NeurIPS 2024

Cross-Domain Graph Data Scaling: A Showcase with Diffusion Models

Wenzhuo Tang, Haitao Mao, Danial Dervovic, Ivan Brugere, Saumitra Mishra, Yuying Xie, Jiliang Tang

Main figure for Cross-Domain Graph Data Scaling: A Showcase with Diffusion Models

Abstract

Models for natural language and images benefit from data scaling behavior: the more data fed into the model, the better they perform. This 'better with more' phenomenon enables the effectiveness of large-scale pre-training on vast amounts of data. However, current graph pre-training methods struggle to scale up data due to heterogeneity across graphs. To achieve effective data scaling, we aim to develop a general model that is able to capture diverse data patterns of graphs and can be utilized to adaptively help the downstream tasks. To this end, we propose UniAug, a universal graph structure augmentor built on a diffusion model. We first pre-train a discrete diffusion model on thousands of graphs across domains to learn the graph structural patterns. In the downstream phase, we provide adaptive enhancement by conducting graph structure augmentation with the help of the pre-trained diffusion model via guided generation. By leveraging the pre-trained diffusion model for structure augmentation, we consistently achieve performance improvements across various downstream tasks in a plug-and-play manner. To the best of our knowledge, this study represents the first demonstration of a data-scaling graph structure augmentor on graphs across domains.

Benchmark Results

Tested on 12 datasets 23 baseline values reported too low Non-standard metric on 1 dataset

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 #558 537 places worse
0.9004
best reported
actual #21 vs paper #558 537 places worse
paper 0.8175 ±0.0073
paper 0.8175 ±0.0073 Δ at pub 0.0829
39
SAGE
0.8911 ±0.0012
558
UniAug
0.8178 ±0.0060
This paper
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
44
GCN
actual #44 vs paper #577 533 places worse
0.8033 ±0.0088
best reported
actual #44 vs paper #577 533 places worse
paper 0.7071 ±0.0076
paper 0.7071 ±0.0076 Δ at pub 0.0872 Δ today 0.0962
61
GraphSAGE
0.7923 ±0.0053
350
MLP
0.7289 ±0.0010
549
UniAug
0.7117 ±0.0058
This paper
#ModelAccuracy ↑Paper
1
LGTL
0.9518 ±0.0011
2
MixHop (LO)
0.9513 ±0.0038
3
GraphSAGE (LO)
0.9511 ±0.0036
18
GCN
actual #18 vs paper #502 484 places worse
0.9296 ±0.0015
best reported
actual #18 vs paper #502 484 places worse
paper 0.7953 ±0.0025
116
SAGE
0.8881 ±0.0015
210
MLP
0.8690 ±0.0074
502
UniAug
0.7954 ±0.0035
This paper

TU Dortmund

#ModelAccuracy ↑Paper
1
WL-MLP
0.9954
2
GIN
actual #2 vs paper #305 303 places worse
0.9934
best reported
actual #2 vs paper #305 303 places worse
paper 0.7830 ±0.0320
paper 0.7830 ±0.0320 Δ at pub 0.2104
3
GCN
0.9727
81
Infomax
actual #81 vs paper #366 285 places worse
0.8285 ±0.0016
best reported
actual #81 vs paper #366 285 places worse
paper 0.7694 ±0.0148
paper 0.7694 ±0.0148 Δ at pub 0.0591
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
148
GraphAug
actual #148 vs paper #247 99 places worse
0.8160 ±0.0010
best reported
actual #148 vs paper #247 99 places worse
paper 0.7953 ±0.0321

Difference within reported uncertainty; not counted as underperformance.

paper 0.7953 ±0.0321 Δ at pub 0.0207
191
UniAug
0.8054 ±0.0177
This paper
200
GraphMAE
actual #200 vs paper #261 61 places worse
0.8042 ±0.0035
best reported
actual #200 vs paper #261 61 places worse
paper 0.7908 ±0.0272

Difference within reported uncertainty; not counted as underperformance.

paper 0.7908 ±0.0272 Δ at pub 0.0132 Δ today 0.0134
204
FLAG
actual #204 vs paper #261 57 places worse
0.8040 ±0.0020
best reported
actual #204 vs paper #261 57 places worse
paper 0.7903 ±0.0375

