Rethinking and Simplifying Bootstrapped Graph Latents

Wangbin Sun, Jintang Li, Liang Chen, Bingzhe Wu, Yatao Bian, Zibin Zheng

Main figure for Rethinking and Simplifying Bootstrapped Graph Latents

Abstract

Graph contrastive learning (GCL) has emerged as a representative paradigm in graph self-supervised learning, where negative samples are commonly regarded as the key to preventing model collapse and producing distinguishable representations. Recent studies have shown that GCL without negative samples can achieve state-of-the-art performance as well as scalability improvement, with bootstrapped graph latent (BGRL) as a prominent step forward. However, BGRL relies on a complex architecture to maintain the ability to scatter representations, and the underlying mechanisms enabling the success remain largely unexplored. In this paper, we introduce an instance-level decorrelation perspective to tackle the aforementioned issue and leverage it as a springboard to reveal the potential unnecessary model complexity within BGRL. Based on our findings, we present SGCL, a simple yet effective GCL framework that utilizes the outputs from two consecutive iterations as positive pairs, eliminating the negative samples. SGCL only requires a single graph augmentation and a single graph encoder without additional parameters. Extensive experiments conducted on various graph benchmarks demonstrate that SGCL can achieve competitive performance with fewer parameters, lower time and space costs, and significant convergence speedup..

Proposed method: SGCL

Benchmark Results

Tested on 8 datasets 25 baseline values reported too low

Tables show presented results in global context (best 3 papers + GCN + MLP).

Classic

#ModelAccuracy ↑Paper
1
GraphTARIF
0.9703 ±0.0019
2
GAT
actual #2 vs paper #275 273 places worse
0.9669 ±0.0014
best reported
actual #2 vs paper #275 273 places worse
paper 0.9256 ±0.0035
3
GAT+T
0.9660 ±0.0007
7
SAGE
0.9643 ±0.0027
8
GCN
actual #8 vs paper #292 284 places worse
0.9632 ±0.0008
best reported
actual #8 vs paper #292 284 places worse
paper 0.9242 ±0.0022
130
AFGRL
actual #130 vs paper #189 59 places worse
0.9361 ±0.0020
best reported
actual #130 vs paper #189 59 places worse
paper 0.9322 ±0.0028

Difference within reported uncertainty; not counted as underperformance.

paper 0.9322 ±0.0028 Δ at pub 0.0039
157
SGCL
0.9346 ±0.0030
This paper
164
GraphMAE
actual #164 vs paper #164
0.9341 ±0.0010
actual #164 vs paper #164
paper 0.9341 ±0.0010
172
BGRL
actual #172 vs paper #198 26 places worse
0.9337 ±0.0021
best reported
actual #172 vs paper #198 26 places worse
paper 0.9317 ±0.0030

Difference within reported uncertainty; not counted as underperformance.

paper 0.9317 ±0.0030 Δ at pub 0.0020
186
CCA-SSG
actual #186 vs paper #201 15 places worse
0.9325 ±0.0021
best reported
actual #186 vs paper #201 15 places worse
paper 0.9314 ±0.0014

Difference within reported uncertainty; not counted as underperformance.

paper 0.9314 ±0.0014 Δ at pub 0.0011
191
GCA
actual #191 vs paper #277 86 places worse
0.9320 ±0.0060
best reported
actual #191 vs paper #277 86 places worse
paper 0.9253 ±0.0016
203
GRACE
actual #203 vs paper #288 85 places worse
0.9313 ±0.0017
best reported
actual #203 vs paper #288 85 places worse
paper 0.9246 ±0.0018
paper 0.9246 ±0.0018 Δ at pub 0.0034 Δ today 0.0067
206
MVGRL
actual #206 vs paper #359 153 places worse
0.9310 ±0.0040
best reported
actual #206 vs paper #359 153 places worse
paper 0.9174 ±0.0007
213
DGI
actual #213 vs paper #366 153 places worse
0.9309 ±0.0008
best reported
actual #213 vs paper #366 153 places worse
paper 0.9161 ±0.0022
263
COSTA
actual #263 vs paper #275 12 places worse
0.9267 ±0.0016
best reported
actual #263 vs paper #275 12 places worse
paper 0.9256 ±0.0045

