IJCAI 2025

Explainable Graph Representation Learning via Graph Pattern Analysis

Xudong Wang, Ziheng Sun, Chris Ding, Jicong Fan

Main figure for 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.

Proposed method: PXGL-GNN

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

#ModelAccuracy ↑Paper
1
MSH-GNN
0.9910 ±0.0030
2
ID-GNN+BEC
0.9830 ±0.0360
3
SupCosine
0.9830 ±0.0250
20
SAGNN
actual #20 vs paper #39 19 places worse
0.9520 ±0.0300
best reported
actual #20 vs paper #39 19 places worse
paper 0.9324 ±0.0251

Difference within reported uncertainty; not counted as underperformance.

paper 0.9324 ±0.0251 Δ at pub 0.0196
39
GIN
actual #39 vs paper #466 427 places worse
0.9330 ±0.0290
best reported
actual #39 vs paper #466 427 places worse
paper 0.8453 ±0.0238
paper 0.8453 ±0.0238 Δ at pub 0.0877
50
SAN
0.9265 ±0.0153
This paper
63
GCN
0.9220 ±0.0440
100
ICL
0.9134 ±0.0219
This paper
158
GraphSAGE
actual #158 vs paper #408 250 places worse
0.9040 ±0.0780
best reported
actual #158 vs paper #408 250 places worse
paper 0.8635 ±0.0131

Difference within reported uncertainty; not counted as underperformance.

paper 0.8635 ±0.0131 Δ at pub 0.0405
239
DiffPool
actual #239 vs paper #400 161 places worse
0.8940 ±0.0460
best reported
actual #239 vs paper #400 161 places worse
paper 0.8672 ±0.0195

Difference within reported uncertainty; not counted as underperformance.

paper 0.8672 ±0.0195 Δ at pub 0.0268
266
S2GAE
actual #266 vs paper #266
0.8927 ±0.0153
actual #266 vs paper #266
paper 0.8927 ±0.0153

Improvement within reported uncertainty; not highlighted.

paper 0.8927 ±0.0153 Δ at pub 0.0101
361
SubGNN
0.8752 ±0.0237
This paper
403
MLP
0.8660 ±0.0495
425
DGCNN
actual #425 vs paper #479 54 places worse
0.8583 ±0.0116
best reported
actual #425 vs paper #479 54 places worse
paper 0.8429 ±0.0116

Difference within reported uncertainty; not counted as underperformance.

paper 0.8429 ±0.0116 Δ at pub 0.0154 Δ today 0.0154
#ModelAccuracy ↑Paper
1
WL-MLP
0.9954
2
GIN
actual #2 vs paper #443 441 places worse
0.9934
best reported
actual #2 vs paper #443 441 places worse
paper 0.7336 ±0.0178
paper 0.7336 ±0.0178 Δ at pub 0.2598
3
GCN
0.9727
5
DiffPool
actual #5 vs paper #405 400 places worse
0.9210 ±0.0260
best reported
actual #5 vs paper #405 400 places worse
paper 0.7542 ±0.0216
paper 0.7542 ±0.0216 Δ at pub 0.1668
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
actual #112 vs paper #112
0.8237 ±0.0224
actual #112 vs paper #112
paper 0.8237 ±0.0224

Improvement within reported uncertainty; not highlighted.

paper 0.8237 ±0.0224 Δ at pub 0.0157
131
GraphSAGE
actual #131 vs paper #325 194 places worse
0.8200 ±0.0100
best reported
actual #131 vs paper #325 194 places worse
paper 0.7793 ±0.0204
paper 0.7793 ±0.0204 Δ at pub 0.0407
165
SAGNN
0.8129 ±0.0122
This paper
373
DGCNN
actual #373 vs paper #417 44 places worse
0.7650 ±0.0190
best reported
actual #373 vs paper #417 44 places worse
paper 0.7481 ±0.0153

Difference within reported uncertainty; not counted as underperformance.