Difference within reported uncertainty; not counted as underperformance.

paper 0.7903 ±0.0375 Δ at pub 0.0137
265
CtxtPred
0.7899 ±0.0129
This paper
268
S-Mixup
0.7891 ±0.0161
This paper
301
JOAO
actual #301 vs paper #367 66 places worse
0.7840 ±0.0050
best reported
actual #301 vs paper #367 66 places worse
paper 0.7687 ±0.0227

Difference within reported uncertainty; not counted as underperformance.

paper 0.7687 ±0.0227 Δ at pub 0.0153
325
D-SLA
0.7795 ±0.0211
This paper
326
EdgePred
actual #326 vs paper #326
0.7782 ±0.0295
actual #326 vs paper #326
paper 0.7782 ±0.0295
paper 0.7782 ±0.0295 Δ at pub 0.0341
331
AttrMask
0.7767 ±0.0253
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
#ModelAccuracy ↑Paper
1
MSH-GNN
0.9410 ±0.0330
2
GRDL
0.8260 ±0.0120
3
GMN
0.8225
32
GIN
actual #32 vs paper #349 317 places worse
0.7880 ±0.0410
best reported
actual #32 vs paper #349 317 places worse
paper 0.7332 ±0.0403

Difference within reported uncertainty; not counted as underperformance.

paper 0.7332 ±0.0403 Δ at pub 0.0548
67
SAGE
0.7726 ±0.0228
149
MLP
0.7600 ±0.0320
195
UniAug
0.7547 ±0.0250
This paper
213
GraphMAE
actual #213 vs paper #453 240 places worse
0.7530 ±0.0050
best reported
actual #213 vs paper #453 240 places worse
paper 0.7045 ±0.0419
265
GraphCL
actual #265 vs paper #308 43 places worse
0.7489 ±0.0065
best reported
actual #265 vs paper #308 43 places worse
paper 0.7417 ±0.0034

Difference within reported uncertainty; not counted as underperformance.

paper 0.7417 ±0.0034 Δ at pub 0.0072
281
S-Mixup
0.7461 ±0.0508
This paper
283
JOAO
actual #283 vs paper #428 145 places worse
0.7460 ±0.0040
best reported
actual #283 vs paper #428 145 places worse
paper 0.7157 ±0.0531

Difference within reported uncertainty; not counted as underperformance.

paper 0.7157 ±0.0531 Δ at pub 0.0303 Δ today 0.0303
297
FLAG
actual #297 vs paper #297
0.7431 ±0.0421
actual #297 vs paper #297
paper 0.7431 ±0.0421
paper 0.7431 ±0.0421 Δ at pub 0.0341
303
GraphAug
actual #303 vs paper #303
0.7421 ±0.0370
actual #303 vs paper #303
paper 0.7421 ±0.0370

Improvement within reported uncertainty; not highlighted.

paper 0.7421 ±0.0370 Δ at pub 0.0201
361
AttrMask
0.7310 ±0.0390
This paper
402
CtxtPred
0.7221 ±0.0460
This paper
412
D-SLA
0.7197 ±0.0417
This paper
433
Infomax
0.7130 ±0.0518
This paper
436
EdgePred
0.7122 ±0.0353
This paper
#ModelAccuracy ↑Paper
1
WL-MLP
0.9792
2
MSH-GNN
0.9640 ±0.0070
3
CoCN
0.8722 ±0.0013
19
GraphAug
actual #19 vs paper #227 208 places worse
0.8290 ±0.0020
best reported
actual #19 vs paper #227 208 places worse
paper 0.7602 ±0.0267
paper 0.7602 ±0.0267 Δ at pub 0.0688
22
GraphMAE
actual #22 vs paper #109 87 places worse
0.8270 ±0.0100
best reported
actual #22 vs paper #109 87 places worse
paper 0.8032 ±0.0046
paper 0.8032 ±0.0046 Δ today 0.0238
23
GCN
0.8260 ±0.0220
30
GIN
actual #30 vs paper #256 226 places worse
0.8220 ±0.0210
best reported
actual #30 vs paper #256 226 places worse
paper 0.7454 ±0.0241
80
GraphCL
actual #80 vs paper #260 180 places worse
0.8108 ±0.0017
best reported
actual #80 vs paper #260 180 places worse
paper 0.7423 ±0.0021
paper 0.7423 ±0.0021 Δ at pub 0.0685
81
Infomax
actual #81 vs paper #242 161 places worse
0.8104 ±0.0012
best reported
actual #81 vs paper #242 161 places worse
paper 0.7544 ±0.0112
paper 0.7544 ±0.0112 Δ at pub 0.0560
110
FLAG
actual #110 vs paper #248 138 places worse
0.8030 ±0.0060
best reported
actual #110 vs paper #248 138 places worse
paper 0.7532 ±0.0313
paper 0.7532 ±0.0313 Δ at pub 0.0498
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
211
UniAug
0.7700 ±0.0202
This paper
230
D-SLA
0.7599 ±0.0208
This paper
232
S-Mixup
0.7589 ±0.0326
This paper
235
AttrMask
0.7564 ±0.0152
This paper
236
CtxtPred
0.7560 ±0.0149
This paper
248
JOAO
actual #248 vs paper #253 5 places worse
0.7535 ±0.0093
best reported
actual #248 vs paper #253 5 places worse
paper 0.7477 ±0.0171

