TMLR 2025

Diffusion on Graph: Augmentation of Graph Structure for Node Classification

Yancheng Wang, Changyu Liu, Yingzhen Yang

Main figure for Diffusion on Graph: Augmentation of Graph Structure for Node Classification

Abstract

Graph diffusion models have recently been proposed to synthesize entire graphs, such as molecule graphs. Although existing methods have shown great performance in generating entire graphs for graph-level learning tasks, no graph diffusion models have been developed to generate synthetic graph structures, that is, synthetic nodes and associated edges within a given graph, for node-level learning tasks. Inspired by the research in the computer vision literature using synthetic data for enhanced performance, we propose Diffusion on Graph (DoG), which generates synthetic graph structures to boost the performance of GNNs. The synthetic graph structures generated by DoG are combined with the original graph to form an augmented graph for the training of node-level learning tasks, such as node classification and graph contrastive learning (GCL). To improve the efficiency of the generation process, a Bi-Level Neighbor Map Decoder (BLND) is introduced in DoG. To mitigate the adverse effect of the noise introduced by the synthetic graph structures, a low-rank regularization method is proposed for the training of graph neural networks (GNNs) on the augmented graphs. Extensive experiments on various graph datasets for semi-supervised node classification and graph contrastive learning have been conducted to demonstrate the effectiveness of DoG with low-rank regularization. The code of DoG is available at.

Proposed method: DoG

Benchmark Results

Tested on 7 datasets 13 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 #558 537 places worse
0.9004
best reported
actual #21 vs paper #558 537 places worse
paper 0.8170 ±0.0040
paper 0.8170 ±0.0040 Δ at pub 0.0834
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
108
APPNP
actual #108 vs paper #389 281 places worse
0.8787
best reported
actual #108 vs paper #389 281 places worse
paper 0.8330 ±0.0050
best at pub: Orthogonal Graph Neural Networks (AAAI 2021)
paper 0.8330 ±0.0050 Δ at pub 0.0457 Δ today 0.0457
233
SGFormer
actual #233 vs paper #251 18 places worse
0.8482 ±0.0085
best reported
actual #233 vs paper #251 18 places worse
paper 0.8450 ±0.0080

Difference within reported uncertainty; not counted as underperformance.

paper 0.8450 ±0.0080 Δ today 0.0032
291
Exphormer
0.8410 ±0.0080
This paper
366
S^2GC
0.8350 ±0.0020
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
20
APPNP
actual #20 vs paper #474 454 places worse
0.8142 ±0.0026
best reported
actual #20 vs paper #474 454 places worse
paper 0.7180 ±0.0050
paper 0.7180 ±0.0050 Δ at pub 0.0962
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 #588 544 places worse
0.8033 ±0.0088
best reported
actual #44 vs paper #588 544 places worse
paper 0.7050 ±0.0030
paper 0.7050 ±0.0030 Δ at pub 0.0983
61
GraphSAGE
0.7923 ±0.0053
89
SGFormer
actual #89 vs paper #373 284 places worse
0.7798 ±0.0091
best reported
actual #89 vs paper #373 284 places worse
paper 0.7260 ±0.0040
paper 0.7260 ±0.0040 Δ at pub 0.0538
264
S^2GC
0.7360 ±0.0050
This paper
344
Exphormer
0.7290 ±0.0040
This paper
350
MLP
0.7289 ±0.0010
#ModelAccuracy ↑Paper
1
LGTL
0.9518 ±0.0011
2
MixHop (LO)
0.9513 ±0.0038
3
GraphSAGE (LO)
0.9511 ±0.0036
17
APPNP
actual #17 vs paper #439 422 places worse
0.9355 ±0.0060
best reported
actual #17 vs paper #439 422 places worse
paper 0.8010 ±0.0020
paper 0.8010 ±0.0020 Δ at pub 0.1345
18
GCN
actual #18 vs paper #524 506 places worse
0.9296 ±0.0015
best reported
actual #18 vs paper #524 506 places worse
paper 0.7940 ±0.0040
20
GAT
actual #20 vs paper #585 565 places worse
0.9233 ±0.0018
best reported
actual #20 vs paper #585 565 places worse
paper 0.7900 ±0.0030
56
SGFormer
actual #56 vs paper #418 362 places worse
0.9037 ±0.0020
best reported
actual #56 vs paper #418 362 places worse
paper 0.8030 ±0.0060
105
Exphormer
actual #105 vs paper #296 191 places worse
0.8906 ±0.0024
best reported
actual #105 vs paper #296 191 places worse
paper 0.8320 ±0.0060
116
SAGE
0.8881 ±0.0015
210
MLP
0.8690 ±0.0074
433
S^2GC
0.8020 ±0.0050
This paper
#ModelAccuracy ↑Paper
1
DoG
0.9690 ±0.0030
This paper
2
GWN-fa
0.9667 ±0.0026
3
GWN-sym
0.9666 ±0.0026
6
GraphSAGE
0.9593 ±0.0025
8
Exphormer
actual #8 vs paper #10 2 places worse
0.9580 ±0.0020
best reported
actual #8 vs paper #10 2 places worse
paper 0.9570 ±0.0020

Difference within reported uncertainty; not counted as underperformance.

