Extract the Knowledge of Graph Neural Networks and Go Beyond it: An Effective Knowledge Distillation Framework
Abstract
Semi-supervised learning on graphs is an important problem in the machine learning area. In recent years, state-of-the-art classification methods based on graph neural networks (GNNs) have shown their superiority over traditional ones such as label propagation. However, the sophisticated architectures of these neural models will lead to a complex prediction mechanism, which could not make full use of valuable prior knowledge lying in the data, e.g., structurally correlated nodes tend to have the same class. In this paper, we propose a framework based on knowledge distillation to address the above issues. Our framework extracts the knowledge of an arbitrary learned GNN model (teacher model), and injects it into a well-designed student model. The student model is built with two simple prediction mechanisms, i.e., label propagation and feature transformation, which naturally preserves structure-based and feature-based prior knowledge, respectively. In specific, we design the student model as a trainable combination of parameterized label propagation and feature transformation modules. As a result, the learned student can benefit from both prior knowledge and the knowledge in GNN teachers for more effective predictions. Moreover, the learned student model has a more interpretable prediction process than GNNs. We conduct experiments on five public benchmark datasets and employ seven GNN models including GCN, GAT, APPNP, SAGE, SGC, GCNII and GLP as the teacher models. Experimental results show that the learned student model can consistently outperform its corresponding teacher model by $1.4\
Benchmark Results
Tested on 4 datasets 14 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphSAGE+CNA | 0.9418
±0.0033 | |
| 2 | GCN+CNA | 0.9366
±0.0048 | |
| 3 | TransformerConv | 0.9350
±0.0058 | |
| 21 | GCN | 0.9004 best reported | best at pub: SplineCNN: Fast Geometric Deep Learning with Continuous B-Spline Kernels (2017) best today: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 39 | SAGE | 0.8911
±0.0012 best reported | best today: Efficient Text-Attributed Graph Learning through Selective Annotation and Graph Alignment (TMLR 2025) |
| 44 | GAT | 0.8897
±0.0014 best reported | best at pub: Learned Low Precision Graph Neural Networks (2020) |
| 45 | GCNII | 0.8893
±0.0137 best reported | best today: Large Language Model Meets Graph Neural Network in Knowledge Distillation (AAAI 2024) |
| 108 | APPNP | 0.8787 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) best today: Feature Transportation Improves Graph Neural Networks (AAAI 2023) |
| 141 | GraphSAGE | 0.8708
±0.0085 | |
| 191 | CPF-tra | 0.8590 | This paper |
| 194 | CPF-ind | 0.8581 | This paper |
| 223 | SGC | 0.8509
±0.0648 best reported | best at pub: Learning Conjoint Attentions for Graph Neural Nets (NeurIPS 2021) |
| 269 | FT | 0.8431 | This paper |
| 338 | GLP | 0.8365 | This paper |
| 724 | MLP | 0.7768 | |
| 746 | PLP | 0.7663 | This paper |
| # | 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) |
| 35 | GAT | 0.8080
±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 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 | |
| 96 | SGC | 0.7765
±0.0012 best reported | best at pub: Deep Learning on Graphs: A Survey (2018) |
| 113 | CPF-ind | 0.7696 | This paper |
| 114 | CPF-tra | 0.7696 | This paper |
| 138 | FT | 0.7597 | This paper |
| 166 | GLP | 0.7536 | This paper |
| 259 | SAGE | 0.7361
±0.0190 best reported | best today: Efficient Tuning and Inference for Large Language Models on Textual Graphs (IJCAI 2024) Difference within reported uncertainty; not counted as underperformance. |
| 350 | MLP | 0.7289
±0.0010 | |
| 680 | PLP | 0.6812 | This paper |
| # | 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) |
| 20 | GAT | 0.9233
±0.0018 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 58 | GCNII | 0.9030
±0.0043 best reported | |
| 116 | SAGE | 0.8881
±0.0015 best reported | best today: Efficient Text-Attributed Graph Learning through Selective Annotation and Graph Alignment (TMLR 2025) |
| 125 | GraphSAGE | 0.8864
±0.0030 | |
| 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 | |
| 326 | CPF-tra | 0.8210 | This paper |
| 354 | CPF-ind | 0.8133 | This paper |
| 371 | FT | 0.8102 | This paper |
| 381 | GLP | 0.8088 | This paper |
| 845 | PLP | 0.6913 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9461
±0.0017 | |
| 2 | GCN | 0.9412
±0.0008 best reported | best at pub: Learning on Attribute-Missing Graphs (2020) |
| 3 | GAT | 0.9398
±0.0022 best reported | best at pub: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) |
| 8 | SAGE | 0.9351
±0.0006 best reported | |
| 46 | GraphSAGE | 0.9120
±0.0029 | |
| 52 | GCNII | 0.8325 | best today: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) |
| 58 | APPNP | 0.9093
±0.0018 best reported | best at pub: A Unified View on Graph Neural Networks as Graph Signal Denoising (2020) |
| 82 | SGC | 0.9022
±0.0021 best reported | |
| 319 | CPF-ind | 0.8467 | This paper |
| 320 | MLP | 0.8463 | |
| 328 | CPF-tra | 0.8447 | This paper |
| 346 | FT | 0.8411 | This paper |
| 447 | PLP | 0.7628 | This paper |