Difference within reported uncertainty; not counted as underperformance.

paper 0.7477 ±0.0171 Δ at pub 0.0058
256
EdgePred
actual #256 vs paper #256
0.7464 ±0.0224
actual #256 vs paper #256
paper 0.7464 ±0.0224
paper 0.7464 ±0.0224 Δ at pub 0.0984
#ModelAccuracy ↑Paper
1
GMN
0.7866
2
MemGNN
0.7550
3
TFGW SP
0.7510 ±0.0500
13
UniAug
0.7150 ±0.0585
This paper
17
GatedGCN
0.7000 ±0.0494
22
FLAG
0.6835 ±0.0745
This paper
26
GraphSAGE
0.6817 ±0.0545
27
GraphAug
0.6814 ±0.0792
This paper
32
GIN
actual #32 vs paper #40 8 places worse
0.6767 ±0.0583
best reported
actual #32 vs paper #40 8 places worse
paper 0.6600 ±0.0752
best at pub: GNNBenchmark (JMLR 2023)

Difference within reported uncertainty; not counted as underperformance.

paper 0.6600 ±0.0752 Δ at pub 0.0167
35
S-Mixup
0.6685 ±0.0704
This paper
124
MLP
0.5583 ±0.0352
212
JOAO
actual #212 vs paper #278 66 places worse
0.3460 ±0.0106
best reported
actual #212 vs paper #278 66 places worse
paper 0.2217 ±0.0367
paper 0.2217 ±0.0367 Δ at pub 0.1243
259
AttrMask
0.2366 ±0.0609
This paper
266
GraphMAE
0.2300 ±0.0364
This paper
269
D-SLA
0.2267 ±0.0421
This paper
273
Infomax
0.2250 ±0.0676
This paper
279
EdgePred
0.2200 ±0.0332
This paper
282
CtxtPred
0.2167 ±0.0387
This paper

Heterophilic Graphs

#ModelAccuracy ↑Paper
1
P^2GNN
0.9672 ±0.0147
2
DoG
0.9660 ±0.0210
3
GPF-plus
0.9583 ±0.0419
34
MLP
0.9230 ±0.0070
53
GraphSAGE
0.9000 ±0.0365
257
GCN
actual #257 vs paper #454 197 places worse
0.7933 ±0.0447
best reported
actual #257 vs paper #454 197 places worse
paper 0.6378 ±0.0480
best today: Graph Wave Networks (WWW 2025)
paper 0.6378 ±0.0480 Δ at pub 0.1462 Δ today 0.1555
287
UniAug + Half-Hop
0.7703 ±0.0427
This paper
331
GraphMAE
actual #331 vs paper #454 123 places worse
0.7432 ±0.0456
best reported
actual #331 vs paper #454 123 places worse
paper 0.6370 ±0.0551
paper 0.6370 ±0.0551 Δ today 0.1062
346
UniAug
0.7351 ±0.0506
This paper
351
MVGRL
actual #351 vs paper #480 129 places worse
0.7301 ±0.0552
best reported
actual #351 vs paper #480 129 places worse
paper 0.6170 ±0.0394
367
Half-Hop
0.7235 ±0.0427
This paper
369
GRACE
actual #369 vs paper #456 87 places worse
0.6354 ±0.0257
actual #369 vs paper #456 87 places worse
paper 0.6354 ±0.0257
409
BGRL
actual #409 vs paper #435 26 places worse
0.6578 ±0.0266
actual #409 vs paper #435 26 places worse
paper 0.6578 ±0.0266
468
JOAO
actual #468 vs paper #550 82 places worse
0.6245 ±0.0296
best reported
actual #468 vs paper #550 82 places worse
paper 0.5706 ±0.0343

