Dirichlet Energy Enhancement of Graph Neural Networks by Framelet Augmentation
Abstract
Graph convolutions have been a pivotal element in learning graph representations. However, recursively aggregating neighboring information with graph convolutions leads to indistinguishable node features in deep layers, which is known as the over-smoothing issue. The performance of graph neural networks decays fast as the number of stacked layers increases, and the Dirichlet energy associated with the graph decreases to zero as well. In this work, we introduce a framelet system into the analysis of Dirichlet energy and take a multi-scale perspective to leverage the Dirichlet energy and alleviate the over-smoothing issue. Specifically, we develop a Framelet Augmentation strategy by adjusting the update rules with positive and negative increments for low-pass and high-passes respectively. Based on that, we design the Energy Enhanced Convolution (EEConv), which is an effective and practical operation that is proved to strictly enhance Dirichlet energy. From a message-passing perspective, EEConv inherits multi-hop aggregation property from the framelet transform and takes into account all hops in the multi-scale representation, which benefits the node classification tasks over heterophilous graphs. Experiments show that deep GNNs with EEConv achieve state-of-the-art performance over various node classification datasets, especially for heterophilous graphs, while also lifting the Dirichlet energy as the network goes deeper.
Benchmark Results
Tested on 2 datasets 6 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. |
| 61 | FAGCN | 0.8961
±0.0152 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) Difference within reported uncertainty; not counted as underperformance. |
| 70 | GCNII | 0.8918
±0.0443 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: Piecewise Constant Spectral Graph Neural Network (TMLR 2025) |
| 189 | SAGE | 0.8269 | |
| 196 | UFG | 0.8230
±0.0090 best reported | best at pub: Unifying over-smoothing and over-squashing in graph neural networks: A physics informed approach and beyond (2023) Difference within reported uncertainty; not counted as underperformance. |
| 197 | EE-UFG | 0.8230
±0.0320 | This paper |
| 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. |
| 220 | EGNN | 0.8134
±0.0156 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: Simplified PCNet with Robustness (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) |
| 276 | MixHop | 0.7784
±0.0773 best reported | best at pub: Graph Pointer Neural Networks (AAAI 2021) best today: Graph Navier–Stokes Networks (2026) Difference within reported uncertainty; not counted as underperformance. |
| 499 | PairNorm | 0.6030
±0.0430 | This paper |
| # | 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 | |
| 35 | GCNII | 0.8918
±0.0396 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 38 | FAGCN | 0.8852
±0.0133 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 117 | EGNN | 0.8380
±0.0460 | prev best: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) Improvement within reported uncertainty; not highlighted. |
| 129 | UFG | 0.8320
±0.0030 best reported | |
| 138 | SAGE | 0.8269 | |
| 142 | GRAND | 0.8220
±0.0710 | prev best: Understanding convolution on graphs via energies (TMLR 2022) Improvement within reported uncertainty; not highlighted. |
| 147 | EE-UFG | 0.8220
±0.0280 | This paper |
| 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) |
| 183 | MixHop | 0.7950
±0.0630 best reported | best at pub: Label-Wise Graph Convolutional Network for Heterophilic Graphs (2021) Difference within reported uncertainty; not counted as underperformance. |
| 389 | PairNorm | 0.5892
±0.0315 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. |
