Graph Neural Networks Inspired by Classical Iterative Algorithms
Abstract
Despite the recent success of graph neural networks (GNN), common architectures often exhibit significant limitations, including sensitivity to oversmoothing, long-range dependencies, and spurious edges, e.g., as can occur as a result of graph heterophily or adversarial attacks. To at least partially address these issues within a simple transparent framework, we consider a new family of GNN layers designed to mimic and integrate the update rules of two classical iterative algorithms, namely, proximal gradient descent and iterative reweighted least squares (IRLS). The former defines an extensible base GNN architecture that is immune to oversmoothing while nonetheless capturing long-range dependencies by allowing arbitrary propagation steps. In contrast, the latter produces a novel attention mechanism that is explicitly anchored to an underlying end-to-end energy function, contributing stability with respect to edge uncertainty. When combined we obtain an extremely simple yet robust model that we evaluate across disparate scenarios including standardized benchmarks, adversarially-perturbated graphs, graphs with heterophily, and graphs involving long-range dependencies. In doing so, we compare against SOTA GNN approaches that have been explicitly designed for the respective task, achieving competitive or superior node classification accuracy. Our code is available at https://github.com/FFTYYY/TWIRLS.
Benchmark Results
Tested on 6 datasets 19 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) |
| 36 | GCNII | 0.8076
±0.0030 best reported | best at pub: Extract the Knowledge of Graph Neural Networks and Go Beyond it: An Effective Knowledge Distillation Framework (WWW 2021) 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 | |
| 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 | best at pub: Deep Learning on Graphs: A Survey (2018) |
| 223 | TWIRLS base | 0.7420
±0.0045 | This paper |
| 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 | |
| 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 | 0.8030
±0.0040 | prev best: Extract the Knowledge of Graph Neural Networks and Go Beyond it: An Effective Knowledge Distillation Framework (WWW 2021) best today: Graph Neural Reaction Diffusion Models Submitted to the editors June 2023. Accepted in March 2024. (2024) Improvement within reported uncertainty; not highlighted. |
| 116 | SAGE | 0.8881
±0.0015 | |
| 141 | SGC | 0.8832
±0.0055 best reported | best at pub: Learning Conjoint Attentions for Graph Neural Nets (NeurIPS 2021) |
| 210 | MLP | 0.8690
±0.0074 | |
| 226 | DAGNN | 0.8640 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 397 | TWIRLS | 0.8070
±0.0050 | This paper |
Heterophilic Graphs
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9672
±0.0147 | |
| 2 | DoG | 0.9660
±0.0210 | |
| 3 | GPF-plus | 0.9583
±0.0419 | |
| 34 | MLP | 0.9230
±0.0070 best reported | |
| 40 | H2GCN | 0.9189
±0.0393 best reported | best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) Difference within reported uncertainty; not counted as underperformance. |
| 47 | TWIRLS | 0.9131
±0.0336 best reported | best today: Simplified PCNet with Robustness (2024) |
| 53 | GraphSAGE | 0.8243
±0.0614 | |
| 189 | SAGE | 0.8269 | |
| 212 | TWIRLS-base | 0.8162
±0.0551 | This paper |
| 211 | GAT | 0.8162
±0.0645 best reported | best at pub: Heterophilic Graphs (ICLR 2020) best today: Equivariance Everywhere All At Once: A Recipe for Graph Foundation Models (2025) |
| 257 | GCN | 0.7933
±0.0447 best reported | best at pub: Non-Local Graph Neural Networks (2020) best today: Graph Wave Networks (WWW 2025) |
| 415 | Geom-GCN | 0.6760 best reported | best at pub: Non-Local Graph Neural Networks (2020) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9541
±0.0272 | |
| 2 | ACM-GCN | 0.9480
±0.0380 | |
| 3 | RF-GCN | 0.9429 | |
| 24 | MLP | 0.9136
±0.0070 best reported | best at pub: Non-Local Graph Neural Networks (2020) best today: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 27 | TWIRLS | 0.8983
±0.0229 best reported | best today: Simplified PCNet with Robustness (2024) Difference within reported uncertainty; not counted as underperformance. |
| 68 | H2GCN | 0.8623
±0.0471 best reported | best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) Difference within reported uncertainty; not counted as underperformance. |
| 122 | TWIRLS-base | 0.8351
±0.0730 | This paper |
| 138 | SAGE | 0.8269 | |
| 157 | GraphSAGE | 0.7595
±0.0501 | |
| 158 | GAT | 0.8190
±0.0540 best reported | best at pub: NCGNN: Node-Level Capsule Graph Neural Network for Semisupervised Classification (2020) best today: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 170 | GCN | 0.8082
±0.0360 best reported | best at pub: NCGNN: Node-Level Capsule Graph Neural Network for Semisupervised Classification (2020) best today: Bayesian Neighborhood Adaptation for Graph Neural Networks (TMLR 2025) |
| 342 | Geom-GCN | 0.6081 | prev best: Non-Local Graph Neural Networks (2020) best today: Steering Graph Neural Networks with Pinning Control (2023) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DiGGR | 0.4535
±0.0353 | |
| 2 | TRIGON | 0.4402
±0.0028 | |
| 3 | DoG | 0.4320
±0.0120 | |
| 42 | MLP | 0.4026
±0.0108 best reported | best at pub: NCGNN: Node-Level Capsule Graph Neural Network for Semisupervised Classification (2020) best today: Heterophily-Aware Graph Attention Network (2023) |
| 68 | GraphSAGE | 0.3423
±0.0099 | prev best: Complete the Missing Half: Augmenting Aggregation Filtering with Diversification for Graph Convolutional Networks (NeurIPS 2020) best today: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) |
| 71 | H2GCN | 0.3885
±0.0117 best reported | best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 85 | TWIRLS | 0.3813
±0.0081 best reported | best today: Simplified PCNet with Robustness (2024) Difference within reported uncertainty; not counted as underperformance. |
| 87 | Geom-GCN | 0.3810 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) |
| 130 | TWIRLS-base | 0.3710
±0.0107 | This paper |
| 135 | GCN | 0.3690 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) |
| 182 | GAT | 0.3605
±0.0035 best reported | best at pub: Non-Local Graph Neural Networks (2020) best today: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) |
| 266 | GIN | 0.3410
±0.0030 |