Difference within reported uncertainty; not counted as underperformance.

paper 0.5706 ±0.0343 Δ today 0.0539
497
AttrMask
0.6054 ±0.0582
This paper
502
D-SLA
0.5993 ±0.0429
This paper
518
EdgePred
0.5937 ±0.0511
This paper
528
CtxtPred
0.5892 ±0.0432
This paper
530
Infomax
0.5887 ±0.0406
This paper
#ModelAccuracy ↑Paper
1
P^2GNN
0.9541 ±0.0272
2
ACM-GCN
0.9480 ±0.0380
3
RF-GCN
0.9429
24
MLP
0.9136 ±0.0070
138
SAGE
0.8269
170
GCN
actual #170 vs paper #382 212 places worse
0.8082 ±0.0360
best reported
actual #170 vs paper #382 212 places worse
paper 0.5941 ±0.0603
paper 0.5941 ±0.0603 Δ at pub 0.2074 Δ today 0.2141
231
GraphMAE
actual #231 vs paper #414 183 places worse
0.7514 ±0.0965
best reported
actual #231 vs paper #414 183 places worse
paper 0.5731 ±0.0211
paper 0.5731 ±0.0211 Δ today 0.1783
264
UniAug + Half-Hop
0.7243 ±0.0581
This paper
299
UniAug
0.6811 ±0.0672
This paper
340
MVGRL
actual #340 vs paper #424 84 places worse
0.6430
best reported
actual #340 vs paper #424 84 places worse
paper 0.5619 ±0.0242
357
Half-Hop
0.6246 ±0.0758
This paper
415
BGRL
actual #415 vs paper #420 5 places worse
0.5730
best reported
actual #415 vs paper #420 5 places worse
paper 0.5667 ±0.0213

Difference within reported uncertainty; not counted as underperformance.

paper 0.5667 ±0.0213 Δ at pub 0.0063
423
GRACE
actual #423 vs paper #423
0.5639 ±0.0211
actual #423 vs paper #423
paper 0.5639 ±0.0211

Improvement within reported uncertainty; not highlighted.

paper 0.5639 ±0.0211 Δ at pub 0.0153
477
JOAO
actual #477 vs paper #553 76 places worse
0.5102 ±0.0096
best reported
actual #477 vs paper #553 76 places worse
paper 0.4013 ±0.0860

Difference within reported uncertainty; not counted as underperformance.

paper 0.4013 ±0.0860 Δ today 0.1089
528
AttrMask
0.4486 ±0.0543
This paper
543
EdgePred
0.4270 ±0.0551
This paper
552
D-SLA
0.4105 ±0.0688
This paper
553
CtxtPred
0.4081 ±0.0778
This paper
555
Infomax
0.3919 ±0.1275
This paper
#ModelAccuracy ↑Paper
1
DiGGR
0.4535 ±0.0353
2
TRIGON
0.4402 ±0.0028
3
DoG
0.4320 ±0.0120
6
UniAug - PolyGCL
0.4301 ±0.0127
This paper
35
PolyGCL
0.4115 ±0.0088
This paper
42
MLP
0.4026 ±0.0108
68
GraphSAGE
0.3899 ±0.0085
135
GCN
actual #135 vs paper #336 201 places worse
0.3690
best reported
actual #135 vs paper #336 201 places worse
paper 0.3058 ±0.0129
paper 0.3058 ±0.0129 Δ at pub 0.0632
235
UniAug + Half-Hop
0.3497 ±0.0055
This paper
247
MVGRL
actual #247 vs paper #315 68 places worse
0.3464 ±0.0020
best reported
actual #247 vs paper #315 68 places worse
paper 0.3137 ±0.0083
paper 0.3137 ±0.0083 Δ at pub 0.0072 Δ today 0.0327
251
GRACE
actual #251 vs paper #393 142 places worse
0.3450 ±0.0110
best reported
actual #251 vs paper #393 142 places worse
paper 0.2814 ±0.0081
paper 0.2814 ±0.0081 Δ at pub 0.0636
270
Half-Hop
0.3395 ±0.0068
This paper
285
UniAug
0.3311 ±0.0157
This paper
299
GraphMAE
actual #299 vs paper #373 74 places worse
0.3215 ±0.0133
best reported
actual #299 vs paper #373 74 places worse
paper 0.2897 ±0.0027
paper 0.2897 ±0.0027 Δ today 0.0318
356
BGRL
actual #356 vs paper #357 1 place worse
0.2986
best reported
actual #356 vs paper #357 1 place worse
paper 0.2980 ±0.0031