paper 0.9570 ±0.0020 Δ at pub 0.0010
12
GCN
actual #12 vs paper #82 70 places worse
0.9514 ±0.0025
best reported
actual #12 vs paper #82 70 places worse
paper 0.9290 ±0.0010
best today: Graph Wave Networks (WWW 2025)
paper 0.9290 ±0.0010 Δ at pub 0.0070 Δ today 0.0224
21
GAT
actual #21 vs paper #36 15 places worse
0.9437 ±0.0028
best reported
actual #21 vs paper #36 15 places worse
paper 0.9360 ±0.0070
best today: Graph Wave Networks (WWW 2025)

Difference within reported uncertainty; not counted as underperformance.

paper 0.9360 ±0.0070 Δ at pub 0.0020 Δ today 0.0077
25
APPNP
actual #25 vs paper #25
0.9400 ±0.0030
actual #25 vs paper #25
paper 0.9400 ±0.0030

Improvement within reported uncertainty; not highlighted.

paper 0.9400 ±0.0030 Δ at pub 0.0016
31
S^2GC
actual #31 vs paper #31
0.9380 ±0.0010
actual #31 vs paper #31
paper 0.9380 ±0.0010
paper 0.9380 ±0.0010 Δ at pub 0.0220
34
SGFormer
0.9370 ±0.0040
This paper
43
DGI
actual #43 vs paper #113 70 places worse
0.9350 ±0.0030
best reported
actual #43 vs paper #113 70 places worse
paper 0.9220 ±0.0060
paper 0.9220 ±0.0060 Δ at pub 0.0130
51
GCA
actual #51 vs paper #152 101 places worse
0.9332 ±0.0012
best reported
actual #51 vs paper #152 101 places worse
paper 0.9100
53
BGRL
actual #53 vs paper #54 1 place worse
0.9331 ±0.0013
best reported
actual #53 vs paper #54 1 place worse
paper 0.9330 ±0.0010

Difference within reported uncertainty; not counted as underperformance.

paper 0.9330 ±0.0010 Δ at pub 0.0001 Δ today 0.0001
57
SGCL
actual #57 vs paper #57
0.9330 ±0.0020
actual #57 vs paper #57
paper 0.9330 ±0.0020

Improvement within reported uncertainty; not highlighted.

paper 0.9330 ±0.0020 Δ at pub 0.0001
63
GraphMAE
actual #63 vs paper #69 6 places worse
0.9300 ±0.0010
actual #63 vs paper #69 6 places worse
paper 0.9300 ±0.0010

Improvement within reported uncertainty; not highlighted.

paper 0.9300 ±0.0010 Δ at pub 0.0004
88
MLP
0.9280 ±0.0020
98
GGD
actual #98 vs paper #98
0.9270 ±0.0040
actual #98 vs paper #98
paper 0.9270 ±0.0040
paper 0.9270 ±0.0040 Δ at pub 0.0040
116
MVGRL
actual #116 vs paper #118 2 places worse
0.9211 ±0.0012
best reported
actual #116 vs paper #118 2 places worse
paper 0.9210 ±0.0010

Difference within reported uncertainty; not counted as underperformance.

paper 0.9210 ±0.0010 Δ at pub 0.0001 Δ today 0.0001
152
GMI
actual #152 vs paper #152
0.9108 ±0.0056
best reported
actual #152 vs paper #152
paper 0.9100

Difference within reported uncertainty; not counted as underperformance.

paper 0.9100 Δ at pub 0.0008

Heterophilic Graphs

#ModelAccuracy ↑Paper
1
P^2GNN
0.9672 ±0.0147
2
DoG
0.9660 ±0.0210
This paper
3
GPF-plus
0.9583 ±0.0419
5
ACM-GCN
actual #5 vs paper #5
0.9510 ±0.0320
actual #5 vs paper #5
paper 0.9510 ±0.0320
34
MLP
0.9230 ±0.0070
53
GraphSAGE
0.9000 ±0.0365
#ModelAccuracy ↑Paper
1
DiGGR
0.4535 ±0.0353
2
TRIGON
0.4402 ±0.0028
3
DoG
0.4320 ±0.0120
This paper
16
ACM-GCN
actual #16 vs paper #24 8 places worse
0.4160 ±0.0110
actual #16 vs paper #24 8 places worse
paper 0.4160 ±0.0110
paper 0.4160 ±0.0110 Δ at pub 0.0500
42
MLP
0.4026 ±0.0108
68
GraphSAGE
0.3899 ±0.0085
#ModelAccuracy ↑Paper
1
Hetero-S (GAT 8-layer)
0.8693
2
Dir-GNN+CNA
0.8586 ±0.0180
3
GAT
0.8560
28
ACM-GCN
actual #28 vs paper #62 34 places worse
0.6900 ±0.0170
actual #28 vs paper #62 34 places worse
paper 0.6900 ±0.0170

Improvement within reported uncertainty; not highlighted.

paper 0.6900 ±0.0170 Δ at pub 0.0207 Δ today 0.0576
50
DoG
0.7060 ±0.0140
This paper
52
GCN
0.7033
169
MLP
0.5429
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 Best today — OK at publication; today's leaderboard best is elsewhere