Dual-perspective Cross Contrastive Learning in Graph Transformers

Zelin Yao, Chuang Liu, Xueqi Ma, Mukun Chen, Jia Wu, Xiantao Cai, Bo Du, Wenbin Hu

Main figure for Dual-perspective Cross Contrastive Learning in Graph Transformers

Abstract

Graph contrastive learning (GCL) is a popular method for leaning graph representations by maximizing the consistency of features across augmented views. Traditional GCL methods utilize single-perspective (i.e. data or model-perspective) augmentation to generate positive samples, restraining the diversity of positive samples. In addition, these positive samples may be unreliable due to uncontrollable augmentation strategies that potentially alter the semantic information. To address these challenges, this paper proposed a innovative framework termed dual-perspective cross graph contrastive learning (DC-GCL), which incorporates three modifications designed to enhance positive sample diversity and reliability: 1) We propose dual-perspective augmentation strategy that provide the model with more diverse training data, enabling the model effective learning of feature consistency across different views. 2) From the data perspective, we slightly perturb the original graphs using controllable data augmentation, effectively preserving their semantic information. 3) From the model perspective, we enhance the encoder by utilizing more powerful graph transformers instead of graph neural networks. Based on the model's architecture, we propose three pruning-based strategies to slightly perturb the encoder, providing more reliable positive samples. These modifications collectively form the DC-GCL's foundation and provide more diverse and reliable training inputs, offering significant improvements over traditional GCL methods. Extensive experiments on various benchmarks demonstrate that DC-GCL consistently outperforms different baselines on various datasets and tasks..

Proposed method: DC-GCL

Benchmark Results

Tested on 9 datasets 24 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
154
DC-GCL
0.9050 ±0.0155
This paper
159
WL
actual #159 vs paper #596 437 places worse
0.9040 ±0.0570
best reported
actual #159 vs paper #596 437 places worse
paper 0.8072 ±0.0300
paper 0.8072 ±0.0300 Δ at pub 0.0968
211
iGCL
0.8980 ±0.0120
This paper
222
JOAOv2
actual #222 vs paper #353 131 places worse
0.8967 ±0.0524
best reported
actual #222 vs paper #353 131 places worse
paper 0.8767 ±0.0079

Difference within reported uncertainty; not counted as underperformance.

paper 0.8767 ±0.0079 Δ at pub 0.0200
229
DRGCL
0.8950 ±0.0060
This paper
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
272
SimGRACE
actual #272 vs paper #272
0.8910 ±0.0140
best reported
actual #272 vs paper #272
paper 0.8901 ±0.0131

Difference within reported uncertainty; not counted as underperformance.

paper 0.8901 ±0.0131 Δ at pub 0.0009
310
DualGCL
0.8850 ±0.0090
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
365
DGK
0.8744 ±0.0272
This paper
378
GraphTrans
actual #378 vs paper #378
0.8722 ±0.0705
actual #378 vs paper #378
paper 0.8722 ±0.0705

Improvement within reported uncertainty; not highlighted.

paper 0.8722 ±0.0705 Δ at pub 0.0568
403
MLP
0.8660 ±0.0495
444
GL
actual #444 vs paper #577 133 places worse
0.8520 ±0.0090
best reported
actual #444 vs paper #577 133 places worse
paper 0.8166 ±0.0211
paper 0.8166 ±0.0211 Δ at pub 0.0354
448
GraphGPS
0.8500 ±0.0316
This paper
#ModelAccuracy ↑Paper
1
WL-MLP
0.9954
2
GIN
0.9934
3
GCN
0.9727
12
WL
actual #12 vs paper #223 211 places worse
0.8590 ±0.0010
best reported
actual #12 vs paper #223 211 places worse
paper 0.8001 ±0.0050
best at pub: Propagation Kernels (2014)
paper 0.8001 ±0.0050 Δ at pub 0.0589
35
GraphGPS
0.8421 ±0.0225
This paper
97
iGCL
0.8270 ±0.0040
This paper
100
GraphTrans
actual #100 vs paper #100
0.8260 ±0.0120
actual #100 vs paper #100
paper 0.8260 ±0.0120

Improvement within reported uncertainty; not highlighted.

