Recognizing Predictive Substructures with Subgraph Information Bottleneck
Abstract
The emergence of Graph Convolutional Network (GCN) has greatly boosted the progress of graph learning. However, two disturbing factors, noise and redundancy in graph data, and lack of interpretation for prediction results, impede further development of GCN. One solution is to recognize a predictive yet compressed subgraph to get rid of the noise and redundancy and obtain the interpretable part of the graph. This setting of subgraph is similar to the information bottleneck (IB) principle, which is less studied on graph-structured data and GCN. Inspired by the IB principle, we propose a novel subgraph information bottleneck (SIB) framework to recognize such subgraphs, named IB-subgraph. However, the intractability of mutual information and the discrete nature of graph data makes the objective of SIB notoriously hard to optimize. To this end, we introduce a bilevel optimization scheme coupled with a mutual information estimator for irregular graphs. Moreover, we propose a continuous relaxation for subgraph selection with a connectivity loss for stabilization. We further theoretically prove the error bound of our estimation scheme for mutual information and the noise-invariant nature of IB-subgraph. Extensive experiments on graph learning and large-scale point cloud tasks demonstrate the superior property of IB-subgraph.
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: CogDL: A Comprehensive Library for Graph Deep Learning (WWW 2021) best today: ProtGNN: Towards Self-Explaining Graph Neural Networks (AAAI 2021) |
| 63 | GCN | 0.9220
±0.0440 best reported | best at pub: Hierarchical Graph Capsule Network (AAAI 2020) 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 | 0.9000
±0.0224 best reported | best at pub: CogDL: A Comprehensive Library for Graph Deep Learning (WWW 2021) 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. |
| 239 | DiffPool | 0.8940
±0.0460 best reported | best at pub: CogDL: A Comprehensive Library for Graph Deep Learning (WWW 2021) 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 | |
| 495 | GIN+SIB | 0.8390
±0.0640 | This paper |
| 589 | EdgePool | 0.8101
±0.0082 best reported | best at pub: Graph Information Bottleneck for Subgraph Recognition (ICLR 2020) best today: Embedding Graphs on Grassmann Manifold (2022) Difference within reported uncertainty; not counted as underperformance. |
| 673 | GCN+SIB | 0.7760
±0.0750 | This paper |
| 698 | GraphSAGE+SIB | 0.7600
±0.0740 | This paper |
| 708 | GAT+SIB+DropEdge | 0.7540
±0.0850 | This paper |
| 719 | GAT+SIB | 0.7490
±0.0970 | This paper |
| 718 | SAGE | 0.7490
±0.0870 | |
| 722 | ASAPool | 0.7430
±0.0770 | This paper |
| 723 | GAT +DropEdge | 0.7430
±0.0810 | 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: Hierarchical Graph Capsule Network (AAAI 2020) 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 at pub: Graph Information Bottleneck for Subgraph Recognition (ICLR 2020) best today: Embedding Graphs on Grassmann Manifold (2022) Difference within reported uncertainty; not counted as underperformance. |
| 264 | GIN+SIB | 0.7490
±0.0510 | This paper |
| 273 | GCN+SIB | 0.7480
±0.0460 | This paper |
| 331 | GAT+SIB | 0.7370
±0.0440 | This paper |
| 332 | GAT+SIB+DropEdge | 0.7370
±0.0370 | This paper |
| 349 | GraphSAGE+SIB | 0.7340
±0.0430 | This paper |
| 373 | AttPool | 0.7280
±0.0410 | This paper |
| 397 | ASAPool | 0.7232
±0.0291 best reported | best at pub: Graph Information Bottleneck for Subgraph Recognition (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. |
| 438 | GAT +DropEdge | 0.7110
±0.0430 | This paper |
| # | 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 | 0.7407
±0.0453 best reported | best at pub: Graph Information Bottleneck for Subgraph Recognition (ICLR 2020) best today: Pooling Architecture Search for Graph Classification (2021) Difference within reported uncertainty; not counted as underperformance. |
| 61 | GIN+SIB | 0.7370
±0.0700 | This paper |
| 78 | DiffPool | 0.7314
±0.0070 best reported | best at pub: Graph Information Bottleneck for Subgraph Recognition (ICLR 2020) best today: Cluster-wise Graph Transformer with Dual-granularity Kernelized Attention (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 81 | GAT+SIB+DropEdge | 0.7310
±0.0030 | This paper |
| 86 | GAT+SIB | 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. |
| 102 | GCN+SIB | 0.7220
±0.0390 | This paper |
| 100 | AttPool | 0.7220
±0.0470 | This paper |
| 103 | SAGE | 0.7217
±0.0529 | |
| 104 | SortPool | 0.7212
±0.0112 best reported | best at pub: Graph Information Bottleneck for Subgraph Recognition (ICLR 2020) best today: Cluster-wise Graph Transformer with Dual-granularity Kernelized Attention (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 111 | GraphSAGE+SIB | 0.7190
±0.0520 | This paper |
| 120 | ASAPool | 0.7150
±0.0440 | This paper |
| 127 | GAT +DropEdge | 0.7100
±0.0410 | This paper |
