BiKT: Unleashing the potential of GNNs via Bi-directional Knowledge Transfer
Abstract
Based on the message-passing paradigm, there has been an amount of research proposing diverse and impressive feature propagation mechanisms to improve the performance of GNNs. However, less focus has been put on feature transformation, another major operation of the message-passing framework. In this paper, we first empirically investigate the performance of the feature transformation operation in several typical GNNs. Unexpectedly, we notice that GNNs do not completely free up the power of the inherent feature transformation operation. By this observation, we propose the Bi-directional Knowledge Transfer (BiKT), a plug-and-play approach to unleash the potential of the feature transformation operations without modifying the original architecture. Taking the feature transformation operation as a derived representation learning model that shares parameters with the original GNN, the direct prediction by this model provides a topological-agnostic knowledge feedback that can further instruct the learning of GNN and the feature transformations therein. On this basis, BiKT not only allows us to acquire knowledge from both the GNN and its derived model but promotes each other by injecting the knowledge into the other. In addition, a theoretical analysis is further provided to demonstrate that BiKT improves the generalization bound of the GNNs from the perspective of domain adaption. An extensive group of experiments on up to 7 datasets with 5 typical GNNs demonstrates that BiKT brings up to 0.5\
Benchmark Results
Tested on 3 datasets 3 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9461
±0.0017 | |
| 2 | GCN | 0.9412
±0.0008 best reported | best at pub: Clarify Confused Nodes via Separated Learning (2023) |
| 3 | GAT | 0.9398
±0.0022 best reported | |
| 8 | SAGE | 0.9351
±0.0006 | |
| 52 | GCNII | 0.8482
±0.0100 | prev best: Extract the Knowledge of Graph Neural Networks and Go Beyond it: An Effective Knowledge Distillation Framework (WWW 2021) best today: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) Improvement within reported uncertainty; not highlighted. |
| 126 | FAGCN | 0.8968
±0.0097 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 292 | BiKT-GCN | 0.8592
±0.0126 | This paper |
| 303 | BiKT-GCNII | 0.8540
±0.0107 | This paper |
| 311 | BiKT-FAGCN | 0.8507
±0.0115 | This paper |
| 320 | MLP | 0.8463 | |
| 327 | BiKT-GAT | 0.8448
±0.0117 | This paper |
| 336 | BiKT-MLP_GCNII | 0.8439
±0.0091 | This paper |
| 366 | BiKT-MixHop | 0.8358
±0.0117 | This paper |
| 384 | BiKT-MLP_MixHop | 0.8296
±0.0115 | This paper |
| 389 | BiKT-MLP_GAT | 0.8268
±0.0147 | This paper |
| 415 | BiKT-MLP_GCN | 0.8126
±0.0174 | This paper |
| 432 | MixHop | 0.7952
±0.0210 best reported | best at pub: Towards Deep Attention in Graph Neural Networks: Problems and Remedies (ICML 2023) Difference within reported uncertainty; not counted as underperformance. |
| 437 | BiKT-MLP_FAGCN | 0.7868
±0.0195 | This paper |
| 464 | MLP_GCN | 0.7269
±0.0091 | This paper |
| 467 | MLP_MixHop | 0.7130
±0.0131 | This paper |
| 468 | MLP_GCNII | 0.7128
±0.0110 | This paper |
| 474 | MLP_FAGCN | 0.7014
±0.0119 | This paper |
| 476 | MLP_GAT | 0.6968
±0.0109 | This paper |
TU Dortmund
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MSH-GNN | 0.9910
±0.0030 | |
| 2 | ID-GNN+BEC | 0.9830
±0.0360 | |
| 3 | SupCosine | 0.9830
±0.0250 | |
| 39 | GIN | 0.9330
±0.0290 best reported | best at pub: ProtGNN: Towards Self-Explaining Graph Neural Networks (AAAI 2021) Difference within reported uncertainty; not counted as underperformance. |
| 63 | GCN | 0.9220
±0.0440 best reported | best at pub: Breaking the Limits of Message Passing Graph Neural Networks (ICML 2021) best today: Depth-Adaptive Graph Neural Networks via Learnable Bakry-Émery Curvature (KDD 2025) Difference within reported uncertainty; not counted as underperformance. |
| 158 | GraphSAGE | 0.9040
±0.0780 | |
| 182 | BiKT-GIN | 0.9013
±0.0728 | This paper |
| 374 | BiKT-GCN | 0.8726
±0.0501 | This paper |
| 403 | MLP | 0.8660
±0.0495 |
OGB
| # | Model | ROC-AUC ↑ | Paper |
|---|---|---|---|
| 1 | Multi-RF Fusion with Multi-GNN Blending | 0.8476
±0.0002 | |
| 2 | HyperFusion | 0.8475
±0.0003 | |
| 3 | PAS+FPs | 0.8420
±0.0015 | |
| 9 | GatedGCN | 0.8090
±0.0160 | |
| 109 | GIN | 0.7780
±0.0182 best reported | best at pub: GRPE: Relative Positional Encoding for Graph Transformer (2022) Difference within reported uncertainty; not counted as underperformance. |
| 141 | BiKT-GCN | 0.7715
±0.0122 | This paper |
| 160 | GraphSAGE | 0.7690
±0.0136 | |
| 180 | BiKT-GIN | 0.7647
±0.0181 | This paper |
| 184 | GCN | 0.7630
±0.0030 best reported | best at pub: Motif-based Graph Representation Learning with Application to Chemical Molecules (2022) Difference within reported uncertainty; not counted as underperformance. |
