ENGAGE: Explanation Guided Data Augmentation for Graph Representation Learning

Yucheng Shi, Kaixiong Zhou, Ninghao Liu

Main figure for ENGAGE: Explanation Guided Data Augmentation for Graph Representation Learning

Abstract

The recent contrastive learning methods, due to their effectiveness in representation learning, have been widely applied to modeling graph data. Random perturbation is widely used to build contrastive views for graph data, which however, could accidentally break graph structures and lead to suboptimal performance. In addition, graph data is usually highly abstract, so it is hard to extract intuitive meanings and design more informed augmentation schemes. Effective representations should preserve key characteristics in data and abandon superfluous information. In this paper, we propose ENGAGE (ExplaNation Guided data AuGmEntation), where explanation guides the contrastive augmentation process to preserve the key parts in graphs and explore removing superfluous information. Specifically, we design an efficient unsupervised explanation method called smoothed activation map as the indicator of node importance in representation learning. Then, we design two data augmentation schemes on graphs for perturbing structural and feature information, respectively. We also provide justification for the proposed method in the framework of information theories. Experiments of both graph-level and node-level tasks, on various model architectures and on different real-world graphs, are conducted to demonstrate the effectiveness and flexibility of ENGAGE. The code of ENGAGE can be found here [1]..

Benchmark Results

Tested on 8 datasets 40 baseline values reported too low

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

Classic

#ModelAccuracy ↑Paper
1
GraphSAGE+CNA
0.9418 ±0.0033
2
GCN+CNA
0.9366 ±0.0048
3
TransformerConv
0.9350 ±0.0058
21
GCN
actual #21 vs paper #573 552 places worse
0.9004
best reported
actual #21 vs paper #573 552 places worse
paper 0.8150
paper 0.8150 Δ at pub 0.0567 Δ today 0.0854
39
SAGE
0.8911 ±0.0012
44
GAT
actual #44 vs paper #424 380 places worse
0.8897 ±0.0014
best reported
actual #44 vs paper #424 380 places worse
paper 0.8300 ±0.0070
paper 0.8300 ±0.0070 Δ at pub 0.0590 Δ today 0.0597
156
MVGRL
actual #156 vs paper #156
0.8680 ±0.0050
actual #156 vs paper #156
paper 0.8680 ±0.0050
177
DGI
actual #177 vs paper #486 309 places worse
0.8630 ±0.0020
best reported
actual #177 vs paper #486 309 places worse
paper 0.8230 ±0.0060
paper 0.8230 ±0.0060 Δ at pub 0.0400
302
EG-SimCLR(GCN)
0.8407 ±0.0018
This paper
359
GRACE(GAT)
0.8357 ±0.0055
This paper
379
EG-Simsiam(GCN)
0.8346 ±0.0056
This paper
435
DeepWalk
actual #435 vs paper #814 379 places worse
0.8290
best reported
actual #435 vs paper #814 379 places worse
paper 0.7070 ±0.0060
paper 0.7070 ±0.0060 Δ at pub 0.1220
454
RD-Simsiam(GCN)
0.8265 ±0.0062
This paper
654
GAE
actual #654 vs paper #810 156 places worse
0.8011 ±0.0022
best reported
actual #654 vs paper #810 156 places worse
paper 0.7150 ±0.0040
paper 0.7150 ±0.0040 Δ at pub 0.0861
724
MLP
0.7768
#ModelAccuracy ↑Paper
1
CNA
0.9575 ±0.0058
2
IS-GIB
0.9390 ±0.0187
3
EERM
0.9112 ±0.0145
35
GAT
actual #35 vs paper #388 353 places worse
0.8080 ±0.0026
best reported
actual #35 vs paper #388 353 places worse
paper 0.7250 ±0.0070
paper 0.7250 ±0.0070 Δ at pub 0.0830
44
GCN
actual #44 vs paper #603 559 places worse
0.8033 ±0.0088
best reported
actual #44 vs paper #603 559 places worse
paper 0.7030
61
GraphSAGE
0.7923 ±0.0053
66
DGI
actual #66 vs paper #474 408 places worse
0.7890 ±0.0020
best reported
actual #66 vs paper #474 408 places worse
paper 0.7180 ±0.0070
paper 0.7180 ±0.0070 Δ at pub 0.0710
87
MVGRL
actual #87 vs paper #292 205 places worse
0.7808 ±0.0006
best reported
actual #87 vs paper #292 205 places worse
paper 0.7330 ±0.0050
350
MLP
0.7289 ±0.0010
417
EG-SimCLR(GCN)
0.7240 ±0.0046
This paper
488
GRACE(GAT)
0.7170 ±0.0055
This paper
514
EG-Simsiam(GCN)
0.7149 ±0.0031
This paper
577
RD-Simsiam(GCN)
0.7072 ±0.0064
This paper
692
DeepWalk
actual #692 vs paper #864 172 places worse
0.6785 ±0.0079
best reported
actual #692 vs paper #864 172 places worse
paper 0.5140 ±0.0050
paper 0.5140 ±0.0050 Δ at pub 0.1645
739
GAE
actual #739 vs paper #757 18 places worse
0.6639 ±0.0024
best reported
actual #739 vs paper #757 18 places worse
paper 0.6580 ±0.0040

