HAT-GAE: Self-Supervised Graph Auto-encoders with Hierarchical Adaptive Masking and Trainable Corruption

Chengyu Sun, Liang Hu, Hongtu Li, Shuai Li, Tuohang Li, Ling Chi

Main figure for HAT-GAE: Self-Supervised Graph Auto-encoders with Hierarchical Adaptive Masking and Trainable Corruption

Abstract

[S U M M A R Y] Self-supervised auto-encoders have emerged as a successful framework for representation learning in computer vision and natural language processing in recent years, However, their application to graph data has been met with limited performance due to the non-Euclidean and complex structure of graphs in comparison to images or text, as well as the limitations of conventional auto-encoder architectures. In this paper, we investigate factors impacting the performance of auto-encoders on graph data and propose a novel auto-encoder model for graph representation learning. Our model incorporates a hierarchical adaptive masking mechanism to incrementally increase the difficulty of training in order to mimic the process of human cognitive learning, and a trainable corruption scheme to enhance the robustness of learned representations. Through extensive experimentation on ten benchmark datasets, we demonstrate the superiority of our proposed method over state-of-the-art graph representation learning models.

Benchmark Results

Tested on 6 datasets 16 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 #247 245 places worse
0.9669 ±0.0014
best reported
actual #2 vs paper #247 245 places worse
paper 0.9276 ±0.0017
3
GAT+T
0.9660 ±0.0007
7
SAGE
0.9643 ±0.0027
8
GCN
actual #8 vs paper #544 536 places worse
0.9632 ±0.0008
best reported
actual #8 vs paper #544 536 places worse
paper 0.7719 ±0.0021
140
HAT-GAE
0.9358 ±0.0024
This paper
164
GraphMAE
actual #164 vs paper #218 54 places worse
0.9301 ±0.0026
actual #164 vs paper #218 54 places worse
paper 0.9301 ±0.0026
paper 0.9301 ±0.0026 Δ at pub 0.0230 Δ today 0.0040
172
BGRL
actual #172 vs paper #263 91 places worse
0.9337 ±0.0021
best reported
actual #172 vs paper #263 91 places worse
paper 0.9265 ±0.0031
paper 0.9265 ±0.0031 Δ at pub 0.0072
186
CCA-SSG
actual #186 vs paper #329 143 places worse
0.9325 ±0.0021
best reported
actual #186 vs paper #329 143 places worse
paper 0.9210 ±0.0013
paper 0.9210 ±0.0013 Δ at pub 0.0115
203
GRACE
actual #203 vs paper #524 321 places worse
0.9313 ±0.0017
best reported
actual #203 vs paper #524 321 places worse
paper 0.8221 ±0.0022
paper 0.8221 ±0.0022 Δ at pub 0.1059 Δ today 0.1092
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 0.9177 ±0.0014
213
DGI
actual #213 vs paper #367 154 places worse
0.9309 ±0.0008
best reported
actual #213 vs paper #367 154 places worse
paper 0.9159 ±0.0017
227
HAT-GAE-TC
0.9292 ±0.0018
This paper
264
HAT-GAE-HM
0.9265 ±0.0011
This paper
348
GATE
0.9191 ±0.0014
This paper
352
GAE
actual #352 vs paper #506 154 places worse
0.9185 ±0.0006
best reported
actual #352 vs paper #506 154 places worse
paper 0.8527 ±0.0011
paper 0.8527 ±0.0011 Δ at pub 0.0658
390
MLP
0.9128 ±0.0063
398
InfoGCL
0.9117 ±0.0022
This paper
437
HAT-GAE-AM
0.9039 ±0.0020
This paper
471
GPT-GNN
0.8927 ±0.0028
This paper
#ModelAccuracy ↑Paper
1
GraphTARIF
0.9461 ±0.0017
2
GCN
actual #2 vs paper #268 266 places worse
0.9412 ±0.0008
best reported
actual #2 vs paper #268 266 places worse
paper 0.8655 ±0.0031
paper 0.8655 ±0.0031 Δ at pub 0.0130 Δ today 0.0757
3
GAT
actual #3 vs paper #254 251 places worse
0.9398 ±0.0022
best reported
actual #3 vs paper #254 251 places worse
paper 0.8699 ±0.0027
8
SAGE
0.9351 ±0.0006
79
BGRL
actual #79 vs paper #143 64 places worse
0.9034 ±0.0019
best reported
actual #79 vs paper #143 64 places worse
paper 0.8939 ±0.0011
paper 0.8939 ±0.0011 Δ at pub 0.0095 Δ today 0.0095
100
GraphMAE
actual #100 vs paper #193 93 places worse
0.8832 ±0.0016
actual #100 vs paper #193 93 places worse
paper 0.8832 ±0.0016
paper 0.8832 ±0.0016 Δ at pub 0.0716 Δ today 0.0170
139
GRACE
actual #139 vs paper #235 96 places worse
0.8953 ±0.0035
best reported
actual #139 vs paper #235 96 places worse
paper 0.8751 ±0.0012
paper 0.8751 ±0.0012 Δ at pub 0.0202 Δ today 0.0202
159
CCA-SSG
actual #159 vs paper #256 97 places worse
0.8896 ±0.0013
best reported
actual #159 vs paper #256 97 places worse
paper 0.8696 ±0.0028
paper 0.8696 ±0.0028 Δ at pub 0.0178 Δ today 0.0200
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 ±0.0024
183
HAT-GAE
0.8855 ±0.0018
This paper
210
DGI
actual #210 vs paper #352 142 places worse
0.8798 ±0.0081
best reported
actual #210 vs paper #352 142 places worse
paper 0.8399 ±0.0030
225
HAT-GAE-TC
0.8769 ±0.0026
This paper
227
HAT-GAE-HM
0.8767 ±0.0016
This paper
240
HAT-GAE-AM
0.8741 ±0.0003
This paper
239
InfoGCL
0.8741 ±0.0034
This paper
262
GATE
0.8671 ±0.0029
This paper
264
GAE
actual #264 vs paper #428 164 places worse
0.8666 ±0.0007
best reported
actual #264 vs paper #428 164 places worse
paper 0.8020 ±0.0021
paper 0.8020 ±0.0021 Δ at pub 0.0646
320
MLP
0.8463
377
GPT-GNN
0.8336 ±0.0015
This paper
#ModelF1 ↑Paper
1
EnGCN
0.9714 ±0.0003
2
SAGN+SLE
0.9710
3
GAMLP(JK)
0.9704 ±0.0001
14
GraphSAGE
0.9660
36
HAT-GAE
0.9606 ±0.0010
This paper
38
GraphMAE
actual #38 vs paper #42 4 places worse
0.9601 ±0.0008
best reported
actual #38 vs paper #42 4 places worse
paper 0.9589 ±0.0024