Difference within reported uncertainty; not counted as underperformance.

paper 0.9256 ±0.0045 Δ today 0.0011
390
MLP
actual #390 vs paper #535 145 places worse
0.9128 ±0.0063
best reported
actual #390 vs paper #535 145 places worse
paper 0.7853
paper 0.7853 Δ at pub 0.1275
#ModelAccuracy ↑Paper
1
GraphTARIF
0.9461 ±0.0017
2
GCN
actual #2 vs paper #269 267 places worse
0.9412 ±0.0008
best reported
actual #2 vs paper #269 267 places worse
paper 0.8651 ±0.0054
paper 0.8651 ±0.0054 Δ at pub 0.0321 Δ today 0.0761
3
GAT
actual #3 vs paper #256 253 places worse
0.9398 ±0.0022
best reported
actual #3 vs paper #256 253 places worse
paper 0.8693 ±0.0029
8
SAGE
0.9351 ±0.0006
65
SGCL
0.9070 ±0.0030
This paper
79
BGRL
0.9034 ±0.0019
This paper
100
GraphMAE
actual #100 vs paper #111 11 places worse
0.8988 ±0.0010
actual #100 vs paper #111 11 places worse
paper 0.8988 ±0.0010
paper 0.8988 ±0.0010 Δ at pub 0.0154
112
AFGRL
0.8988 ±0.0033
This paper
139
GRACE
actual #139 vs paper #270 131 places worse
0.8953 ±0.0035
best reported
actual #139 vs paper #270 131 places worse
paper 0.8650 ±0.0033
paper 0.8650 ±0.0033 Δ at pub 0.0303 Δ today 0.0303
159
CCA-SSG
actual #159 vs paper #171 12 places worse
0.8896 ±0.0013
best reported
actual #159 vs paper #171 12 places worse
paper 0.8874 ±0.0028

Difference within reported uncertainty; not counted as underperformance.

paper 0.8874 ±0.0028 Δ today 0.0022
160
GCA
0.8894 ±0.0015
This paper
179
MVGRL
actual #179 vs paper #235 56 places worse
0.8861 ±0.0064
best reported
actual #179 vs paper #235 56 places worse
paper 0.8752 ±0.0011
192
COSTA
actual #192 vs paper #193 1 place worse
0.8837 ±0.0022
best reported
actual #192 vs paper #193 1 place worse
paper 0.8832 ±0.0003

Difference within reported uncertainty; not counted as underperformance.

paper 0.8832 ±0.0003 Δ at pub 0.0005
210
DGI
actual #210 vs paper #354 144 places worse
0.8798 ±0.0081
best reported
actual #210 vs paper #354 144 places worse
paper 0.8395 ±0.0047
320
MLP
actual #320 vs paper #455 135 places worse
0.8463
best reported
actual #320 vs paper #455 135 places worse
paper 0.7381
#ModelAccuracy ↑Paper
1
GrokFormer
0.9831 ±0.0018
2
PolyFormer
0.9808 ±0.0027
3
SGFormer
0.9796 ±0.0081
6
GAT
actual #6 vs paper #122 116 places worse
0.9782 ±0.0028
best reported
actual #6 vs paper #122 116 places worse
paper 0.9547 ±0.0015
paper 0.9547 ±0.0015 Δ at pub 0.0116 Δ today 0.0235
9
GCN
actual #9 vs paper #90 81 places worse
0.9774 ±0.0035
best reported
actual #9 vs paper #90 81 places worse
paper 0.9565 ±0.0016
paper 0.9565 ±0.0016 Δ at pub 0.0085 Δ today 0.0209
17
SAGE
0.9739 ±0.0018
58
MLP
actual #58 vs paper #210 152 places worse
0.9597 ±0.0007
best reported
actual #58 vs paper #210 152 places worse
paper 0.9358
63
GCA
actual #63 vs paper #80 17 places worse
0.9590 ±0.0020
best reported
actual #63 vs paper #80 17 places worse
paper 0.9573 ±0.0003

