.6040 ±0.0070 Δ at pub 0.0010
222
No Pre-train
0.5730 ±0.0160
This paper
#ModelROC-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
actual #28 vs paper #131 103 places worse
0.7140 ±0.0180
best reported
actual #28 vs paper #131 103 places worse
paper 0.6390 ±0.0060
paper 0.6390 ±0.0060 Δ at pub 0.0750
30
EdgePred
actual #30 vs paper #127 97 places worse
0.7120 ±0.0110
best reported
actual #30 vs paper #127 97 places worse
paper 0.6410 ±0.0060
paper 0.6410 ±0.0060 Δ at pub 0.0710
31
JOAO
actual #31 vs paper #165 134 places worse
0.7110 ±0.0140
best reported
actual #31 vs paper #165 134 places worse
paper 0.6290 ±0.0050
paper 0.6290 ±0.0050 Δ at pub 0.0820
35
InfoGraph
actual #35 vs paper #168 133 places worse
0.7050
best reported
actual #35 vs paper #168 133 places worse
paper 0.6270 ±0.0040
paper 0.6270 ±0.0040 Δ at pub 0.0780
42
GraphCL
actual #42 vs paper #178 136 places worse
0.6960 ±0.0230
best reported
actual #42 vs paper #178 136 places worse
paper 0.6240 ±0.0060
paper 0.6240 ±0.0060 Δ at pub 0.0720
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
actual #148 vs paper #149 1 place worse
0.6333 ±0.0017
best reported
actual #148 vs paper #149 1 place worse
paper 0.6330 ±0.0020

Difference within reported uncertainty; not counted as underperformance.

paper 0.6330 ±0.0020 Δ at pub 0.0003 Δ today 0.0003
160
ADGCL
0.6310 ±0.0070
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