Interpretable Prototype-based Graph Information Bottleneck
Abstract
The success of Graph Neural Networks (GNNs) has led to a need for understanding their decision-making process and providing explanations for their predictions, which has given rise to explainable AI (XAI) that offers transparent explanations for black-box models. Recently, the use of prototypes has successfully improved the explainability of models by learning prototypes to imply training graphs that affect the prediction. However, these approaches tend to provide prototypes with excessive information from the entire graph, leading to the exclusion of key substructures or the inclusion of irrelevant substructures, which can limit both the interpretability and the performance of the model in downstream tasks. In this work, we propose a novel framework of explainable GNNs, called interpretable Prototype-based Graph Information Bottleneck (PGIB), that incorporates prototype learning within the information bottleneck framework to provide prototypes with the key subgraph from the input graph that is important for the model prediction. This is the first work that incorporates prototype learning into the process of identifying the key subgraphs that have a critical impact on the prediction performance. Extensive experiments, including qualitative analysis, demonstrate that PGIB outperforms state-of-the-art methods in terms of both prediction performance and explainability. The source code of PGIB is available at.
Benchmark Results
Tested on 2 datasets 3 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
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 | |
| 8 | GSAT | 0.9637
±0.0215 best reported | |
| 39 | GIN | 0.9330
±0.0290 best reported | best at pub: ProtGNN: Towards Self-Explaining Graph Neural Networks (AAAI 2021) |
| 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) |
| 81 | ProtGNN | 0.9170
±0.0290 best reported | best at pub: ProtGNN: Towards Self-Explaining Graph Neural Networks (AAAI 2021) Difference within reported uncertainty; not counted as underperformance. |
| 158 | GraphSAGE | 0.9040
±0.0780 | |
| 183 | GAT | 0.9010
±0.0580 best reported | best at pub: Breaking the Limits of Message Passing Graph Neural Networks (ICML 2021) best today: The Expressive Power of Graph Neural Networks: A Survey (2023) |
| 299 | GIB | 0.8870
±0.0530 best reported | best at pub: Mind the Label Shift of Augmentation-based Graph OOD Generalization (2023) Difference within reported uncertainty; not counted as underperformance. |
| 403 | MLP | 0.8660
±0.0495 | |
| 592 | VGIB | 0.8100
±0.0663 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MSH-GNN | 0.9410
±0.0330 | |
| 2 | GRDL | 0.8260
±0.0120 | |
| 3 | GMN | 0.8225 | |
| 32 | GIN | 0.7880
±0.0410 best reported | |
| 49 | GAT | 0.7800
±0.0300 best reported | best at pub: CI-GNN: A Granger Causality-Inspired Graph Neural Network for Interpretable Brain Network-Based Psychiatric Diagnosis (2023) Difference within reported uncertainty; not counted as underperformance. |
| 67 | SAGE | 0.7726
±0.0228 | |
| 148 | GCN | 0.7600
±0.0320 best reported | best at pub: CI-GNN: A Granger Causality-Inspired Graph Neural Network for Interpretable Brain Network-Based Psychiatric Diagnosis (2023) best today: Simplifying Graph Convolutional Networks with Redundancy-Free Neighbors (2025) Difference within reported uncertainty; not counted as underperformance. |
| 149 | MLP | 0.7600
±0.0320 | |
| 223 | GIB | 0.7525
±0.0592 | This paper |
| 324 | ProtGNN | 0.7383
±0.0422 | This paper |
| 334 | VGIB | 0.7366
±0.0332 | This paper |
| 460 | GSAT | 0.6964
±0.0471 | This paper |
