A Unified View on Graph Neural Networks as Graph Signal Denoising
Abstract
Graph Neural Networks (GNNs) have risen to prominence in learning representations for graph structured data. A single GNN layer typically consists of a feature transformation and a feature aggregation operation. The former normally uses feed-forward networks to transform features, while the latter aggregates the transformed features over the graph. Numerous recent works have proposed GNN models with different designs in the aggregation operation. In this work, we establish mathematically that the aggregation processes in a group of representative GNN models including GCN, GAT, PPNP, and APPNP can be regarded as (approximately) solving a graph denoising problem with a smoothness assumption. Such a unified view across GNNs not only provides a new perspective to understand a variety of aggregation operations but also enables us to develop a unified graph neural network framework Ugnn. To demonstrate its promising potential, we instantiate a novel GNN model, Ada-Ugnn, derived from Ugnn, to handle graphs with adaptive smoothness across nodes. Comprehensive experiments show the effectiveness of Ada-Ugnn. The implementation of ADA-UGNN is available at.
Benchmark Results
Tested on 6 datasets 7 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: SplineCNN: Fast Geometric Deep Learning with Continuous B-Spline Kernels (2017) best today: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 39 | SAGE | 0.8911
±0.0012 | |
| 44 | GAT | 0.8897
±0.0014 best reported | best at pub: Learned Low Precision Graph Neural Networks (2020) |
| 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 | |
| 35 | GAT | 0.8080
±0.0026 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) best today: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 44 | GCN | 0.8033
±0.0088 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 61 | GraphSAGE | 0.7923
±0.0053 | |
| 350 | MLP | 0.7289
±0.0010 |
| # | 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: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 20 | GAT | 0.9233
±0.0018 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 116 | SAGE | 0.8881
±0.0015 | |
| 210 | MLP | 0.8690
±0.0074 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9703
±0.0019 | |
| 2 | GAT | 0.9033
±0.0120 | prev best: Directed Graph Convolutional Network (2020) best today: Graph Transductive Sharpening: Leveraging Unlabeled Predictions in Node Classification (2026) Improvement within reported uncertainty; not highlighted. |
| 3 | GAT+T | 0.9660
±0.0007 | |
| 7 | SAGE | 0.9643
±0.0027 | |
| 8 | GCN | 0.9632
±0.0008 best reported | best at pub: Learning on Attribute-Missing Graphs (2020) |
| 21 | APPNP | 0.9573
±0.0012 best reported | best at pub: Spectral Graph Attention Network with Fast Eigen-approximation (2020) |
| 377 | ADA-UGNN | 0.9144
±0.0120 | This paper |
| 390 | MLP | 0.9128
±0.0063 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9461
±0.0017 | |
| 2 | GCN | 0.9412
±0.0008 best reported | best at pub: Learning on Attribute-Missing Graphs (2020) |
| 3 | GAT | 0.9398
±0.0022 best reported | best at pub: Learned Low Precision Graph Neural Networks (2020) |
| 8 | SAGE | 0.9351
±0.0006 | |
| 58 | APPNP | 0.8299
±0.0160 | prev best: Adaptive Propagation Graph Convolutional Network (2020) |
| 320 | MLP | 0.8463 | |
| 375 | ADA-UGNN | 0.8340
±0.0130 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DoG | 0.9690
±0.0030 | |
| 2 | GWN-fa | 0.9667
±0.0026 | |
| 3 | GWN-sym | 0.9666
±0.0026 | |
| 6 | GraphSAGE | 0.9593
±0.0025 | |
| 12 | GCN | 0.9514
±0.0025 best reported | best at pub: Unifying Graph Convolutional Neural Networks and Label Propagation (2020) best today: Graph Wave Networks (WWW 2025) |
| 21 | GAT | 0.9437
±0.0028 best reported | best at pub: Unifying Graph Convolutional Neural Networks and Label Propagation (2020) best today: Graph Wave Networks (WWW 2025) |
| 25 | APPNP | 0.9384
±0.0050 | prev best: Spectral Graph Attention Network with Fast Eigen-approximation (2020) |
| 28 | ADA-UGNN | 0.9392
±0.0060 | This paper |
| 88 | MLP | 0.9280
±0.0020 |