Difference within reported uncertainty; not counted as underperformance.

paper 0.9573 ±0.0003 Δ at pub 0.0017
69
BGRL
actual #69 vs paper #80 11 places worse
0.9580 ±0.0040
best reported
actual #69 vs paper #80 11 places worse
paper 0.9573 ±0.0005

Difference within reported uncertainty; not counted as underperformance.

paper 0.9573 ±0.0005 Δ at pub 0.0007
74
SGCL
0.9578 ±0.0011
This paper
78
AFGRL
actual #78 vs paper #88 10 places worse
0.9574 ±0.0010
best reported
actual #78 vs paper #88 10 places worse
paper 0.9569 ±0.0010

Difference within reported uncertainty; not counted as underperformance.

paper 0.9569 ±0.0010 Δ at pub 0.0005
100
COSTA
0.9560 ±0.0002
This paper
106
CCA-SSG
actual #106 vs paper #133 27 places worse
0.9559 ±0.0007
best reported
actual #106 vs paper #133 27 places worse
paper 0.9538 ±0.0006
paper 0.9538 ±0.0006 Δ at pub 0.0021
114
MVRL
actual #114 vs paper #134 20 places worse
0.9553 ±0.0010
best reported
actual #114 vs paper #134 20 places worse
paper 0.9533 ±0.0003
117
GraphMAE
actual #117 vs paper #125 8 places worse
0.9540 ±0.0006
actual #117 vs paper #125 8 places worse
paper 0.9540 ±0.0006

Improvement within reported uncertainty; not highlighted.

paper 0.9540 ±0.0006 Δ at pub 0.0010
167
DGI
actual #167 vs paper #174 7 places worse
0.9489 ±0.0009
best reported
actual #167 vs paper #174 7 places worse
paper 0.9451 ±0.0052

Difference within reported uncertainty; not counted as underperformance.

paper 0.9451 ±0.0052 Δ at pub 0.0006 Δ today 0.0038
#ModelAccuracy ↑Paper
1
GCN
actual #1 vs paper #202 201 places worse
0.9302 ±0.0011
best reported
actual #1 vs paper #202 201 places worse
paper 0.7719 ±0.0012
paper 0.7719 ±0.0012 Δ at pub 0.1583
2
RSE + RGCN (70b)
0.8852 ±0.0019
3
LEMP+T
0.8825
9
SAGE
0.8771
31
GAT
actual #31 vs paper #187 156 places worse
0.8533
best reported
actual #31 vs paper #187 156 places worse
paper 0.7765 ±0.0011
84
GraphMAE
actual #84 vs paper #101 17 places worse
0.7992 ±0.0068
actual #84 vs paper #101 17 places worse
paper 0.7992 ±0.0068
paper 0.7992 ±0.0068 Δ at pub 0.0280
94
GRACE
actual #94 vs paper #175 81 places worse
0.8014 ±0.0048
best reported
actual #94 vs paper #175 81 places worse
paper 0.7797 ±0.0063
paper 0.7797 ±0.0063 Δ at pub 0.0217 Δ today 0.0217
100
BGRL
actual #100 vs paper #100
0.8000 ±0.0010
best reported
actual #100 vs paper #100
paper 0.7998 ±0.0010

Difference within reported uncertainty; not counted as underperformance.

paper 0.7998 ±0.0010 Δ at pub 0.0002 Δ today 0.0002
103
SGCL
0.7985 ±0.0053
This paper
129
COSTA
0.7912 ±0.0002
This paper
130
CCA-SSG
actual #130 vs paper #130
0.7908 ±0.0053
actual #130 vs paper #130
paper 0.7908 ±0.0053

Improvement within reported uncertainty; not highlighted.

