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
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphSAGE+CNA | 0.9418
±0.0033 | |
| 2 | GCN+CNA | 0.9366
±0.0048 | |
| 3 | TransformerConv | 0.9350
±0.0058 | |
| 21 | GCN | 0.9004 best reported | best at pub: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 39 | SAGE | 0.8911
±0.0012 | |
| 558 | UniAug | 0.8178
±0.0060 | This paper |
| 724 | MLP | 0.7768 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | CNA | 0.9575
±0.0058 | |
| 2 | IS-GIB | 0.9390
±0.0187 | |
| 3 | EERM | 0.9112
±0.0145 | |
| 44 | GCN | 0.8033
±0.0088 best reported | best at pub: Gophormer: Ego-Graph Transformer for Node Classification (2021) |
| 61 | GraphSAGE | 0.7923
±0.0053 | |
| 350 | MLP | 0.7289
±0.0010 | |
| 549 | UniAug | 0.7117
±0.0058 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | LGTL | 0.9518
±0.0011 | |
| 2 | MixHop (LO) | 0.9513
±0.0038 | |
| 3 | GraphSAGE (LO) | 0.9511
±0.0036 | |
| 18 | GCN | 0.9296
±0.0015 best reported | best at pub: Node Identifiers: Compact, Discrete Representations for Efficient Graph Learning (ICLR 2024) |
| 116 | SAGE | 0.8881
±0.0015 | |
| 210 | MLP | 0.8690
±0.0074 | |
| 502 | UniAug | 0.7954
±0.0035 | This paper |
TU Dortmund
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9954 | |
| 2 | GIN | 0.9934 best reported | best at pub: 1-WL Expressiveness Is (Almost) All You Need (2022) |
| 3 | GCN | 0.9727 | |
| 81 | Infomax | 0.8285
±0.0016 best reported | best at pub: Label-invariant Augmentation for Semi-Supervised Graph Classification (NeurIPS 2022) |
| 104 | GraphCL | 0.8250
±0.0013 best reported | best at pub: Label-invariant Augmentation for Semi-Supervised Graph Classification (NeurIPS 2022) |
| 131 | GraphSAGE | 0.8200
±0.0100 | |
| 148 | GraphAug | 0.8160
±0.0010 best reported | best at pub: Automated Data Augmentations for Graph Classification (ICLR 2022) Difference within reported uncertainty; not counted as underperformance. |
| 191 | UniAug | 0.8054
±0.0177 | This paper |
| 200 | GraphMAE | 0.8042
±0.0035 best reported | best at pub: GraphMAE: Self-Supervised Masked Graph Autoencoders (KDD 2022) best today: Self-Supervised Graph Learning via Spectral Bootstrapping and Laplacian-Based Augmentations (2025) Difference within reported uncertainty; not counted as underperformance. |
| 204 | FLAG | 0.8040
±0.0020 best reported | best at pub: Automated Data Augmentations for Graph Classification (ICLR 2022) Difference within reported uncertainty; not counted as underperformance. |
| 265 | CtxtPred | 0.7899
±0.0129 | This paper |
| 268 | S-Mixup | 0.7891
±0.0161 | This paper |
| 301 | JOAO | 0.7840
±0.0050 best reported | best at pub: Omni-Granular Ego-Semantic Propagation for Self-Supervised Graph Representation Learning (ICML 2022) Difference within reported uncertainty; not counted as underperformance. |
| 325 | D-SLA | 0.7795
±0.0211 | This paper |
| 326 | EdgePred | 0.7782
±0.0295 | prev best: SGL-PT: A Strong Graph Learner with Graph Prompt Tuning (2023) |
| 331 | AttrMask | 0.7767
±0.0253 | This paper |
| 338 | InfoGraph | 0.7750
±0.0074 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) Difference within reported uncertainty; not counted as underperformance. |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MSH-GNN | 0.9410
±0.0330 | |
| 2 | GRDL | 0.8260
±0.0120 | |
| 3 | GMN | 0.8225 | |
| 32 | GIN | 0.7880
±0.0410 best reported | best at pub: Permutation-Invariant graph partitioning: How graph neural networks capture structural interactions? (2023) Difference within reported uncertainty; not counted as underperformance. |
| 67 | SAGE | 0.7726
±0.0228 | |
| 149 | MLP | 0.7600
±0.0320 | |
| 195 | UniAug | 0.7547
±0.0250 | This paper |
| 213 | GraphMAE | 0.7530