paper 0.8260 ±0.0120 Δ at pub 0.0056
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
141
SimGRACE
actual #141 vs paper #258 117 places worse
0.8180 ±0.0015
best reported
actual #141 vs paper #258 117 places worse
paper 0.7912 ±0.0044
paper 0.7912 ±0.0044 Δ at pub 0.0268
146
JOAOv2
actual #146 vs paper #303 157 places worse
0.8170 ±0.0026
best reported
actual #146 vs paper #303 157 places worse
paper 0.7836 ±0.0053
paper 0.7836 ±0.0053 Δ at pub 0.0334
210
DGK
0.8031 ±0.0046
This paper
235
DualGCL
0.7980 ±0.0030
This paper
242
DC-GCL
0.7962 ±0.0037
This paper
277
DRGCL
0.7870 ±0.0040
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
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
#ModelAccuracy ↑Paper
1
MSH-GNN
0.9410 ±0.0330
2
GRDL
0.8260 ±0.0120
3
GMN
0.8225
32
GIN
0.7880 ±0.0410
112
DC-GCL
0.7645 ±0.0026
This paper
149
MLP
0.7600 ±0.0320
170
GraphGPS
0.7577 ±0.0219
This paper
178
DGK
actual #178 vs paper #349 171 places worse
0.7568 ±0.0054
best reported
actual #178 vs paper #349 171 places worse
paper 0.7330 ±0.0082
best today: Hierarchical Graph Capsule Network (AAAI 2020)
paper 0.7330 ±0.0082 Δ at pub 0.0238 Δ today 0.0238
189
DualGCL
0.7560 ±0.0050
This paper
190
WL
actual #190 vs paper #369 179 places worse
0.7560 ±0.0040
best reported
actual #190 vs paper #369 179 places worse
paper 0.7292 ±0.0056
paper 0.7292 ±0.0056 Δ at pub 0.0268
209
SimGRACE
0.7535 ±0.0009
This paper
226
DRGCL
0.7520 ±0.0060
This paper
231
GraphTrans
actual #231 vs paper #231
0.7518 ±0.0336
actual #231 vs paper #231
paper 0.7518 ±0.0336

Improvement within reported uncertainty; not highlighted.

paper 0.7518 ±0.0336 Δ at pub 0.0006
265
GraphCL
actual #265 vs paper #296 31 places worse
0.7489 ±0.0065
best reported
actual #265 vs paper #296 31 places worse
paper 0.7439 ±0.0045

Difference within reported uncertainty; not counted as underperformance.

paper 0.7439 ±0.0045 Δ at pub 0.0050
275
iGCL
0.7480 ±0.0050
This paper
283
JOAO
actual #283 vs paper #288 5 places worse
0.7460 ±0.0040
best reported
actual #283 vs paper #288 5 places worse
paper 0.7455 ±0.0041

Difference within reported uncertainty; not counted as underperformance.