Difference within reported uncertainty; not counted as underperformance.

paper 0.2980 ±0.0031 Δ at pub 0.0006
431
AttrMask
0.2531 ±0.0103
This paper
441
JOAO
0.2417 ±0.0502
This paper
443
CtxtPred
0.2397 ±0.0263
This paper
448
D-SLA
0.2374 ±0.0406
This paper
452
Infomax
0.2330 ±0.0437
This paper
457
EdgePred
0.2299 ±0.0622
This paper
#ModelAccuracy ↑Paper
1
IBG-NN
0.7763 ±0.0179
2
Dir-GNN+CNA
0.7747 ±0.0128
3
DHGNN
0.7684 ±0.0161
44
GraphMAE
actual #44 vs paper #173 129 places worse
0.6113 ±0.0060
best reported
actual #44 vs paper #173 129 places worse
paper 0.3913 ±0.0201
paper 0.3913 ±0.0201 Δ today 0.2200
46
GCN
actual #46 vs paper #173 127 places worse
0.6067
best reported
actual #46 vs paper #173 127 places worse
paper 0.3911 ±0.0174
paper 0.3911 ±0.0174 Δ at pub 0.2156
50
MVGRL
actual #50 vs paper #215 165 places worse
0.6009 ±0.0044
best reported
actual #50 vs paper #215 165 places worse
paper 0.3532 ±0.0132
paper 0.3532 ±0.0132 Δ at pub 0.0343 Δ today 0.2477
108
BGRL
actual #108 vs paper #222 114 places worse
0.4624 ±0.0070
best reported
actual #108 vs paper #222 114 places worse
paper 0.3477 ±0.0201
120
SAGE
0.4460 ±0.0130
147
UniAug
0.4190 ±0.0190
This paper
154
GRACE
actual #154 vs paper #229 75 places worse
0.4109 ±0.0085
best reported
actual #154 vs paper #229 75 places worse
paper 0.3365 ±0.0251
172
MLP
0.3930 ±0.0079
177
UniAug + Half-Hop
0.3879 ±0.0261
This paper
196
Half-Hop
0.3734 ±0.0218
This paper
234
JOAO
0.3172 ±0.0703
This paper
240
AttrMask
0.3063 ±0.0168
This paper
246
D-SLA
0.2850 ±0.0690
This paper
249
EdgePred
0.2794 ±0.0841
This paper
253
Infomax
0.2752 ±0.0909
This paper
256
CtxtPred
0.2626 ±0.0750
This paper

MoleculeNet

FreeSolv

Global leaderboard →
Non-default metric. This paper reports MAE; the dataset default is RMSE. Values below use MAE only.

Sorted by MAE. Highlighted rows are from other papers.

#ModelMAE ↓Paper
1
DCT
1.3390 ±0.0750
This paper
2
UniAug
1.4480 ±0.0490
This paper
3
FLAG
1.5650 ±0.0980
This paper
4
GIN
1.6130 ±0.1550
This paper
5
GINE
1.6390 ±0.1460
This paper
6
GREA
1.8290 ±0.3680
This paper
7
JOAO
3.2920 ±0.1170
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