±0.0050 best reported | best at pub: Graph Learning with Distributional Edge Layouts (2024) |
| 265 | GraphCL | 0.7489
±0.0065 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) Difference within reported uncertainty; not counted as underperformance. |
| 281 | S-Mixup | 0.7461
±0.0508 | This paper |
| 283 | JOAO | 0.7460
±0.0040 best reported | best at pub: GPS: graph contrastive learning via multi-scale augmented views from adversarial pooling (2024) best today: Balancing Graph Embedding Smoothness in Self-Supervised Learning via Information-Theoretic Decomposition (WWW 2025) Difference within reported uncertainty; not counted as underperformance. |
| 297 | FLAG | 0.7431
±0.0421 | prev best: Automated Data Augmentations for Graph Classification (ICLR 2022) |
| 303 | GraphAug | 0.7421
±0.0370 | prev best: Automated Data Augmentations for Graph Classification (ICLR 2022) Improvement within reported uncertainty; not highlighted. |
| 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 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9792 | |
| 2 | MSH-GNN | 0.9640
±0.0070 | |
| 3 | CoCN | 0.8722
±0.0013 | |
| 19 | GraphAug | 0.8290
±0.0020 best reported | best at pub: Automated Data Augmentations for Graph Classification (ICLR 2022) |
| 22 | GraphMAE | 0.8270
±0.0100 best reported | best at pub: GraphMAE: Self-Supervised Masked Graph Autoencoders (KDD 2022) best today: Revisiting Graph Autoencoders as Implicit Contrastive Learners (KDD 2024) |
| 23 | GCN | 0.8260
±0.0220 | |
| 30 | GIN | 0.8220
±0.0210 best reported | best at pub: On the Equivalence between Graph Isomorphism Testing and Function Approximation with GNNs (NeurIPS 2019) best today: Scalable Expressiveness through Preprocessed Graph Perturbations (2024) |
| 80 | GraphCL | 0.8108
±0.0017 best reported | best at pub: Label-invariant Augmentation for Semi-Supervised Graph Classification (NeurIPS 2022) |
| 81 | Infomax | 0.8104
±0.0012 best reported | best at pub: Label-invariant Augmentation for Semi-Supervised Graph Classification (NeurIPS 2022) |
| 110 | FLAG | 0.8030
±0.0060 best reported | best at pub: Automated Data Augmentations for Graph Classification (ICLR 2022) |
| 146 | InfoGraph | 0.7940 best reported | best at pub: CogDL: A Comprehensive Library for Graph Deep Learning (WWW 2021) |
| 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 | 0.7535
±0.0093 best reported | best at pub: Spectral Augmentation for Self-Supervised Learning on Graphs (ICLR 2022) Difference within reported uncertainty; not counted as underperformance. |
| 256 | EdgePred | 0.7464
±0.0224 | prev best: SGL-PT: A Strong Graph Learner with Graph Prompt Tuning (2023) |
| # | Model | Accuracy ↑ | 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 | 0.6767
±0.0583 best reported | best at pub: GNNBenchmark (JMLR 2023) Difference within reported uncertainty; not counted as underperformance. |
| 35 | S-Mixup | 0.6685
±0.0704 | This paper |
| 124 | MLP | 0.5583
±0.0352 | |
| 212 | JOAO | 0.3460
±0.0106 best reported | best at pub: Graph Contrastive Learning with Cohesive Subgraph Awareness (WWW 2024) |
| 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
| # | Model | Accuracy ↑ | 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 | 0.7933
±0.0447 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) best today: Graph Wave Networks (WWW 2025) |
| 287 | UniAug + Half-Hop | 0.7703
±0.0427 | This paper |
| 331 | GraphMAE | 0.7432
±0.0456 best reported | best today: Disentangled Generative Graph Representation Learning (2024) |
| 346 | UniAug | 0.7351
±0.0506 | This paper |
| 351 | MVGRL | 0.7301
±0.0552 best reported | |
| 367 | Half-Hop | 0.7235
±0.0427 | This paper |
| 369 | GRACE | 0.6354
±0.0257 | |
| 409 | BGRL | 0.6578
±0.0266 | |
| 468 | JOAO | 0.6245