paper 0.7455 ±0.0041 Δ at pub 0.0005 Δ today 0.0005
294
InfoGraph
0.7444 ±0.0031
This paper
309
JOAOv2
0.7407 ±0.0110
This paper
#ModelAccuracy ↑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
32
JOAOv2
actual #32 vs paper #305 273 places worse
0.8216 ±0.0017
best reported
actual #32 vs paper #305 273 places worse
paper 0.6933 ±0.0034
paper 0.6933 ±0.0034 Δ at pub 0.1283
37
SimGRACE
actual #37 vs paper #286 249 places worse
0.8188 ±0.0023
best reported
actual #37 vs paper #286 249 places worse
paper 0.7172 ±0.0082
paper 0.7172 ±0.0082 Δ at pub 0.1016
63
GraphGPS
0.8140 ±0.0026
This paper
80
GraphCL
actual #80 vs paper #290 210 places worse
0.8108 ±0.0017
best reported
actual #80 vs paper #290 210 places worse
paper 0.7136 ±0.0115
paper 0.7136 ±0.0115 Δ at pub 0.0972
130
DC-GCL
0.7983 ±0.0043
This paper
131
GraphTrans
0.7981 ±0.0084
This paper
146
InfoGraph
actual #146 vs paper #295 149 places worse
0.7940
best reported
actual #146 vs paper #295 149 places worse
paper 0.7065 ±0.0113
paper 0.7065 ±0.0113 Δ at pub 0.0875
151
MLP
0.7920 ±0.0240
248
JOAO
actual #248 vs paper #305 57 places worse
0.7535 ±0.0093
best reported
actual #248 vs paper #305 57 places worse
paper 0.6950 ±0.0036
paper 0.6950 ±0.0036 Δ at pub 0.0585
249
DualGCL
0.7530 ±0.0040
This paper
285
iGCL
0.7200 ±0.0080
This paper
296
DRGCL
0.7060 ±0.0080
This paper
#ModelAccuracy ↑Paper
1
GC-GNN (GCN)
0.9210 ±0.0810
2
SUGAR
0.8403 ±0.0133
3
Ortho-g-U-Nets
0.8387
15
SAGE
0.8088 ±0.0233
35
DC-GCL
0.7943 ±0.0063
This paper
58
GraphCL
0.7862 ±0.0040
This paper
65
DRGCL
0.7840 ±0.0070
This paper
93
SimGRACE
0.7744 ±0.0111
This paper
94
JOAOv2
0.7740 ±0.0115
This paper
98
JOAO
0.7732 ±0.0054
This paper
119
GraphGPS
0.7598 ±0.0153
This paper
134
GraphTrans
0.7524 ±0.0483
This paper
148
InfoGraph
actual #148 vs paper #157 9 places worse
0.7424 ±0.0086
best reported
actual #148 vs paper #157 9 places worse
paper 0.7285 ±0.0178

Difference within reported uncertainty; not counted as underperformance.

paper 0.7285 ±0.0178 Δ at pub 0.0139
#ModelAccuracy ↑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
actual #23 vs paper #43 20 places worse
0.9169 ±0.0070
best reported
actual #23 vs paper #43 20 places worse
paper 0.8953 ±0.0084
paper 0.8953 ±0.0084 Δ at pub 0.0216
24
JOAO
actual #24 vs paper #63 39 places worse
0.9166 ±0.0059
best reported
actual #24 vs paper #63 39 places worse
paper 0.8529 ±0.0135
paper 0.8529 ±0.0135 Δ at pub 0.0637
29
DC-GCL
0.9104 ±0.0045
This paper
31
DRGCL
0.9080 ±0.0030
This paper
44
SimGRACE
0.8951 ±0.0089
This paper
46
InfoGraph
actual #46 vs paper #68 22 places worse
0.8939 ±0.0181
best reported
actual #46 vs paper #68 22 places worse
paper 0.8250 ±0.0142
paper 0.8250 ±0.0142 Δ at pub 0.0689
49
JOAOv2
actual #49 vs paper #58 9 places worse
0.8879 ±0.0065
best reported
actual #49 vs paper #58 9 places worse
paper 0.8642 ±0.0145
paper 0.8642 ±0.0145 Δ at pub 0.0237
50
GraphTrans
0.8858 ±0.0130
This paper
51
GraphGPS
0.8840 ±0.0115
This paper
73
DGK
0.7804 ±0.0039
This paper
75
GL
0.7734 ±0.0018
This paper
85
WL
0.6882 ±0.0041
This paper

MoleculeNet

#ModelROC-AUC ↑Paper
1
ProtoMol
0.9140 ±0.0030
2
MMSG
0.9080 ±0.0050
3
MemGNN
0.9070
43
GIN
0.8646 ±0.0081
100
JOAO
actual #100 vs paper #226 126 places worse
0.8340 ±0.0330
best reported
actual #100 vs paper #226 126 places worse
paper 0.7730 ±0.0050
paper 0.7730 ±0.0050 Δ at pub 0.0610
178
DC-GCL
0.7990 ±0.0170
This paper
186
ContextPred
0.7960 ±0.0120
This paper
191
AttrMasking
0.7930 ±0.0160
This paper
213
GraphCL
actual #213 vs paper #248 35 places worse
0.7820 ±0.0120
best reported
actual #213 vs paper #248 35 places worse
paper 0.7540 ±0.0140
paper 0.7540 ±0.0140 Δ at pub 0.0280
214
DRGCL
0.7820 ±0.0100
This paper
225
Infomax
actual #225 vs paper #243 18 places worse
0.7780 ±0.0046
best reported
actual #225 vs paper #243 18 places worse
paper 0.7590 ±0.0160