paper 0.7481 ±0.0153 Δ at pub 0.0169
#ModelAccuracy ↑Paper
1
MSH-GNN
0.9410 ±0.0330
2
GRDL
0.8260 ±0.0120
3
GMN
0.8225
7
DiffPool
actual #7 vs paper #144 137 places worse
0.8161 ±0.0232
best reported
actual #7 vs paper #144 137 places worse
paper 0.7607 ±0.0162
22
SAGNN
actual #22 vs paper #183 161 places worse
0.7980 ±0.0380
best reported
actual #22 vs paper #183 161 places worse
paper 0.7561 ±0.0228

Difference within reported uncertainty; not counted as underperformance.

paper 0.7561 ±0.0228 Δ at pub 0.0419
32
GIN
actual #32 vs paper #349 317 places worse
0.7880 ±0.0410
best reported
actual #32 vs paper #349 317 places worse
paper 0.7338 ±0.0216

Difference within reported uncertainty; not counted as underperformance.

paper 0.7338 ±0.0216 Δ at pub 0.0542
67
SAGE
0.7726 ±0.0228
110
S2GAE
actual #110 vs paper #110
0.7647 ±0.0112
actual #110 vs paper #110
paper 0.7647 ±0.0112

Improvement within reported uncertainty; not highlighted.

paper 0.7647 ±0.0112 Δ at pub 0.0010
124
SubGNN
0.7638 ±0.0157
This paper
132
DGCNN
actual #132 vs paper #190 58 places worse
0.7626
best reported
actual #132 vs paper #190 58 places worse
paper 0.7553 ±0.0214
best at pub: Orthogonal Graph Neural Networks (AAAI 2021)

Difference within reported uncertainty; not counted as underperformance.

paper 0.7553 ±0.0214 Δ at pub 0.0073
149
MLP
0.7600 ±0.0320
155
GraphSAGE
actual #155 vs paper #302 147 places worse
0.7590 ±0.0320
best reported
actual #155 vs paper #302 147 places worse
paper 0.7421 ±0.0185

Difference within reported uncertainty; not counted as underperformance.

paper 0.7421 ±0.0185 Δ at pub 0.0169 Δ today 0.0169
183
SAN
0.7562 ±0.0239
This paper
199
ICL
0.7544 ±0.0126
This paper
#ModelAccuracy ↑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
actual #21 vs paper #21
0.8273 ±0.0192
actual #21 vs paper #21
paper 0.8273 ±0.0192
paper 0.8273 ±0.0192 Δ at pub 0.0828
23
GCN
0.8260 ±0.0220
27
S2GAE
actual #27 vs paper #27
0.8235 ±0.0234
actual #27 vs paper #27
paper 0.8235 ±0.0234

Improvement within reported uncertainty; not highlighted.

paper 0.8235 ±0.0234 Δ at pub 0.0015
30
GIN
actual #30 vs paper #232 202 places worse
0.8220 ±0.0210
best reported
actual #30 vs paper #232 202 places worse
paper 0.7583 ±0.0129
paper 0.7583 ±0.0129 Δ at pub 0.0637
33
DiffPool
actual #33 vs paper #165 132 places worse
0.8213 ±0.0043
best reported
actual #33 vs paper #165 132 places worse
paper 0.7877 ±0.0136
paper 0.7877 ±0.0136 Δ at pub 0.0336
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
actual #136 vs paper #222 86 places worse
0.7970 ±0.0170
best reported
actual #136 vs paper #222 86 places worse
paper 0.7637 ±0.0211

Difference within reported uncertainty; not counted as underperformance.

paper 0.7637 ±0.0211 Δ at pub 0.0333 Δ today 0.0333
151
MLP
0.7920 ±0.0240
191
DGCNN
actual #191 vs paper #191
0.7759 ±0.0224
actual #191 vs paper #191
paper 0.7759 ±0.0224

Improvement within reported uncertainty; not highlighted.

paper 0.7759 ±0.0224 Δ at pub 0.0014
SOTA performance (not significantly different from the best) Proposed method (this paper) Baseline / comparison (this paper) Global context (other papers) Best at pub — reported result worse than the best known when published (best reported in green) Best at pub — reported value improved over the best known when published