Teaching MLP More Graph Information: A Three-stage Multitask Knowledge Distillation Framework.
Abstract
We study the challenging problem for inference tasks on large-scale graph datasets of Graph Neural Networks: huge time and memory consumption, and try to overcome it by reducing reliance on graph structure. Even though distilling graph knowledge to student MLP is an excellent idea, it faces two major problems of positional information loss and low generalization. To solve the problems, we propose a new three-stage multitask distillation framework. In detail, we use Positional Encoding to capture positional information. Also, we introduce Neural Heat Kernels responsible for graph data processing in GNN and utilize hidden layer outputs matching for better performance of student MLP's hidden layers. To the best of our knowledge, it is the first work to include hidden layer distillation for student MLP on graphs and to combine graph Positional Encoding with MLP. We test its performance and robustness with several settings and draw the conclusion that our work can outperform well with good stability.
Benchmark Results
Tested on 5 datasets 13 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: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 39 | SAGE | 0.8911
±0.0012 best reported | best at pub: Efficient Tuning and Inference for Large Language Models on Textual Graphs (IJCAI 2024) 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) |
| 141 | GraphSAGE | 0.8708
±0.0085 | |
| 611 | KMP+PE | 0.8097
±0.0103 | This paper |
| 636 | KMP(GAT) | 0.8044
±0.0113 | This paper |
| 665 | GLNN(GAT) | 0.7989
±0.0144 | This paper |
| 685 | SA-MLP | 0.7933
±0.0155 | This paper |
| 724 | MLP | 0.7768 best reported | best at pub: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | CNA | 0.9575
±0.0058 | |
| 2 | IS-GIB | 0.9390
±0.0187 | |
| 3 | EERM | 0.9112
±0.0145 | |
| 35 | GAT | 0.8080
±0.0026 best reported | best at pub: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 44 | GCN | 0.8033
±0.0088 best reported | best at pub: Gophormer: Ego-Graph Transformer for Node Classification (2021) |
| 61 | GraphSAGE | 0.7923
±0.0053 | |
| 350 | MLP | 0.7289
±0.0010 | |
| 362 | KMP(GAT) | 0.7272
±0.0118 | This paper |
| 406 | GLNN(GAT) | 0.7244
±0.0163 | 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 | |
| 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) |
| 116 | SAGE | 0.8881
±0.0015 best reported | best at pub: Marginal Nodes Matter: Towards Structure Fairness in Graphs (KDD 2023) best today: Efficient Text-Attributed Graph Learning through Selective Annotation and Graph Alignment (TMLR 2025) |
| 125 | GraphSAGE | 0.8864
±0.0030 | |
| 210 | MLP | 0.8690
±0.0074 best reported | best at pub: On the Equivalence of Graph Convolution and Mixup (TMLR 2023) |
| 645 | KMP(GCN) | 0.7848
±0.0190 | This paper |
| 685 | GLNN(GCN) | 0.7794
±0.0295 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9703
±0.0019 | |
| 2 | GAT | 0.9669
±0.0014 best reported | |
| 3 | GAT+T | 0.9660
±0.0007 | |
| 7 | SAGE | 0.9643
±0.0027 best reported | best at pub: Training MLPs on Graphs without Supervision (2024) |
| 8 | GCN | 0.9632
±0.0008 best reported | |
| 56 | GraphSAGE | 0.9508
±0.0026 | |
| 197 | KMP(GAT) | 0.9319
±0.0078 | This paper |
| 221 | GLNN(GAT) | 0.9301
±0.0094 | This paper |
| 305 | KMP+PE | 0.9238
±0.0082 | This paper |
| 390 | MLP | 0.9128
±0.0063 best reported | best at pub: Clarify Confused Nodes via Separated Learning (2023) |
| 418 | SA-MLP | 0.9067
±0.0093 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9461
±0.0017 | |
| 2 | GCN | 0.9412
±0.0008 | |
| 3 | GAT | 0.9398
±0.0022 | |
| 8 | SAGE | 0.9351
±0.0006 | |
| 310 | KMP+PE | 0.8510
±0.0166 | This paper |
| 318 | KMP(SAGE) | 0.8475
±0.0110 | This paper |
| 320 | MLP | 0.8463 |
