SE-GSL: A General and Effective Graph Structure Learning Framework through Structural Entropy Optimization
Abstract
Graph Neural Networks (GNNs) are de facto solutions to structural data learning. However, it is susceptible to low-quality and unreliable structure, which has been a norm rather than an exception in real-world graphs. Existing graph structure learning (GSL) frameworks still lack robustness and interpretability. This paper proposes a general GSL framework, SE-GSL, through structural entropy and the graph hierarchy abstracted in the encoding tree. Particularly, we exploit the one-dimensional structural entropy to maximize embedded information content when auxiliary neighbourhood attributes is fused to enhance the original graph. A new scheme of constructing optimal encoding trees is proposed to minimize the uncertainty and noises in the graph whilst assuring proper community partition in hierarchical abstraction. We present a novel sample-based mechanism for restoring the graph structure via node structural entropy distribution. It increases the connectivity among nodes with larger uncertainty in lower-level communities. \ SE-GSL\ is compatible with various GNN models and enhances the robustness towards noisy and heterophily structures. Extensive experiments show significant improvements in the effectiveness and robustness of structure learning and node representation learning.
Benchmark Results
Tested on 3 datasets 16 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 | |
| 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) |
| 193 | SE-GSL | 0.8249
±0.0480 | This paper |
| 204 | H_2GCN-2 | 0.8216
±0.0528 | This paper |
| 211 | GAT | 0.8162
±0.0645 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) 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: Understanding convolution on graphs via energies (TMLR 2022) best today: When Graph Neural Networks Meet Dynamic Mode Decomposition (ICLR 2024) |
| 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) |
| 273 | GEN | 0.7830
±0.0800 best reported | best at pub: ES-GNN: Generalizing Graph Neural Networks Beyond Homophily with Edge Splitting (2022) Difference within reported uncertainty; not counted as underperformance. |
| 276 | MixHop | 0.7784
±0.0773 best reported | best at pub: Graph Pointer Neural Networks (AAAI 2021) best today: Graph Navier–Stokes Networks (2026) |
| 514 | DropEdge | 0.5946
±0.0811 best reported | best today: A Signed Graph Approach to Understanding and Mitigating Oversmoothing in GNNs (NeurIPS 2025) Difference within reported uncertainty; not counted as underperformance. |
| 557 | GDC | 0.5642
±0.0399 | 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) |
| 138 | SAGE | 0.8269 | |
| 142 | GRAND | 0.8246
±0.0709 best reported | best at pub: Understanding convolution on graphs via energies (TMLR 2022) best today: Graph Navier–Stokes Networks (2026) |
| 158 | GAT | 0.8190
±0.0540 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 168 | GEN | 0.8100
±0.0390 best reported | best at pub: ES-GNN: Generalizing Graph Neural Networks Beyond Homophily with Edge Splitting (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) |
| 230 | SE-GSL | 0.7521
±0.0554 | This paper |
| 374 | DropEdge | 0.6054
±0.0530 best reported | best today: Graph Neural Networks with a Distribution of Parametrized Graphs (ICML 2023) Difference within reported uncertainty; not counted as underperformance. |
| 381 | GDC | 0.5946
±0.0435 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DiGGR | 0.4535
±0.0353 | |
| 2 | TRIGON | 0.4402
±0.0028 | |
| 3 | DoG | 0.4320
±0.0120 | |
| 38 | GCNII | 0.4082
±0.0179 best reported | best at pub: Understanding convolution on graphs via energies (TMLR 2022) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 42 | MLP | 0.4026
±0.0108 | |
| 68 | GraphSAGE | 0.3899
±0.0085 | |
| 119 | GEN | 0.3730
±0.0140 best reported | best at pub: ES-GNN: Generalizing Graph Neural Networks Beyond Homophily with Edge Splitting (2022) 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) |
| 144 | DropEdge | 0.3680
±0.0290 best reported | |
| 162 | MixHop | 0.3648
±0.0120 best reported | best at pub: Deformable Graph Transformer (2022) best today: Towards Deep Attention in Graph Neural Networks: Problems and Remedies (ICML 2023) |
| 171 | SE-GSL | 0.3634
±0.0207 | This paper |
| 182 | GAT | 0.3605
±0.0035 best reported | best at pub: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) |
| 203 | GRAND | 0.3562
±0.0101 best reported | best at pub: Understanding convolution on graphs via energies (TMLR 2022) best today: Graph Navier–Stokes Networks (2026) |
| 380 | GDC | 0.2874
±0.0076 | This paper |