Difference within reported uncertainty; not counted as underperformance.

paper 0.9589 ±0.0024 Δ at pub 0.0012
39
GAT
actual #39 vs paper #41 2 places worse
0.9600 ±0.0010
best reported
actual #39 vs paper #41 2 places worse
paper 0.9595 ±0.0021

Difference within reported uncertainty; not counted as underperformance.

paper 0.9595 ±0.0021 Δ at pub 0.0005
58
GCN
actual #58 vs paper #62 4 places worse
0.9530 ±0.0010
best reported
actual #58 vs paper #62 4 places worse
paper 0.9514 ±0.0011

Difference within reported uncertainty; not counted as underperformance.

paper 0.9514 ±0.0011 Δ at pub 0.0016
63
CCA-SSG
actual #63 vs paper #63
0.9511 ±0.0018
actual #63 vs paper #63
paper 0.9511 ±0.0018

Improvement within reported uncertainty; not highlighted.

paper 0.9511 ±0.0018 Δ at pub 0.0004
64
GATE
0.9510 ±0.0031
This paper
68
GRACE
actual #68 vs paper #68
0.9501 ±0.0036
actual #68 vs paper #68
paper 0.9501 ±0.0036

Improvement within reported uncertainty; not highlighted.

paper 0.9501 ±0.0036 Δ at pub 0.0017
74
BGRL
actual #74 vs paper #78 4 places worse
0.9490 ±0.0400
best reported
actual #74 vs paper #78 4 places worse
paper 0.9431 ±0.0023

Difference within reported uncertainty; not counted as underperformance.

paper 0.9431 ±0.0023 Δ at pub 0.0059
79
MVGRL
0.9421 ±0.0010
This paper
82
DGI
actual #82 vs paper #86 4 places worse
0.9414 ±0.0003
best reported
actual #82 vs paper #86 4 places worse
paper 0.9391 ±0.0014
paper 0.9391 ±0.0014 Δ at pub 0.0023
95
InfoGCL
0.9356 ±0.0033
This paper
98
GPT-GNN
0.9351 ±0.0020
This paper
117
GAE
0.9027 ±0.0022
This paper
#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 #114 108 places worse
0.9782 ±0.0028
best reported
actual #6 vs paper #114 108 places worse
paper 0.9551 ±0.0016
paper 0.9551 ±0.0016 Δ at pub 0.0069 Δ today 0.0231
9
GCN
actual #9 vs paper #116 107 places worse
0.9774 ±0.0035
best reported
actual #9 vs paper #116 107 places worse
paper 0.9550 ±0.0024
paper 0.9550 ±0.0024 Δ at pub 0.0100 Δ today 0.0224
17
SAGE
0.9739 ±0.0018
58
MLP
0.9597 ±0.0007
69
BGRL
actual #69 vs paper #122 53 places worse
0.9580 ±0.0040
best reported
actual #69 vs paper #122 53 places worse
paper 0.9549 ±0.0031