paper 0.7908 ±0.0053 Δ at pub 0.0043
143
AFGRL
actual #143 vs paper #187 44 places worse
0.7890 ±0.0060
best reported
actual #143 vs paper #187 44 places worse
paper 0.7762 ±0.0049
paper 0.7762 ±0.0049 Δ today 0.0128
151
DGI
actual #151 vs paper #228 77 places worse
0.7865 ±0.0690
best reported
actual #151 vs paper #228 77 places worse
paper 0.7535 ±0.0014

Difference within reported uncertainty; not counted as underperformance.

paper 0.7535 ±0.0014 Δ at pub 0.0005 Δ today 0.0330
162
GCA
actual #162 vs paper #163 1 place worse
0.7840 ±0.0013
best reported
actual #162 vs paper #163 1 place worse
paper 0.7835 ±0.0005

Difference within reported uncertainty; not counted as underperformance.

paper 0.7835 ±0.0005 Δ at pub 0.0005 Δ today 0.0005
190
MVGRL
actual #190 vs paper #191 1 place worse
0.7757 ±0.0046
best reported
actual #190 vs paper #191 1 place worse
paper 0.7752 ±0.0008

Difference within reported uncertainty; not counted as underperformance.

paper 0.7752 ±0.0008 Δ today 0.0005
237
MLP
actual #237 vs paper #252 15 places worse
0.7469 ±0.0085
best reported
actual #237 vs paper #252 15 places worse
paper 0.7198
#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
12
GCN
actual #12 vs paper #67 55 places worse
0.9514 ±0.0025
best reported
actual #12 vs paper #67 55 places worse
paper 0.9303 ±0.0031
best today: Graph Wave Networks (WWW 2025)
paper 0.9303 ±0.0031 Δ at pub 0.0057 Δ today 0.0211
21
GAT
actual #21 vs paper #107 86 places worse
0.9437 ±0.0028
best reported
actual #21 vs paper #107 86 places worse
paper 0.9231 ±0.0024
best today: Graph Wave Networks (WWW 2025)
paper 0.9231 ±0.0024 Δ at pub 0.0149 Δ today 0.0206
43
DGI
actual #43 vs paper #114 71 places worse
0.9350 ±0.0030
best reported
actual #43 vs paper #114 71 places worse
paper 0.9215 ±0.0063
48
CCA-SSG
actual #48 vs paper #50 2 places worse
0.9337 ±0.0020
best reported
actual #48 vs paper #50 2 places worse
paper 0.9332 ±0.0022

Difference within reported uncertainty; not counted as underperformance.

paper 0.9332 ±0.0022 Δ at pub 0.0005
51
GCA
actual #51 vs paper #63 12 places worse
0.9332 ±0.0012
best reported
actual #51 vs paper #63 12 places worse
paper 0.9310 ±0.0001
53
BGRL
0.9331 ±0.0013
This paper
57
SGCL
actual #57 vs paper #58 1 place worse
0.9330 ±0.0020
best reported
actual #57 vs paper #58 1 place worse
paper 0.9329 ±0.0017

Difference within reported uncertainty; not counted as underperformance.

paper 0.9329 ±0.0017 Δ today 0.0001
56
AFGRL
actual #56 vs paper #58 2 places worse
0.9330 ±0.0020
best reported
actual #56 vs paper #58 2 places worse
paper 0.9327 ±0.0017

Difference within reported uncertainty; not counted as underperformance.

paper 0.9327 ±0.0017 Δ today 0.0003
63
GraphMAE
actual #63 vs paper #73 10 places worse
0.9296 ±0.0009
actual #63 vs paper #73 10 places worse
paper 0.9296 ±0.0009
69
GRACE
actual #69 vs paper #114 45 places worse
0.9301 ±0.0003
best reported
actual #69 vs paper #114 45 places worse
paper 0.9217 ±0.0004
paper 0.9217 ±0.0004 Δ at pub 0.0076 Δ today 0.0084
76
COSTA
0.9295 ±0.0012
This paper
88
MLP
actual #88 vs paper #158 70 places worse
0.9280 ±0.0020
best reported
actual #88 vs paper #158 70 places worse
paper 0.9037
118
MVRL
0.9211 ±0.0012
This paper

