GADPN: Graph Adaptive Denoising and Perturbation Networks via Singular Value Decomposition

Hao Deng, Bo Liu

Main figure for GADPN: Graph Adaptive Denoising and Perturbation Networks via Singular Value Decomposition

Abstract

While Graph Neural Networks (GNNs) excel on graph-structured data, their performance is fundamentally limited by the quality of the observed graph, which often contains noise, missing links, or structural properties misaligned with GNNs' underlying assumptions. To address this, graph structure learning aims to infer a more optimal topology. Existing methods, however, often incur high computational costs due to complex generative models and iterative joint optimization, limiting their practical utility. In this paper, we propose GADPN, a simple yet effective graph structure learning framework that adaptively refines graph topology via low-rank denoising and generalized structural perturbation. Our approach makes two key contributions: (1) we introduce Bayesian optimization to adaptively determine the optimal denoising strength, tailoring the process to each graph's homophily level; and (2) we extend the structural perturbation method to arbitrary graphs via Singular Value Decomposition (SVD), overcoming its original limitation to symmetric structures. Extensive experiments on benchmark datasets demonstrate that GADPN not only achieves state-of-the-art performance but does so with significantly improved efficiency. It shows particularly strong gains on challenging disassortative graphs, validating its ability to robustly learn enhanced graph structures across diverse network types.

Benchmark Results

Tested on 5 datasets 35 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 #606 585 places worse
0.9004
best reported
actual #21 vs paper #606 585 places worse
paper 0.8100
paper 0.8100 Δ at pub 0.0904
39
SAGE
0.8911 ±0.0012
44
GAT
actual #44 vs paper #558 514 places worse
0.8897 ±0.0014
best reported
actual #44 vs paper #558 514 places worse
paper 0.8170
50
FAGCN
actual #50 vs paper #530 480 places worse
0.8885 ±0.0136
best reported
actual #50 vs paper #530 480 places worse
paper 0.8200
best at pub: Language is All a Graph Needs (2023)
paper 0.8200 Δ at pub 0.0685 Δ today 0.0685
108
APPNP
actual #108 vs paper #456 348 places worse
0.8787
best reported
actual #108 vs paper #456 348 places worse
paper 0.8260
best at pub: Orthogonal Graph Neural Networks (AAAI 2021)
paper 0.8260 Δ at pub 0.0527 Δ today 0.0527
141
GraphSAGE
actual #141 vs paper #656 515 places worse
0.8708 ±0.0085
best reported
actual #141 vs paper #656 515 places worse
paper 0.8000
paper 0.8000 Δ at pub 0.0708
223
SGC
actual #223 vs paper #656 433 places worse
0.8509 ±0.0648
best reported
actual #223 vs paper #656 433 places worse
paper 0.8000

Difference within reported uncertainty; not counted as underperformance.

paper 0.8000 Δ at pub 0.0509
303
GATv2
actual #303 vs paper #573 270 places worse
0.8406 ±0.0083
best reported
actual #303 vs paper #573 270 places worse
paper 0.8150
346
AGNN
actual #346 vs paper #589 243 places worse
0.8360 ±0.0030
best reported
actual #346 vs paper #589 243 places worse
paper 0.8120
paper 0.8120 Δ at pub 0.0240
413
GADPN
0.8320
This paper
569
GEN
actual #569 vs paper #589 20 places worse
0.8166 ±0.0091
best reported
actual #569 vs paper #589 20 places worse
paper 0.8120

Difference within reported uncertainty; not counted as underperformance.

paper 0.8120 Δ at pub 0.0046
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 #550 530 places worse
0.8142 ±0.0026
best reported
actual #20 vs paper #550 530 places worse
paper 0.7110
paper 0.7110 Δ at pub 0.1032
35
GAT
actual #35 vs paper #616 581 places worse
0.8080 ±0.0026
best reported
actual #35 vs paper #616 581 places worse
paper 0.7010
paper 0.7010 Δ at pub 0.1070
44
GCN
actual #44 vs paper #550 506 places worse
0.8033 ±0.0088
best reported
actual #44 vs paper #550 506 places worse
paper 0.7110
60
FAGCN
actual #60 vs paper #720 660 places worse
0.7928 ±0.0170
best reported
actual #60 vs paper #720 660 places worse
paper 0.6700
61
GraphSAGE
actual #61 vs paper #624 563 places worse
0.7923 ±0.0053
best reported
actual #61 vs paper #624 563 places worse
paper 0.6990
paper 0.6990 Δ at pub 0.0933
96
SGC
actual #96 vs paper #528 432 places worse
0.7765 ±0.0012
best reported
actual #96 vs paper #528 432 places worse
paper 0.7130
242
AGNN
actual #242 vs paper #639 397 places worse
0.7380 ±0.0070
best reported
actual #242 vs paper #639 397 places worse
paper 0.6940
paper 0.6940 Δ at pub 0.0440
259
SAGE
0.7361 ±0.0190
303
GEN
actual #303 vs paper #570 267 places worse
0.7321 ±0.0062
best reported
actual #303 vs paper #570 267 places worse
paper 0.7080
paper 0.7080 Δ at pub 0.0241
350
MLP
0.7289 ±0.0010
356
GADPN
0.7280
This paper
585
GATv2
actual #585 vs paper #585
0.7060
actual #585 vs paper #585
paper 0.7060
paper 0.7060 Δ at pub 0.0070