Difference within reported uncertainty; not counted as underperformance.

paper 0.9549 ±0.0031 Δ at pub 0.0031
77
GRACE
actual #77 vs paper #144 67 places worse
0.9574 ±0.0006
best reported
actual #77 vs paper #144 67 places worse
paper 0.9521 ±0.0010
paper 0.9521 ±0.0010 Δ at pub 0.0018 Δ today 0.0053
106
CCA-SSG
actual #106 vs paper #204 98 places worse
0.9559 ±0.0007
best reported
actual #106 vs paper #204 98 places worse
paper 0.9386 ±0.0010
paper 0.9386 ±0.0010 Δ at pub 0.0173
109
HAT-GAE
0.9557 ±0.0021
This paper
117
GraphMAE
actual #117 vs paper #136 19 places worse
0.9550 ±0.0010
best reported
actual #117 vs paper #136 19 places worse
paper 0.9530 ±0.0032

Difference within reported uncertainty; not counted as underperformance.

paper 0.9530 ±0.0032 Δ today 0.0020
125
MVGRL
actual #125 vs paper #125
0.9544 ±0.0027
actual #125 vs paper #125
paper 0.9544 ±0.0027

Improvement within reported uncertainty; not highlighted.

paper 0.9544 ±0.0027 Δ at pub 0.0011
146
GAE
actual #146 vs paper #270 124 places worse
0.9520 ±0.0010
best reported
actual #146 vs paper #270 124 places worse
paper 0.9089 ±0.0024
paper 0.9089 ±0.0024 Δ at pub 0.0403 Δ today 0.0431
167
DGI
actual #167 vs paper #178 11 places worse
0.9489 ±0.0009
best reported
actual #167 vs paper #178 11 places worse
paper 0.9443 ±0.0026
170
HAT-GAE-TC
0.9469 ±0.0015
This paper
198
InfoGCL
0.9401 ±0.0025
This paper
201
HAT-GAE-HM
0.9395 ±0.0017
This paper
216
GATE
0.9352 ±0.0041
This paper
225
HAT-GAE-AM
0.9328 ±0.0003
This paper
226
GPT-GNN
0.9327 ±0.0016
This paper
#ModelF1 ↑Paper
1
GAMLP(JK)
0.9982 ±0.0001
2
GraphCON-GCN
0.9960
3
GCNII
0.9953 ±0.0001
21
GCN
actual #21 vs paper #109 88 places worse
0.9850
best reported
actual #21 vs paper #109 88 places worse
paper 0.7565 ±0.0025
best at pub: Graph-Coupled Oscillator Networks (ICML 2022)
paper 0.7565 ±0.0025 Δ at pub 0.2285
57
GAT
actual #57 vs paper #57
0.9732 ±0.0032
actual #57 vs paper #57
paper 0.9732 ±0.0032

Improvement within reported uncertainty; not highlighted.

paper 0.9732 ±0.0032 Δ at pub 0.0002
92
GIN
0.8724 ±0.0002
109
GAE
actual #109 vs paper #136 27 places worse
0.7570
best reported
actual #109 vs paper #136 27 places worse
paper 0.6751 ±0.0035
paper 0.6751 ±0.0035 Δ at pub 0.0819
112
HAT-GAE
0.7472 ±0.0028
This paper
114
GraphMAE
actual #114 vs paper #114
0.7450 ±0.0029
best reported
actual #114 vs paper #114
paper 0.7439 ±0.0019

Difference within reported uncertainty; not counted as underperformance.

paper 0.7439 ±0.0019 Δ at pub 0.0011 Δ today 0.0011
117
BGRL
actual #117 vs paper #117
0.7363 ±0.0016
best reported
actual #117 vs paper #117
paper 0.7352 ±0.0016

Difference within reported uncertainty; not counted as underperformance.