±0.0296 best reported | best today: Learn Beneficial Noise as Graph Augmentation (ICML 2025) Difference within reported uncertainty; not counted as underperformance. |
| 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 |
| # | Model | Accuracy ↑ | 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 | 0.8082
±0.0360 best reported | best at pub: Differentiable Cluster Graph Neural Network (2024) best today: Bayesian Neighborhood Adaptation for Graph Neural Networks (TMLR 2025) |
| 231 | GraphMAE | 0.7514
±0.0965 best reported | best today: Disentangled Generative Graph Representation Learning (2024) |
| 264 | UniAug + Half-Hop | 0.7243
±0.0581 | This paper |
| 299 | UniAug | 0.6811
±0.0672 | This paper |
| 340 | MVGRL | 0.6430 best reported | best at pub: Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating (AAAI 2022) |
| 357 | Half-Hop | 0.6246
±0.0758 | This paper |
| 415 | BGRL | 0.5730 best reported | best at pub: Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating (AAAI 2022) Difference within reported uncertainty; not counted as underperformance. |
| 423 | GRACE | 0.5639
±0.0211 | prev best: Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating (AAAI 2022) Improvement within reported uncertainty; not highlighted. |
| 477 | JOAO | 0.5102
±0.0096 best reported | best today: Learn Beneficial Noise as Graph Augmentation (ICML 2025) Difference within reported uncertainty; not counted as underperformance. |
| 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 |
| # | Model | Accuracy ↑ | 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 | 0.3690 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) |
| 235 | UniAug + Half-Hop | 0.3497
±0.0055 | This paper |
| 247 | MVGRL | 0.3464
±0.0020 best reported | best at pub: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) best today: Frequency-Corrupt Based Graph Self-Supervised Learning (WWW 2026) |
| 251 | GRACE | 0.3450
±0.0110 best reported | best at pub: Graph Contrastive Learning under Heterophily via Graph Filters (2023) |
| 270 | Half-Hop | 0.3395
±0.0068 | This paper |
| 285 | UniAug | 0.3311
±0.0157 | This paper |
| 299 | GraphMAE | 0.3215
±0.0133 best reported | best today: Frequency-Corrupt Based Graph Self-Supervised Learning (WWW 2026) |
| 356 | BGRL | 0.2986 best reported | best at pub: Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating (AAAI 2022) Difference within reported uncertainty; not counted as underperformance. |
| 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 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | IBG-NN | 0.7763
±0.0179 | |
| 2 | Dir-GNN+CNA | 0.7747
±0.0128 | |
| 3 | DHGNN | 0.7684
±0.0161 | |
| 44 | GraphMAE | 0.6113
±0.0060 best reported | best today: Frequency-Corrupt Based Graph Self-Supervised Learning (WWW 2026) |
| 46 | GCN | 0.6067 best reported | best at pub: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 50 | MVGRL | 0.6009
±0.0044 best reported | best at pub: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) best today: Frequency-Corrupt Based Graph Self-Supervised Learning (WWW 2026) |
| 108 | BGRL | 0.4624
±0.0070 best reported | best at pub: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) best today: Rethinking Graph Contrastive Learning through Relative Similarity Preservation (IJCAI 2025) |
| 120 | SAGE | 0.4460
±0.0130 | |
| 147 | UniAug | 0.4190
±0.0190 | This paper |
| 154 | GRACE | 0.4109
±0.0085 best reported | best at pub: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) best today: Rethinking Graph Contrastive Learning through Relative Similarity Preservation (IJCAI 2025) |
| 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 →Sorted by MAE. Highlighted rows are from other papers.
| # | Model | MAE ↓ | 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 |
