Explainable Graph Representation Learning via Graph Pattern Analysis
Abstract
Explainable artificial intelligence (XAI) is an important area in the AI community, and interpretability is crucial for building robust and trustworthy AI models. While previous work has explored model-level and instance-level explainable graph learning, there has been limited investigation into explainable graph representation learning. In this paper, we focus on representation-level explainable graph learning and ask a fundamental question: What specific information about a graph is captured in graph representations? Our approach is inspired by graph kernels, which evaluate graph similarities by counting substructures within specific graph patterns. Although the pattern counting vector can serve as an explainable representation, it has limitations such as ignoring node features and being high-dimensional. To address these limitations, we introduce a framework (PXGL-GNN) for learning and explaining graph representations through graph pattern analysis. We start by sampling graph substructures of various patterns. Then, we learn the representations of these patterns and combine them using a weighted sum, where the weights indicate the importance of each graph pattern's contribution. We also provide theoretical analyses of our methods, including robustness and generalization. In our experiments, we show how to learn and explain graph representations for real-world data using pattern analysis. Additionally, we compare our method against multiple baselines in both supervised and unsupervised learning tasks to demonstrate its effectiveness.
Benchmark Results
Tested on 4 datasets 7 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 | |
| 20 | SAGNN | 0.9520
±0.0300 best reported | best at pub: The Expressive Power of Graph Neural Networks: A Survey (2023) Difference within reported uncertainty; not counted as underperformance. |
| 39 | GIN | 0.9330
±0.0290 best reported | best at pub: ProtGNN: Towards Self-Explaining Graph Neural Networks (AAAI 2021) |
| 50 | SAN | 0.9265
±0.0153 | This paper |
| 63 | GCN | 0.9220
±0.0440 | |
| 100 | ICL | 0.9134
±0.0219 | This paper |
| 158 | GraphSAGE | 0.9040
±0.0780 best reported | best at pub: Asynchronous Neural Networks for Learning in Graphs (2022) Difference within reported uncertainty; not counted as underperformance. |
| 239 | DiffPool | 0.8940
±0.0460 best reported | best at pub: Graph Classification via Reference Distribution Learning: Theory and Practice (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 266 | S2GAE | 0.8927
±0.0153 | prev best: Generative and Contrastive Paradigms Are Complementary for Graph Self-Supervised Learning (2023) Improvement within reported uncertainty; not highlighted. |
| 361 | SubGNN | 0.8752
±0.0237 | This paper |
| 403 | MLP | 0.8660
±0.0495 | |
| 425 | DGCNN | 0.8583
±0.0116 best reported | best at pub: Deep Learning on Attributed Graphs: A Journey from Graphs to Their Embeddings and Back (2018) best today: Graph Structure Refinement with Energy-based Contrastive Learning (AAAI 2024) Difference within reported uncertainty; not counted as underperformance. |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9954 | |
| 2 | GIN | 0.9934 best reported | best at pub: 1-WL Expressiveness Is (Almost) All You Need (2022) |
| 3 | GCN | 0.9727 | |
| 5 | DiffPool | 0.9210
±0.0260 best reported | best at pub: Where to Mask: Structure-Guided Masking for Graph Masked Autoencoders (IJCAI 2024) |
| 53 | ICL | 0.8345
±0.0178 | This paper |
| 72 | SAN | 0.8307
±0.0154 | This paper |
| 101 | SubGNN | 0.8258
±0.0179 | This paper |
| 112 | S2GAE | 0.8237
±0.0224 | prev best: Generative and Contrastive Paradigms Are Complementary for Graph Self-Supervised Learning (2023) Improvement within reported uncertainty; not highlighted. |
| 131 | GraphSAGE | 0.8200
±0.0100 best reported | best at pub: Weisfeiler and Leman Go Infinite: Spectral and Combinatorial Pre-Colorings (TMLR 2022) |
| 165 | SAGNN | 0.8129
±0.0122 | This paper |
| 373 | DGCNN | 0.7650
±0.0190 best reported | best at pub: GraphCrop: Subgraph Cropping for Graph Classification (2020) Difference within reported uncertainty; not counted as underperformance. |
| # | 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 | |
| 22 | SAGNN | 0.7980
±0.0380 best reported | best at pub: The Expressive Power of Graph Neural Networks: A Survey (2023) Difference within reported uncertainty; not counted as underperformance. |
| 32 | GIN | 0.7880
±0.0410 best reported | best at pub: Permutation-Invariant graph partitioning: How graph neural networks capture structural interactions? (2023) Difference within reported uncertainty; not counted as underperformance. |
| 67 | SAGE | 0.7726
±0.0228 | |
| 110 | S2GAE | 0.7647
±0.0112 | prev best: HC-GAE: The Hierarchical Cluster-based Graph Auto-Encoder for Graph Representation Learning (NeurIPS 2024) Improvement within reported uncertainty; not highlighted. |
| 124 | SubGNN | 0.7638
±0.0157 | This paper |
| 132 | DGCNN | 0.7626 best reported | best at pub: Orthogonal Graph Neural Networks (AAAI 2021) Difference within reported uncertainty; not counted as underperformance. |
| 149 | MLP | 0.7600
±0.0320 | |
| 155 | GraphSAGE | 0.7590
±0.0320 best reported | best at pub: On Structural Expressive Power of Graph Transformers (KDD 2023) best today: Simplifying Graph Convolutional Networks with Redundancy-Free Neighbors (2025) Difference within reported uncertainty; not counted as underperformance. |
| 183 | SAN | 0.7562
±0.0239 | This paper |
| 199 | ICL | 0.7544
±0.0126 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9792 | |
| 2 | MSH-GNN | 0.9640
±0.0070 | |
| 3 | CoCN | 0.8722
±0.0013 | |
| 11 | PXGL-GNN | 0.8396
±0.0159 | This paper |
| 21 | SAN | 0.8273
±0.0192 | prev best: Beyond Message Passing: Neural Graph Pattern Machine (ICML 2025) |
| 23 | GCN | 0.8260
±0.0220 | |
| 27 | S2GAE | 0.8235
±0.0234 | prev best: Revisiting Graph Autoencoders as Implicit Contrastive Learners (KDD 2024) Improvement within reported uncertainty; not highlighted. |
| 30 | GIN | 0.8220
±0.0210 best reported | best at pub: Scalable Expressiveness through Preprocessed Graph Perturbations (2024) |
| 33 | DiffPool | 0.8213
±0.0043 best reported | best at pub: Scalable Graph Compressed Convolutions (2024) |
| 56 | ICL | 0.8145
±0.0121 | This paper |
| 71 | SubGNN | 0.8126
±0.0153 | This paper |
| 129 | SAGNN | 0.7994
±0.0183 | This paper |
| 136 | GraphSAGE | 0.7970
±0.0170 best reported | best at pub: Quaternion Graph Neural Networks (2020) best today: SignGT: Signed Attention-based Graph Transformer for Graph Representation Learning (2023) Difference within reported uncertainty; not counted as underperformance. |
| 151 | MLP | 0.7920
±0.0240 | |
| 191 | DGCNN | 0.7759
±0.0224 | prev best: CogDL: A Comprehensive Library for Graph Deep Learning (WWW 2021) Improvement within reported uncertainty; not highlighted. |