Difference within reported uncertainty; not counted as underperformance.

paper 0.6580 ±0.0040 Δ at pub 0.0059
#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
paper 0.9256 ±0.0035 Δ at pub 0.0165 Δ today 0.0413
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
paper 0.9242 ±0.0022 Δ at pub 0.0152 Δ today 0.0390
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
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
223
EG-SimCLR(GAT)
0.9297 ±0.0007
This paper
247
EG-Simsiam(GCN)
0.9277 ±0.0014
This paper
251
GRACE(GAT)
0.9274 ±0.0020
This paper
268
RD-Simsiam(GAT)
0.9263 ±0.0012
This paper
352
GAE
actual #352 vs paper #366 14 places worse
0.9185 ±0.0006
best reported
actual #352 vs paper #366 14 places worse
paper 0.9162 ±0.0013
paper 0.9162 ±0.0013 Δ at pub 0.0023
390
MLP
0.9128 ±0.0063
444
DeepWalk
0.9005 ±0.0008
This paper
#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
paper 0.8693 ±0.0029 Δ at pub 0.0281 Δ today 0.0705
8
SAGE
0.9351 ±0.0006
139
GRACE
actual #139 vs paper #193 54 places worse
0.8953 ±0.0035
best reported
actual #139 vs paper #193 54 places worse
paper 0.8836 ±0.0018
paper 0.8836 ±0.0018 Δ at pub 0.0117 Δ today 0.0117
160
GCA
actual #160 vs paper #213 53 places worse
0.8894 ±0.0015
best reported
actual #160 vs paper #213 53 places worse
paper 0.8785 ±0.0031
paper 0.8785 ±0.0031 Δ at pub 0.0109 Δ today 0.0109
177
EG-Simsiam(GCN)
0.8866 ±0.0019
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
182
EG-SimCLR(GAT)
0.8856 ±0.0017
This paper
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
212
RD-Simsiam(GAT)
0.8796 ±0.0027
This paper
264
GAE
actual #264 vs paper #305 41 places worse
0.8666 ±0.0007
best reported
actual #264 vs paper #305 41 places worse
paper 0.8527 ±0.0019
paper 0.8527 ±0.0019 Δ at pub 0.0139
278
DeepWalk
0.8628 ±0.0007
This paper
320
MLP
0.8463

TU Dortmund

#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
77
EG-SimCLR
0.8297 ±0.0020
This paper
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
153
EG-Simsiam
0.8149 ±0.0019
This paper
187
HG-Simsiam
0.8070 ±0.0064
This paper
198
HG-SimCLR
0.8048 ±0.0044
This paper
210
DGK
0.8031 ±0.0046
This paper
241
RD-Simsiam
0.7962 ±0.0059
This paper
262
RD-SimCLR
0.7902 ±0.0052
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
356
MVGRL
0.7700 ±0.0080
This paper
406
graph2vec
actual #406 vs paper #446 40 places worse
0.7540 ±0.0120
best reported
actual #406 vs paper #446 40 places worse
paper 0.7322 ±0.0181

Difference within reported uncertainty; not counted as underperformance.

paper 0.7322 ±0.0181 Δ at pub 0.0218
557
Sub2Vec
actual #557 vs paper #575 18 places worse
0.5976 ±0.0035
best reported
actual #557 vs paper #575 18 places worse
paper 0.5284 ±0.0147
paper 0.5284 ±0.0147 Δ at pub 0.0692
571
Node2Vec
actual #571 vs paper #571
0.5490 ±0.0160
best reported
actual #571 vs paper #571
paper 0.5489 ±0.0161

Difference within reported uncertainty; not counted as underperformance.