OGB

#ModelAccuracy ↑Paper
1
Jacobi
0.8968
2
GPR
0.8953
3
LEMP4HG
0.8939
4
SAGE
0.8933
6
GCN
actual #6 vs paper #250 244 places worse
0.8868
best reported
actual #6 vs paper #250 244 places worse
paper 0.7564 ±0.0021
9
GAT
actual #9 vs paper #164 155 places worse
0.8829
best reported
actual #9 vs paper #164 155 places worse
paper 0.7945 ±0.0059
30
GraphMAE
actual #30 vs paper #335 305 places worse
0.8630 ±0.0007
best reported
actual #30 vs paper #335 305 places worse
paper 0.7023 ±0.0010
paper 0.7023 ±0.0010 Δ at pub 0.0133 Δ today 0.1607
244
SGCL
0.7596 ±0.0011
This paper
300
BGRL
0.7397 ±0.0005
This paper
336
CCA-SSG
0.7018 ±0.0015
This paper
351
MLP
actual #351 vs paper #370 19 places worse
0.6605 ±0.0020
best reported
actual #351 vs paper #370 19 places worse
paper 0.6106 ±0.0006
paper 0.6106 ±0.0006 Δ at pub 0.2312 Δ today 0.0499
#ModelAccuracy ↑Paper
1
GIANT-XRT
0.7612 ±0.0016
2
GEGCN
0.7576 ±0.0064
3
AGDN
0.7522 ±0.0007
15
GAT
actual #15 vs paper #78 63 places worse
0.7365 ±0.0011
best reported
actual #15 vs paper #78 63 places worse
paper 0.7060 ±0.0030
paper 0.7060 ±0.0030 Δ today 0.0305
23
GCN
actual #23 vs paper #52 29 places worse
0.7174 ±0.0029
actual #23 vs paper #52 29 places worse
paper 0.7174 ±0.0029

Improvement within reported uncertainty; not highlighted.

paper 0.7174 ±0.0029 Δ at pub 0.0002 Δ today 0.0126
25
GraphSAGE
0.7277 ±0.0016
52
GraphMAE
0.7175 ±0.0017
This paper
56
BGRL
0.7164 ±0.0012
This paper
74
SGCL
0.7099 ±0.0009
This paper
83
DGI
actual #83 vs paper #102 19 places worse
0.7034 ±0.0016
best reported
actual #83 vs paper #102 19 places worse
paper 0.6510 ±0.0040
paper 0.6510 ±0.0040 Δ at pub 0.0524
88
CCA-SSG
0.6922 ±0.0022
This paper
92
GCA
0.6820 ±0.0020
This paper
93
MVGRL
0.6810 ±0.0010
This paper
107
MLP
actual #107 vs paper #108 1 place worse
0.5630 ±0.0030
actual #107 vs paper #108 1 place worse
paper 0.5630 ±0.0030
#ModelAccuracy ↑Paper
1
LMSPS+LP+MS
0.5784 ±0.0022
2
SeHGNN+emb+ms
0.5719 ±0.0012
3
SeHGNN+ms
0.5671 ±0.0014
47
GAT
actual #47 vs paper #78 31 places worse
0.4860 ±0.0029
best reported
actual #47 vs paper #78 31 places worse
paper 0.3050 ±0.0030
57
GraphSAGE
0.4646 ±0.0060
60
GCN
actual #60 vs paper #78 18 places worse
0.4290 ±0.0050
best reported
actual #60 vs paper #78 18 places worse
paper 0.3010 ±0.0030
74
SGCL
0.3271 ±0.0009
This paper
75
GraphMAE
0.3261 ±0.0011
This paper
76
MLP
actual #76 vs paper #78 2 places worse
0.3243
best reported
actual #76 vs paper #78 2 places worse
paper 0.2210 ±0.0030
paper 0.2210 ±0.0030 Δ at pub 0.1033
77
BGRL
0.3218 ±0.0015
This paper
78
CCA-SSG
0.3178 ±0.0038
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 Improved at pub — later paper surpassed this result Best today — OK at publication; today's leaderboard best is elsewhere