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
| # | 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 | |
| 44 | GAT | 0.8897
±0.0014 best reported | |
| 50 | FAGCN | 0.8885
±0.0136 best reported | best at pub: Language is All a Graph Needs (2023) best today: Large Language Model Meets Graph Neural Network in Knowledge Distillation (AAAI 2024) |
| 108 | APPNP | 0.8787 best reported | best at pub: Orthogonal Graph Neural Networks (AAAI 2021) best today: Feature Transportation Improves Graph Neural Networks (AAAI 2023) |
| 141 | GraphSAGE | 0.8708
±0.0085 best reported | best at pub: Large Language Model Meets Graph Neural Network in Knowledge Distillation (AAAI 2024) |
| 223 | SGC | 0.8509
±0.0648 best reported | best at pub: LOGIN: A Large Language Model Consulted Graph Neural Network Training Framework (2024) Difference within reported uncertainty; not counted as underperformance. |
| 303 | GATv2 | 0.8406
±0.0083 best reported | |
| 346 | AGNN | 0.8360
±0.0030 best reported | best at pub: Reinforcement learning on graphs: A survey (2022) |
| 413 | GADPN | 0.8320 | This paper |
| 569 | GEN | 0.8166
±0.0091 best reported | best at pub: Discovering the Representation Bottleneck of Graph Neural Networks (2022) Difference within reported uncertainty; not counted as underperformance. |
| 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 | |
| 20 | APPNP | 0.8142
±0.0026 best reported | best at pub: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 35 | GAT | 0.8080
±0.0026 best reported | best at pub: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 44 | GCN | 0.8033
±0.0088 best reported | best at pub: NTFormer: A Composite Node Tokenized Graph Transformer for Node Classification (2024) |
| 60 | FAGCN | 0.7928
±0.0170 best reported | best at pub: NTFormer: A Composite Node Tokenized Graph Transformer for Node Classification (2024) |
| 61 | GraphSAGE | 0.7923
±0.0053 best reported | best at pub: Gophormer: Ego-Graph Transformer for Node Classification (2021) |
| 96 | SGC | 0.7765
±0.0012 best reported | |
| 242 | AGNN | 0.7380
±0.0070 best reported | best at pub: Reinforcement learning on graphs: A survey (2022) |
| 259 | SAGE | 0.7361
±0.0190 | |
| 303 | GEN | 0.7321
±0.0062 best reported | best at pub: Discovering the Representation Bottleneck of Graph Neural Networks (2022) |
| 350 | MLP | 0.7289
±0.0010 | |
| 356 | GADPN | 0.7280 | This paper |
| 585 | GATv2 | 0.7060 | prev best: GraphText: Graph Reasoning in Text Space (2023) |
Heterophilic Graphs
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DiGGR | 0.4535
±0.0353 | |
| 2 | TRIGON | 0.4402
±0.0028 | |
| 3 | DoG | 0.4320
±0.0120 | |
| 41 | APPNP | 0.4046
±0.0064 best reported | best at pub: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) |
| 42 | MLP | 0.4026
±0.0108 | |
| 56 | FAGCN | 0.3970 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) |
| 68 | GraphSAGE | 0.3899
±0.0085 best reported | best at pub: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) |
| 119 | GEN | 0.3730
±0.0140 best reported | best at pub: ES-GNN: Generalizing Graph Neural Networks Beyond Homophily with Edge Splitting (2022) |
| 135 | GCN | 0.3690 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) |
| 168 | GADPN | 0.3640 | This paper |
| 182 | GAT | 0.3605
±0.0035 best reported | best at pub: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) |
| 230 | GATv2 | 0.3510
±0.0020 best reported | best at pub: What Can We Learn From MIMO Graph Convolutions? (IJCAI 2025) |
| 237 | SGC | 0.3490
±0.0070 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 266 | GIN | 0.3410
±0.0030 | |
| 298 | AGNN | 0.3220 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | Hetero-S (GAT 8-layer) | 0.8693 | |
| 2 | Dir-GNN+CNA | 0.8586
±0.0180 | |
| 3 | GAT | 0.8560 best reported | best at pub: The Heterophilic Snowflake Hypothesis: Training and Empowering GNNs for Heterophilic Graphs (KDD 2024) |
| 52 | GCN | 0.7033 best reported | best at pub: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 76 | SGC | 0.6710
±0.0290 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 79 | APPNP | 0.6670
±0.0270 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 107 | FAGCN | 0.6344
±0.0205 best reported | best at pub: Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating (AAAI 2022) |
| 108 | SAGE | 0.6340
±0.0300 | |
| 115 | GraphSAGE | 0.6215
±0.0042 best reported | best at pub: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) |
| 123 | GADPN | 0.6110 | This paper |
| 153 | GEN | 0.5750 | This paper |
| 169 | MLP | 0.5429 | |
| 214 | GATv2 | 0.4710
±0.0030 best reported | best at pub: What Can We Learn From MIMO Graph Convolutions? (IJCAI 2025) |
| 236 | AGNN | 0.4340 | 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 | |
| 46 | GCN | 0.6067 best reported | best at pub: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 67 | GAT | 0.5630
±0.0220 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 68 | APPNP | 0.5590
±0.0290 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 81 | SGC | 0.5230
±0.0230 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 120 | SAGE | 0.4460
±0.0130 | |
| 128 | GraphSAGE | 0.4378
±0.0190 best reported | |
| 139 | FAGCN | 0.4259
±0.0069 best reported | best at pub: Gradient Gating for Deep Multi-Rate Learning on Graphs (ICLR 2022) |
| 168 | GADPN | 0.3960 | This paper |
| 172 | MLP | 0.3930
±0.0079 | |
| 199 | GEN | 0.3680 | This paper |
| 218 | GATv2 | 0.3510
±0.0020 best reported | best at pub: What Can We Learn From MIMO Graph Convolutions? (IJCAI 2025) |
| 254 | AGNN | 0.2740 | This paper |