Heterophilic Graphs

#ModelAccuracy ↑Paper
1
DiGGR
0.4535 ±0.0353
2
TRIGON
0.4402 ±0.0028
3
DoG
0.4320 ±0.0120
41
APPNP
actual #41 vs paper #390 349 places worse
0.4046 ±0.0064
best reported
actual #41 vs paper #390 349 places worse
paper 0.2820
paper 0.2820 Δ at pub 0.1226
42
MLP
0.4026 ±0.0108
56
FAGCN
actual #56 vs paper #278 222 places worse
0.3970
best reported
actual #56 vs paper #278 222 places worse
paper 0.3360
paper 0.3360 Δ at pub 0.0610
68
GraphSAGE
actual #68 vs paper #273 205 places worse
0.3899 ±0.0085
best reported
actual #68 vs paper #273 205 places worse
paper 0.3380
paper 0.3380 Δ at pub 0.0519
119
GEN
actual #119 vs paper #290 171 places worse
0.3730 ±0.0140
best reported
actual #119 vs paper #290 171 places worse
paper 0.3280
135
GCN
actual #135 vs paper #376 241 places worse
0.3690
best reported
actual #135 vs paper #376 241 places worse
paper 0.2890
paper 0.2890 Δ at pub 0.0800
168
GADPN
0.3640
This paper
182
GAT
actual #182 vs paper #385 203 places worse
0.3605 ±0.0035
best reported
actual #182 vs paper #385 203 places worse
paper 0.2850
paper 0.2850 Δ at pub 0.0755
230
GATv2
actual #230 vs paper #394 164 places worse
0.3510 ±0.0020
best reported
actual #230 vs paper #394 164 places worse
paper 0.2810
paper 0.2810 Δ at pub 0.0700
237
SGC
actual #237 vs paper #412 175 places worse
0.3490 ±0.0070
best reported
actual #237 vs paper #412 175 places worse
paper 0.2660
paper 0.2660 Δ at pub 0.0830
266
GIN
0.3410 ±0.0030
298
AGNN
actual #298 vs paper #298
0.3220
actual #298 vs paper #298
paper 0.3220
#ModelAccuracy ↑Paper
1
Hetero-S (GAT 8-layer)
0.8693
2
Dir-GNN+CNA
0.8586 ±0.0180
3
GAT
actual #3 vs paper #229 226 places worse
0.8560
best reported
actual #3 vs paper #229 226 places worse
paper 0.4410
52
GCN
actual #52 vs paper #269 217 places worse
0.7033
best reported
actual #52 vs paper #269 217 places worse
paper 0.3440
paper 0.3440 Δ at pub 0.3593
76
SGC
actual #76 vs paper #268 192 places worse
0.6710 ±0.0290
best reported
actual #76 vs paper #268 192 places worse
paper 0.3460
paper 0.3460 Δ at pub 0.3250
79
APPNP
actual #79 vs paper #257 178 places worse
0.6670 ±0.0270
best reported
actual #79 vs paper #257 178 places worse
paper 0.3930
paper 0.3930 Δ at pub 0.2740
107
FAGCN
actual #107 vs paper #257 150 places worse
0.6344 ±0.0205
best reported
actual #107 vs paper #257 150 places worse
paper 0.3930
108
SAGE
0.6340 ±0.0300
115
GraphSAGE
actual #115 vs paper #216 101 places worse
0.6215 ±0.0042
best reported
actual #115 vs paper #216 101 places worse
paper 0.4630
paper 0.4630 Δ at pub 0.1585
123
GADPN
0.6110
This paper
153
GEN
0.5750
This paper
169
MLP
0.5429
214
GATv2
actual #214 vs paper #242 28 places worse
0.4710 ±0.0030
best reported
actual #214 vs paper #242 28 places worse
paper 0.4260
paper 0.4260 Δ at pub 0.0450
236
AGNN
0.4340
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
46
GCN
actual #46 vs paper #250 204 places worse
0.6067
best reported
actual #46 vs paper #250 204 places worse
paper 0.2770
paper 0.2770 Δ at pub 0.3297
67
GAT
actual #67 vs paper #254 187 places worse
0.5630 ±0.0220
best reported
actual #67 vs paper #254 187 places worse
paper 0.2720
paper 0.2720 Δ at pub 0.2910
68
APPNP
actual #68 vs paper #245 177 places worse
0.5590 ±0.0290
best reported
actual #68 vs paper #245 177 places worse
paper 0.2850
paper 0.2850 Δ at pub 0.2740
81
SGC
actual #81 vs paper #250 169 places worse
0.5230 ±0.0230
best reported
actual #81 vs paper #250 169 places worse
paper 0.2780
paper 0.2780 Δ at pub 0.2450
120
SAGE
0.4460 ±0.0130
128
GraphSAGE
actual #128 vs paper #235 107 places worse
0.4378 ±0.0190
best reported
actual #128 vs paper #235 107 places worse
paper 0.3140
139
FAGCN
actual #139 vs paper #254 115 places worse
0.4259 ±0.0069
best reported
actual #139 vs paper #254 115 places worse
paper 0.2700
168
GADPN
0.3960
This paper
172
MLP
0.3930 ±0.0079
199
GEN
0.3680
This paper
218
GATv2
actual #218 vs paper #250 32 places worse
0.3510 ±0.0020
best reported
actual #218 vs paper #250 32 places worse
paper 0.2780
paper 0.2780 Δ at pub 0.0730
254
AGNN
0.2740
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