Towards Understanding Graph Neural Networks: An Algorithm Unrolling Perspective
Abstract
The graph neural network (GNN) has demonstrated its superior performance in various applications. The working mechanism behind it, however, remains mysterious. GNN models are designed to learn effective representations for graph-structured data, which intrinsically coincides with the principle of graph signal denoising (GSD). Algorithm unrolling, a ``learning to optimize'' technique, has gained increasing attention due to its prospects in building efficient and interpretable neural network architectures. In this paper, we introduce a class of unrolled networks built based on truncated optimization algorithms (e.g., gradient descent and proximal gradient descent) for GSD problems. They are shown to be tightly connected to many popular GNN models in that the forward propagations in these GNNs are in fact unrolled networks serving specific GSDs. Besides, the training process of a GNN model can be seen as solving a bilevel optimization problem with a GSD problem at the lower level. Such a connection brings a fresh view of GNNs, as we could try to understand their practical capabilities from their GSD counterparts, and it can also motivate designing new GNN models. Based on the algorithm unrolling perspective, an expressive model named UGDGNN, i.e., unrolled gradient descent GNN, is further proposed which inherits appealing theoretical properties. Extensive numerical simulations on seven benchmark datasets demonstrate that UGDGNN can achieve superior or competitive performance over the state-of-the-art models.
Benchmark Results
Tested on 5 datasets 21 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | 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: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) best today: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 32 | GPRGNN | 0.7164
±0.0047 | |
| 36 | GCNII | 0.8076
±0.0030 best reported | best at pub: GBK-GNN: Gated Bi-Kernel Graph Neural Networks for Modeling Both Homophily and Heterophily (WWW 2021) best today: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 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 | |
| 62 | JKNet | 0.7920 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 75 | DAGNN | 0.7860 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 96 | SGC | 0.7765
±0.0012 best reported | |
| 350 | MLP | 0.7289
±0.0010 | |
| 492 | UGDGNN | 0.7168
±0.0070 | 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 | |
| 17 | APPNP | 0.9355
±0.0060 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 18 | GCN | 0.9296
±0.0015 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 24 | JKNet | 0.9160 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 58 | GCNII | 0.9030
±0.0043 best reported | best at pub: Graph Neural Networks Inspired by Classical Iterative Algorithms (ICML 2021) |
| 101 | GPRGNN | 0.8911
±0.0008 best reported | best today: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 116 | SAGE | 0.8881
±0.0015 | |
| 141 | SGC | 0.8832
±0.0055 best reported | |
| 210 | MLP | 0.8690
±0.0074 | |
| 226 | DAGNN | 0.8640 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 556 | UGDGNN | 0.7922
±0.0035 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9703
±0.0019 | |
| 2 | GAT | 0.9669
±0.0014 | |
| 3 | GAT+T | 0.9660
±0.0007 | |
| 7 | SAGE | 0.9643
±0.0027 | |
| 8 | GCN | 0.9632
±0.0008 best reported | best at pub: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) |
| 21 | APPNP | 0.9573
±0.0012 best reported | |
| 33 | GPRGNN | 0.9549
±0.0014 best reported | |
| 50 | SGC | 0.9511
±0.0009 best reported | best at pub: ROD: Reception-aware Online Distillation for Sparse Graphs (KDD 2021) |
| 87 | GCNII | 0.9430
±0.0020 best reported | best at pub: NCGNN: Node-Level Capsule Graph Neural Network for Semisupervised Classification (2020) best today: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) |
| 260 | DAGNN | 0.9269 best reported | best at pub: NCGNN: Node-Level Capsule Graph Neural Network for Semisupervised Classification (2020) |
| 364 | JKNet | 0.9169 best reported | best at pub: Learned Low Precision Graph Neural Networks (2020) best today: Structure-Aware DropEdge Towards Deep Graph Convolutional Networks (2023) |
| 390 | MLP | 0.9128
±0.0063 | |
| 432 | UGDGNN | 0.9049
±0.0085 | 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) |
| 25 | APPNP | 0.9400
±0.0030 best reported | best at pub: A Unified View on Graph Neural Networks as Graph Signal Denoising (2020) best today: Diffusion on Graph: Augmentation of Graph Structure for Node Classification (TMLR 2025) |
| 91 | DAGNN | 0.9280
±0.0090 best reported | best today: Revisiting the Necessity of Graph Learning and Common Graph Benchmarks (2024) Difference within reported uncertainty; not counted as underperformance. |
| 88 | MLP | 0.9280
±0.0020 | |
| 96 | SGC | 0.9270
±0.0010 best reported | best at pub: Towards Graph Self-Supervised Learning with Contrastive Adjusted Zooming (2021) |
| 104 | GCNII | 0.9241
±0.0050 best reported | |
| 114 | UGDGNN | 0.9218
±0.0066 | This paper |
| 124 | GPRGNN | 0.9203
±0.0061 | This paper |
| 150 | JKNet | 0.9110
±0.0030 best reported | best today: Geometric Evolution Graph Convolutional Networks: Enhancing Graph Representation Learning via Ricci Flow (2026) Difference within reported uncertainty; not counted as underperformance. |