Difference within reported uncertainty; not counted as underperformance.

paper 0.7590 ±0.0160 Δ today 0.0190
231
No-pretrain
actual #231 vs paper #231
0.7700 ±0.0210
actual #231 vs paper #231
paper 0.7700 ±0.0210
paper 0.7700 ±0.0210 Δ at pub 0.0700
242
RGCL
actual #242 vs paper #242
0.7603 ±0.0077
best reported
actual #242 vs paper #242
paper 0.7600 ±0.0080

Difference within reported uncertainty; not counted as underperformance.

paper 0.7600 ±0.0080 Δ at pub 0.0003 Δ today 0.0003
244
SimGRACE
actual #244 vs paper #250 6 places worse
0.7580 ±0.0040
best reported
actual #244 vs paper #250 6 places worse
paper 0.7500 ±0.0170

Difference within reported uncertainty; not counted as underperformance.

paper 0.7500 ±0.0170 Δ at pub 0.0080
255
ADGCL
0.7400 ±0.0220
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 #118 61 places worse
0.8500 ±0.0080
best reported
actual #57 vs paper #118 61 places worse
paper 0.7640 ±0.0340
paper 0.7640 ±0.0340 Δ at pub 0.0860
64
DC-GCL
0.8270 ±0.0360
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 at pub 0.0002
93
ADGCL
actual #93 vs paper #104 11 places worse
0.7980 ±0.0350
best reported
actual #93 vs paper #104 11 places worse
paper 0.7850 ±0.0370

Difference within reported uncertainty; not counted as underperformance.

paper 0.7850 ±0.0370 Δ at pub 0.0130
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
105
DRGCL
0.7820 ±0.0150
This paper
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
123
SimGRACE
actual #123 vs paper #123
0.7560 ±0.0300
actual #123 vs paper #123
paper 0.7560 ±0.0300
paper 0.7560 ±0.0300 Δ at pub 0.0880
151
Infomax
actual #151 vs paper #174 23 places worse
0.7300 ±0.0320
best reported
actual #151 vs paper #174 23 places worse
paper 0.6990 ±0.0300

Difference within reported uncertainty; not counted as underperformance.

paper 0.6990 ±0.0300 Δ at pub 0.0310
162
AttrMasking
0.7180 ±0.0410
This paper
205
No-pretrain
actual #205 vs paper #205
0.6440 ±0.0420
actual #205 vs paper #205
paper 0.6440 ±0.0420

Improvement within reported uncertainty; not highlighted.

paper 0.6440 ±0.0420 Δ at pub 0.0620
#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
actual #80 vs paper #202 122 places worse
0.6330 ±0.0080
best reported
actual #80 vs paper #202 122 places worse
paper 0.5910 ±0.0090
paper 0.5910 ±0.0090 Δ at pub 0.0420
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 0.0126 Δ today 0.0133
120
Infomax
actual #120 vs paper #206 86 places worse
0.6160 ±0.0240
best reported
actual #120 vs paper #206 86 places worse
paper 0.5840 ±0.0080

Difference within reported uncertainty; not counted as underperformance.

paper 0.5840 ±0.0080 Δ at pub 0.0320
128
RGCL
0.6140 ±0.0060
This paper
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
140
DRGCL
0.6110 ±0.0080
This paper
161
DC-GCL
0.6060 ±0.0060
This paper
156
SimGRACE
actual #156 vs paper #156
0.6060 ±0.0100
actual #156 vs paper #156
paper 0.6060 ±0.0100

Improvement within reported uncertainty; not highlighted.

paper 0.6060 ±0.0100 Δ at pub 0.0001
213
No-pretrain
actual #213 vs paper #213
0.5810 ±0.0100
actual #213 vs paper #213
paper 0.5810 ±0.0100

Improvement within reported uncertainty; not highlighted.

paper 0.5810 ±0.0100 Δ at pub 0.0090
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