Graph Information Bottleneck for Subgraph Recognition
Abstract
Given the input graph and its label/property, several key problems of graph learning, such as finding interpretable subgraphs, graph denoising and graph compression, can be attributed to the fundamental problem of recognizing a subgraph of the original one. This subgraph shall be as informative as possible, yet contains less redundant and noisy structure. This problem setting is closely related to the well-known information bottleneck (IB) principle, which, however, has less been studied for the irregular graph data and graph neural networks (GNNs). In this paper, we propose a framework of Graph Information Bottleneck (GIB) for the subgraph recognition problem in deep graph learning. Under this framework, one can recognize the maximally informative yet compressive subgraph, named IB-subgraph. However, the GIB objective is notoriously hard to optimize, mostly due to the intractability of the mutual information of irregular graph data and the unstable optimization process. In order to tackle these challenges, we propose: i) a GIB objective based-on a mutual information estimator for the irregular graph data; ii) a bi-level optimization scheme to maximize the GIB objective; iii) a connectivity loss to stabilize the optimization process. We evaluate the properties of the IB-subgraph in three application scenarios: improvement of graph classification, graph interpretation and graph denoising. Extensive experiments demonstrate that the information-theoretic IB-subgraph enjoys superior graph properties.
Benchmark Results
Tested on 3 datasets 1 baseline value 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 | |
| 39 | GIN | 0.9330
±0.0290 best reported | best at pub: Provably Powerful Graph Networks (NeurIPS 2019) best today: ProtGNN: Towards Self-Explaining Graph Neural Networks (AAAI 2021) |
| 63 | GCN | 0.9220
±0.0440 best reported | best at pub: Graph Neural Networks With Convolutional ARMA Filters (2019) best today: Depth-Adaptive Graph Neural Networks via Learnable Bakry-Émery Curvature (KDD 2025) |
| 158 | GraphSAGE | 0.9040
±0.0780 best reported | best at pub: Graph Neural Networks With Convolutional ARMA Filters (2019) best today: Asynchronous Neural Networks for Learning in Graphs (2022) |
| 183 | GAT | 0.9010
±0.0580 best reported | best at pub: Quaternion Graph Neural Networks (2020) best today: The Expressive Power of Graph Neural Networks: A Survey (2023) |
| 190 | SortPool | 0.8440
±0.1410 | prev best: Fast Graph Representation Learning with PyTorch Geometric (ICLR 2019) Improvement within reported uncertainty; not highlighted. |
| 239 | DiffPool | 0.8940
±0.0460 best reported | best at pub: Fast Graph Representation Learning with PyTorch Geometric (ICLR 2019) best today: Graph Classification via Reference Distribution Learning: Theory and Practice (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 403 | MLP | 0.8660
±0.0495 | |
| 494 | GIN+GIB | 0.8390
±0.0640 | This paper |
| 589 | EdgePool | 0.8101
±0.0082 best reported | best today: Embedding Graphs on Grassmann Manifold (2022) Difference within reported uncertainty; not counted as underperformance. |
| 672 | GCN+GIB | 0.7760
±0.0750 | This paper |
| 697 | GraphSAGE+GIB | 0.7600
±0.0740 | This paper |
| 717 | GAT+GIB | 0.7490
±0.0970 | This paper |
| 718 | SAGE | 0.7490
±0.0870 | |
| 722 | ASAPool | 0.7430
±0.0770 | This paper |
| 750 | AttPool | 0.7210
±0.0860 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MSH-GNN | 0.9410
±0.0330 | |
| 2 | GRDL | 0.8260
±0.0120 | |
| 3 | GMN | 0.8225 | |
| 7 | DiffPool | 0.8161