paper 0.7352 ±0.0016 Δ at pub 0.0011 Δ today 0.0011
119
CCA-SSG
actual #119 vs paper #120 1 place worse
0.7334 ±0.0017
best reported
actual #119 vs paper #120 1 place worse
paper 0.7321 ±0.0023

Difference within reported uncertainty; not counted as underperformance.

paper 0.7321 ±0.0023 Δ at pub 0.0013 Δ today 0.0013
120
GATE
0.7325 ±0.0018
This paper
121
InfoGCL
0.7314 ±0.0010
This paper
122
GPT-GNN
0.7276 ±0.0029
This paper
126
GRACE
actual #126 vs paper #130 4 places worse
0.6971 ±0.0017
best reported
actual #126 vs paper #130 4 places worse
paper 0.6959 ±0.0015

Difference within reported uncertainty; not counted as underperformance.

paper 0.6959 ±0.0015 Δ at pub 0.0012 Δ today 0.0012
136
MVGRL
0.6850 ±0.0021
This paper
148
DGI
actual #148 vs paper #149 1 place worse
0.6380 ±0.0020
best reported
actual #148 vs paper #149 1 place worse
paper 0.6352 ±0.0024

Difference within reported uncertainty; not counted as underperformance.

paper 0.6352 ±0.0024 Δ at pub 0.0028 Δ today 0.0028
173
MLP
0.4620
#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 #103 91 places worse
0.9514 ±0.0025
best reported
actual #12 vs paper #103 91 places worse
paper 0.9242 ±0.0034
best today: Graph Wave Networks (WWW 2025)
paper 0.9242 ±0.0034 Δ at pub 0.0118 Δ today 0.0272
21
GAT
actual #21 vs paper #114 93 places worse
0.9437 ±0.0028
best reported
actual #21 vs paper #114 93 places worse
paper 0.9217 ±0.0036
best today: Graph Wave Networks (WWW 2025)
paper 0.9217 ±0.0036 Δ at pub 0.0163 Δ today 0.0220
43
DGI
actual #43 vs paper #113 70 places worse
0.9221 ±0.0029
actual #43 vs paper #113 70 places worse
paper 0.9221 ±0.0029

Improvement within reported uncertainty; not highlighted.

paper 0.9221 ±0.0029 Δ at pub 0.0001 Δ today 0.0129
48
CCA-SSG
actual #48 vs paper #121 73 places worse
0.9337 ±0.0020
best reported
actual #48 vs paper #121 73 places worse
paper 0.9205 ±0.0019
paper 0.9205 ±0.0019 Δ at pub 0.0132
53
BGRL
actual #53 vs paper #63 10 places worse
0.9331 ±0.0013
best reported
actual #53 vs paper #63 10 places worse
paper 0.9310 ±0.0022

Difference within reported uncertainty; not counted as underperformance.

paper 0.9310 ±0.0022 Δ at pub 0.0021 Δ today 0.0021
62
HAT-GAE
0.9317 ±0.0025
This paper
63
GraphMAE
actual #63 vs paper #92 29 places worse
0.9313 ±0.0015
best reported
actual #63 vs paper #92 29 places worse
paper 0.9279 ±0.0010
paper 0.9279 ±0.0010 Δ today 0.0034
69
GRACE
actual #69 vs paper #82 13 places worse
0.9301 ±0.0003
best reported
actual #69 vs paper #82 13 places worse
paper 0.9290 ±0.0007
paper 0.9290 ±0.0007 Δ at pub 0.0003 Δ today 0.0011
79
HAT-GAE-TC
0.9295 ±0.0005
This paper
88
MLP
0.9280 ±0.0020
95
GPT-GNN
0.9271 ±0.0009
This paper
116
MVGRL
actual #116 vs paper #121 5 places worse
0.9211 ±0.0012
best reported
actual #116 vs paper #121 5 places worse
paper 0.9207 ±0.0019

Difference within reported uncertainty; not counted as underperformance.

paper 0.9207 ±0.0019 Δ at pub 0.0004 Δ today 0.0004
123
GATE
0.9204 ±0.0011
This paper
130
InfoGCL
0.9189 ±0.0024
This paper
147
HAT-GAE-HM
0.9128 ±0.0025
This paper
148
HAT-GAE-AM
0.9120 ±0.0014
This paper
163
GAE
actual #163 vs paper #163
0.9005 ±0.0035
actual #163 vs paper #163
paper 0.9005 ±0.0035

Improvement within reported uncertainty; not highlighted.

paper 0.9005 ±0.0035 Δ at pub 0.0004
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) Improved at pub — later paper surpassed this result Best today — OK at publication; today's leaderboard best is elsewhere