paper 0.5489 ±0.0161 Δ at pub 0.0001 Δ today 0.0001
#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
145
EG-Simsiam
0.7606 ±0.0051
This paper
149
MLP
0.7600 ±0.0320
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
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
197
HG-Simsiam
0.7545 ±0.0072
This paper
200
EG-SimCLR
0.7544 ±0.0065
This paper
202
RD-Simsiam
0.7542 ±0.0050
This paper
209
SimGRACE
0.7535 ±0.0009
This paper
256
HG-SimCLR
0.7493 ±0.0062
This paper
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
282
RD-SimCLR
0.7461 ±0.0056
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 today 0.0005
294
InfoGraph
0.7444 ±0.0031
This paper
309
JOAOv2
0.7407 ±0.0110
This paper
350
graph2vec
0.7330 ±0.0205
This paper
474
Sub2Vec
actual #474 vs paper #517 43 places worse
0.6731 ±0.0050
best reported
actual #474 vs paper #517 43 places worse
paper 0.5303 ±0.0555
paper 0.5303 ±0.0555 Δ at pub 0.1428
514
Node2Vec
actual #514 vs paper #514
0.5750 ±0.0360
best reported
actual #514 vs paper #514
paper 0.5749 ±0.0357

Difference within reported uncertainty; not counted as underperformance.

paper 0.5749 ±0.0357 Δ today 0.0001
#ModelAccuracy ↑Paper
1
WL-MLP
0.9792
2
MSH-GNN
0.9640 ±0.0070
3
CoCN
0.8722 ±0.0013
6
graph2vec
actual #6 vs paper #290 284 places worse
0.8558
best reported
actual #6 vs paper #290 284 places worse
paper 0.7110 ±0.0054
paper 0.7110 ±0.0054 Δ at pub 0.1448
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
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
104
MVGRL
actual #104 vs paper #227 123 places worse
0.8048 ±0.0029
best reported
actual #104 vs paper #227 123 places worse
paper 0.7600 ±0.0120
paper 0.7600 ±0.0120 Δ at pub 0.0042 Δ today 0.0448
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
153
WL
actual #153 vs paper #306 153 places worse
0.7910 ±0.0010
best reported
actual #153 vs paper #306 153 places worse
paper 0.6930 ±0.0344
paper 0.6930 ±0.0344 Δ at pub 0.0980
217
EG-SimCLR
0.7660 ±0.0126
This paper
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
255
EG-Simsiam
0.7473 ±0.0079
This paper
274
DGK
actual #274 vs paper #321 47 places worse
0.7310 ±0.0030
best reported
actual #274 vs paper #321 47 places worse
paper 0.6466 ±0.0050
paper 0.6466 ±0.0050 Δ at pub 0.0844 Δ today 0.0844
278
HG-Simsiam
0.7284 ±0.0091
This paper
282
HG-SimCLR
0.7253 ±0.0097
This paper
306
RD-SimCLR
0.6932 ±0.0154
This paper
315
RD-Simsiam
0.6650 ±0.0231
This paper
325
Sub2Vec
actual #325 vs paper #341 16 places worse
0.6210 ±0.0140
best reported
actual #325 vs paper #341 16 places worse
paper 0.5526 ±0.0154
paper 0.5526 ±0.0154 Δ at pub 0.0684
341
Node2Vec
0.5610 ±0.0020
This paper
#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
best at pub: Graph Contrastive Learning Automated (ICML 2021)
paper 0.8953 ±0.0084 Δ today 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 0.0285 Δ today 0.0637
32
EG-SimCLR
0.9070 ±0.0046
This paper
40
HG-SimCLR
0.8992 ±0.0053
This paper
43
HG-Simsiam
0.8963 ±0.0055
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 0.0616 Δ today 0.0689
48
EG-Simsiam
0.8917 ±0.0043
This paper
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
61
RD-Simsiam
0.8612 ±0.0180
This paper
62
RD-SimCLR
0.8567 ±0.0540
This paper
65
MVGRL
0.8450 ±0.0060
This paper
73
DGK
0.7804 ±0.0039
This paper
80
graph2vec
actual #80 vs paper #80
0.7580 ±0.0100
best reported
actual #80 vs paper #80
paper 0.7578 ±0.0103

Difference within reported uncertainty; not counted as underperformance.

paper 0.7578 ±0.0103 Δ at pub 0.0002 Δ today 0.0002
83
Sub2Vec
actual #83 vs paper #83
0.7150 ±0.0040
best reported
actual #83 vs paper #83
paper 0.7148 ±0.0041

Difference within reported uncertainty; not counted as underperformance.

paper 0.7148 ±0.0041 Δ at pub 0.0002
85
WL
0.6882 ±0.0041
This paper
SOTA performance (not significantly different from the best) 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