±0.0232 best reported | best at pub: Memory-Based Graph Networks (ICLR 2020) |
| 32 | GIN | 0.7880
±0.0410 best reported | best at pub: Multi-grained Semantics-aware Graph Neural Networks (2020) best today: Permutation-Invariant graph partitioning: How graph neural networks capture structural interactions? (2023) Difference within reported uncertainty; not counted as underperformance. |
| 49 | GAT | 0.7800
±0.0300 best reported | |
| 67 | SAGE | 0.7726
±0.0228 | |
| 148 | GCN | 0.7600
±0.0320 best reported | best at pub: Graph Convolutional Networks with EigenPooling (KDD 2019) 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 | |
| 152 | SortPool | 0.7598
±0.0176 best reported | best at pub: Memory-Based Graph Networks (ICLR 2020) best today: Graph Structure Prompt Learning: A Novel Methodology to Improve Performance of Graph Neural Networks (2024) Difference within reported uncertainty; not counted as underperformance. |
| 155 | GraphSAGE | 0.7590
±0.0320 best reported | best at pub: Graph Convolutional Networks with EigenPooling (KDD 2019) best today: Simplifying Graph Convolutional Networks with Redundancy-Free Neighbors (2025) Difference within reported uncertainty; not counted as underperformance. |
| 184 | EdgePool | 0.7560
±0.0240 best reported | best today: Embedding Graphs on Grassmann Manifold (2022) Difference within reported uncertainty; not counted as underperformance. |
| 261 | GIN+GIB | 0.7490
±0.0510 | This paper |
| 272 | GCN+GIB | 0.7480
±0.0460 | This paper |
| 329 | GAT+GIB | 0.7370
±0.0440 | This paper |
| 347 | GraphSAGE+GIB | 0.7340
±0.0430 | This paper |
| 373 | AttPool | 0.7280
±0.0410 | This paper |
| 397 | ASAPool | 0.7232
±0.0291 best reported | best today: Graph Structure Prompt Learning: A Novel Methodology to Improve Performance of Graph Neural Networks (2024) Difference within reported uncertainty; not counted as underperformance. |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | ID-GNN+BEC | 0.8150
±0.0240 | |
| 2 | GIN+BEC | 0.8080
±0.0330 | |
| 3 | GCN+BEC | 0.7990
±0.0340 | |
| 4 | GCN | 0.7980
±0.0230 best reported | best at pub: Contrastive Multi-View Representation Learning on Graphs (ICML 2020) best today: Depth-Adaptive Graph Neural Networks via Learnable Bakry-Émery Curvature (KDD 2025) |
| 14 | GIN | 0.7810
±0.0350 best reported | best at pub: Graph Homomorphism Convolution (ICML 2020) best today: Depth-Adaptive Graph Neural Networks via Learnable Bakry-Émery Curvature (KDD 2025) Difference within reported uncertainty; not counted as underperformance. |
| 56 | GAT | 0.7130
±0.0420 | prev best: Contrastive Multi-View Representation Learning on Graphs (ICML 2020) Improvement within reported uncertainty; not highlighted. |
| 60 | GIN+GIB | 0.7370
±0.0700 | This paper |
| 78 | DiffPool | 0.7314
±0.0070 best reported | best today: Cluster-wise Graph Transformer with Dual-granularity Kernelized Attention (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 84 | GAT+GIB | 0.7290
±0.0460 | This paper |
| 90 | EdgePool | 0.7280
±0.0440 | This paper |
| 99 | GraphSAGE | 0.7230
±0.0530 best reported | best at pub: Contrastive Multi-View Representation Learning on Graphs (ICML 2020) Difference within reported uncertainty; not counted as underperformance. |
| 100 | AttPool | 0.7220
±0.0470 | This paper |
| 101 | GCN+GIB | 0.7220
±0.0390 | This paper |
| 103 | SAGE | 0.7217
±0.0529 | |
| 104 | SortPool | 0.7212
±0.0112 best reported | best today: Cluster-wise Graph Transformer with Dual-granularity Kernelized Attention (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 110 | GraphSAGE+GIB | 0.7190
±0.0520 | This paper |
| 120 | ASAPool | 0.7150
±0.0440 | This paper |
