Steering Graph Neural Networks with Pinning Control
Abstract
In the semi-supervised setting where labeled data are largely limited, it remains to be a big challenge for message passing based graph neural networks (GNNs) to learn feature representations for the nodes with the same class label that is distributed discontinuously over the graph. To resolve the discontinuous information transmission problem, we propose a control principle to supervise representation learning by leveraging the prototypes (i.e., class centers) of labeled data. Treating graph learning as a discrete dynamic process and the prototypes of labeled data as “desired” class representations, we borrow the pinning control idea from automatic control theory to design learning feedback controllers for the feature learning process, attempting to minimize the differences between message passing derived features and the class prototypes in every round so as to generate class-relevant features. Specifically, we equip every node with an optimal controller in each round through learning the matching relationships between nodes and the class prototypes, enabling nodes to rectify the aggregated information from incompatible neighbors in a graph with strong heterophily. Our experiments demonstrate that the proposed PCGCN model achieves better performances than deep GNNs and other competitive heterophily-oriented methods, especially when the graph has very few labels and strong heterophily.
Benchmark Results
Tested on 3 datasets 19 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 | |
| 28 | GPRGNN | 0.9295
±0.0131 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 34 | MLP | 0.9230
±0.0070 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 39 | GGCN | 0.9213
±0.0305 best reported | best at pub: Understanding convolution on graphs via energies (TMLR 2022) best today: Graph Wave Networks (WWW 2025) |
| 53 | GraphSAGE | 0.9000
±0.0365 best reported | best at pub: Heterophily-Aware Graph Attention Network (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) |
| 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) |
| 124 | dynamic pinning control method | 0.8595
±0.0390 | This paper |
| 141 | GloGNN | 0.8524
±0.0490 best reported | best at pub: Finding Global Homophily in Graph Neural Networks When Meeting Heterophily (ICML 2022) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) Difference within reported uncertainty; not counted as underperformance. |
| 150 | H2GCN-1 | 0.8486
±0.0670 | This paper |
| 189 | SAGE | 0.8269 | |
| 203 | H2GCN-2 | 0.8216
±0.0520 | 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) |
| 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 | This paper |
| 325 | LINKX | 0.7460
±0.0837 | This paper |
| 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 | |
| 15 | GGCN | 0.9230
±0.0367 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) Difference within reported uncertainty; not counted as underperformance. |
| 22 | GPRGNN | 0.9157
±0.0196 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) best today: Simplified PCNet with Robustness (2024) Difference within reported uncertainty; not counted as underperformance. |
| 24 | MLP | 0.9136
±0.0070 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 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) |
| 74 | GloGNN | 0.8595
±0.0510 best reported | best at pub: GPNet: Simplifying Graph Neural Networks via Multi-channel Geometric Polynomials (2022) best today: Aggregation-aware MLP: An Unsupervised Approach for Graph Message-passing (2025) Difference within reported uncertainty; not counted as underperformance. |
| 78 | PCGCN | 0.8594
±0.0610 | This paper |
| 123 | LINKX | 0.8346
±0.0061 best reported | best at pub: GPNet: Simplifying Graph Neural Networks via Multi-channel Geometric Polynomials (2022) best today: Differentiable Cluster Graph Neural Network (2024) Difference within reported uncertainty; not counted as underperformance. |
| 138 | SAGE | 0.8269 | |
| 153 | H2GCN-1 | 0.8216
±0.0480 | This paper |
| 154 | H2GCN-2 | 0.8216
±0.0600 | 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. |
| 342 | Geom-GCN | 0.6412 | prev best: Graph Neural Networks Inspired by Classical Iterative Algorithms (ICML 2021) |
| # | 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 best reported | best at pub: Heterophily-Aware Graph Attention Network (2023) |
| 52 | GPRGNN | 0.3992
±0.0067 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 56 | FAGCN | 0.3970 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) |
| 58 | GloGNN | 0.3959
±0.0029 best reported | |
| 62 | GGCN | 0.3929
±0.0048 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) Difference within reported uncertainty; not counted as underperformance. |
| 68 | GraphSAGE | 0.3899
±0.0085 best reported | best at pub: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) best today: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) |
| 87 | Geom-GCN | 0.3810 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) |
| 135 | GCN | 0.3690 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) |
| 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) |
| 164 | dynamic pinning control method | 0.3643
±0.0090 | This paper |
| 165 | PCGCN | 0.3643
±0.0090 | This paper |
| 180 | LINKX | 0.3610
±0.0155 | This paper |
| 182 | GAT | 0.3605
±0.0035 best reported | best at pub: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) |
| 190 | H2GCN-1 | 0.3594
±0.0130 | Improvement within reported uncertainty; not highlighted. |
| 204 | H2GCN-2 | 0.3562
±0.0130 best reported | best at pub: NCGNN: Node-Level Capsule Graph Neural Network for Semisupervised Classification (2020) best today: From Node Interaction to Hop Interaction: New Effective and Scalable Graph Learning Paradigm (2022) Difference within reported uncertainty; not counted as underperformance. |
| 266 | GIN | 0.3410
±0.0030 |
