Understanding Oversmoothing in Diffusion-Based GNNs From the Perspective of Operator Semigroup Theory
Abstract
This paper presents an analytical study of the oversmoothing issue in diffusion-based Graph Neural Networks (GNNs). Generalizing beyond extant approaches grounded in random walk analysis or particle systems, we approach this problem through operator semigroup theory. This theoretical framework allows us to rigorously prove that oversmoothing is intrinsically linked to the ergodicity of the diffusion operator. Relying on semigroup method, we can quantitatively analyze the dynamic of graph diffusion and give a specific mathematical form of the smoothing feature by ergodicity and invariant measure of operator, which improves previous works only show existence of oversmoothing. This finding further poses a general and mild ergodicity-breaking condition, encompassing the various specific solutions previously offered, thereby presenting a more universal and theoretically grounded approach to relieve oversmoothing in diffusion-based GNNs. Additionally, we offer a probabilistic interpretation of our theory, forging a link with prior works and broadening the theoretical horizon. Our experimental results reveal that this ergodicity-breaking term effectively mitigates oversmoothing measured by Dirichlet energy, and simultaneously enhances performance in node classification tasks.
Benchmark Results
Tested on 3 datasets 8 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
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 | |
| 53 | GraphSAGE | 0.9000
±0.0365 best reported | best at pub: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) best today: Graph Neural Networks Need Cluster-Normalize-Activate Modules (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 57 | GREAD | 0.8973
±0.0449 best reported | best today: Graph Neural Reaction Diffusion Models Submitted to the editors June 2023. Accepted in March 2024. (2024) Difference within reported uncertainty; not counted as underperformance. |
| 79 | Ours-Expn | 0.8865
±0.0264 | This paper |
| 82 | GRAFF | 0.8838
±0.0353 best reported | best at pub: Understanding convolution on graphs via energies (TMLR 2022) best today: Graph Navier–Stokes Networks (2026) Difference within reported uncertainty; not counted as underperformance. |
| 102 | Ours-Log | 0.8703
±0.0524 | This paper |
| 167 | Ours-Exp | 0.8406
±0.0459 | This paper |
| 189 | SAGE | 0.8269 | |
| 211 | GAT | 0.8162
±0.0645 best reported | best at pub: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) best today: Equivariance Everywhere All At Once: A Recipe for Graph Foundation Models (2025) |
| 217 | GRAND | 0.8140
±0.0350 best reported | best at pub: Unifying over-smoothing and over-squashing in graph neural networks: A physics informed approach and beyond (2023) best today: When Graph Neural Networks Meet Dynamic Mode Decomposition (ICLR 2024) Difference within reported uncertainty; not counted as underperformance. |
| 257 | GCN | 0.7933
±0.0447 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) best today: Graph Wave Networks (WWW 2025) |
| 376 | CGNN | 0.7140
±0.0410 best reported | best at pub: Understanding convolution on graphs via energies (TMLR 2022) best today: Graph Neural Aggregation-diffusion with Metastability (2024) Difference within reported uncertainty; not counted as underperformance. |
| 499 | PairNorm | 0.6030
±0.0430 best reported | best at pub: Graph-Coupled Oscillator Networks (ICML 2022) Difference within reported uncertainty; not counted as underperformance. |
| # | 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 | |
| 52 | GREAD | 0.8703
±0.0495 best reported | best today: Graph Navier–Stokes Networks (2026) |
| 112 | GRAFF | 0.8405
±0.0610 best reported | best at pub: Understanding convolution on graphs via energies (TMLR 2022) |
| 138 | SAGE | 0.8269 | |
| 142 | GRAND | 0.8246
±0.0709 best reported | best at pub: Dirichlet Energy Enhancement of Graph Neural Networks by Framelet Augmentation (2023) best today: Graph Navier–Stokes Networks (2026) Difference within reported uncertainty; not counted as underperformance. |
| 157 | GraphSAGE | 0.8196
±0.0739 best reported | best at pub: Heterophily-Aware Graph Attention Network (2023) Difference within reported uncertainty; not counted as underperformance. |
| 158 | GAT | 0.8190
±0.0540 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 170 | GCN | 0.8082
±0.0360 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) best today: Bayesian Neighborhood Adaptation for Graph Neural Networks (TMLR 2025) |
| 199 | Ours-Log | 0.7811
±0.0390 | This paper |
| 209 | Ours-Exp | 0.7757
±0.0383 | This paper |
| 221 | Ours-Expn | 0.7648
±0.0271 | This paper |
| 319 | CGNN | 0.6622
±0.0769 | This paper |
| 389 | PairNorm | 0.5892
±0.0315 | This paper |
| # | 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 | |
| 68 | GraphSAGE | 0.3899
±0.0085 best reported | best at pub: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) |
| 96 | GREAD | 0.3790
±0.0117 best reported | best today: Graph Navier–Stokes Networks (2026) Difference within reported uncertainty; not counted as underperformance. |
| 106 | Ours-Expn | 0.3779
±0.0086 | This paper |
| 113 | Ours-Log | 0.3755
±0.0080 | This paper |
| 115 | Ours-Exp | 0.3737
±0.0117 | This paper |
| 129 | GRAFF | 0.3711
±0.0108 best reported | best at pub: Understanding convolution on graphs via energies (TMLR 2022) best today: Graph Neural Reaction Diffusion Models Submitted to the editors June 2023. Accepted in March 2024. (2024) Difference within reported uncertainty; not counted as underperformance. |
| 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: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) |
| 189 | CGNN | 0.3595
±0.0086 | This paper |
| 203 | GRAND | 0.3562
±0.0101 | This paper |
| 266 | GIN | 0.3410
±0.0030 | |
| 408 | PairNorm | 0.2740
±0.0124 | This paper |
