Causality-Driven Disentangled Representation Learning in Multiplex Graphs
Organizations: EPFL, Lausanne, Switzerland · Department of Electrical and Computer Engineering at Michigan State University, East Lansing, MI
Abstract
Learning representations from multiplex graphs, i.e., multi-layer networks where nodes interact through multiple relation types, is challenging due to the entanglement of shared (common) and layer-specific (private) information, which limits generalization and interpretability. In this work, we introduce a causal inference-based framework that disentangles common and private components in a self-supervised manner. CaDeM jointly (i) aligns shared embeddings across layers, (ii) enforces private embeddings to capture layer-specific signals, and (iii) applies backdoor adjustment to ensure that the common embeddings capture only global information while being separated from the private representations. Experiments on synthetic and real-world datasets demonstrate consistent improvements over existing baselines, highlighting the effectiveness of our approach for robust and interpretable multiplex graph representation learning.
Figures & tables
| Embeddings | Final labels | Labels of layer 1 | Labels of layer 2 | Labels of layer 3 | ||||
|---|---|---|---|---|---|---|---|---|
| Macro-F1 | Micro-F1 | Macro-F1 | Micro-F1 | Macro-F1 | Micro-F1 | Macro-F1 | Micro-F1 | |
| Combined embeddings | 0.8178 0.0516 | 0.8200 0.0510 | 0.9611 0.0476 | 0.9600 0.0490 | 0.9799 0.0246 | 0.9800 0.0245 | 0.9770 0.0282 | 0.9800 0.0245 |
| Private embeddings of the 1st layer | 0.8158 0.0545 | 0.8202 0.0511 | 0.9904 0.0191 | 0.9900 0.0200 | 0.4714 0.0917 | 0.4900 0.0663 | 0.2463 0.0533 | 0.2600 0.0374 |
| Private embeddings of the 2nd layer | 0.1946 0.0684 | 0.2200 0.0678 | 0.2502 0.1208 | 0.2600 0.1158 | 0.9476 0.0032 | 0.9500 0.0000 | 0.2774 0.0659 | 0.3500 0.0548 |
| Private embeddings of the 3rd layer | 0.3248 0.0483 | 0.3500 0.0316 | 0.3063 0.0274 | 0.3200 0.0245 | 0.3119 0.0896 | 0.3500 0.0949 | 0.9791 0.0260 | 0.9800 0.0245 |
| Models | Macro F1 | Micro F1 |
|---|---|---|
| DeepWalk | ||
| Node2Vec | ||
| VGAE | ||
| DGI | ||
| MVGRL | ||
| GraphMAE |
| Embeddings | Layer 1 clusters | Layer 2 clusters | ||
|---|---|---|---|---|
| ARI | NMI | ARI | NMI | |
| Common embedding | 0.0099 0.0590 | 0.0077 0.0227 | 0.0362 0.1345 | 0.0261 0.0910 |
| Private embedding of the 1st layer | 0.4935 0.0286 | 0.4066 0.0234 | -0.0734 0.0267 | 0.0348 0.0174 |
| Private embedding of the 2nd layer | -0.0911 0.0911 | 0.0450 0..0450 | 0.6441 0.0644 | 0.5405 0.0135 |
| Task | Embeddings | Macro-F1 score | Micro-F1 score |
|---|---|---|---|
| Multiplex graph classification (3 dynamical classes) | Combined graph embeddings | ||
| Common graph embeddings | |||
| Private graph embeddings (1st layer) | |||
| Private graph embeddings (2nd layer) | |||
| Single-layer graph classification (6 dynamical subclasses) | Private graph embeddings |
| Method | Macro F1 | Micro F1 |
|---|---|---|
| MVGRL | 0.3338 0.0529 | 0.3365 0.0520 |
| DGI | 0.6009 0.0208 | 0.6027 0.0240 |
| HDMI | 0.4038 0.0272 | 0.4188 0.0256 |
| DMG | 0.3983 0.0432 | 0.4032 0.0443 |
| Graph2Vec | 0.6033 0.0264 | 0.6192 0.0325 |
| CaDeM | 0.6628 0.0277 | 0.6659 0.0287 |
| Method | DBLP | IMDB | ACM | Freebase | ||||
|---|---|---|---|---|---|---|---|---|
| Macro-F1 | Micro-F1 | Macro-F1 | Micro-F1 | Macro-F1 | Micro-F1 | Macro-F1 | Micro-F1 | |
| DeepWalk | 0.5488 0.0130 | 0.5653 0.0134 | 0.4651 0.0283 | 0.4794 0.0276 | 0.8505 0.0167 | 0.8499 0.0157 | 0.5993 0.0203 | 0.6638 0.0195 |
| Node2Vec | 0.5433 0.0033 | 0.5681 0.0037 | 0.5663 0.0175 | 0.6000 0.0123 | 0.7249 0.0178 | 0.7226 0.0177 | 0.4732 0.0145 | 0.6254 0.0156 |
| VGAE | 0.8164 0.0105 | 0.8080 0.0101 | 0.6278 0.0142 | 0.6301 0.0129 | 0.9093 0.0084 | 0.9084 0.0085 | 0.5523 0.0112 | 0.6375 0.0052 |
| DGI | 0.7283 0.0130 | 0.7199 0.0120 | 0.5213 0.0658 | 0.5349 0.0548 | 0.9107 0.0128 | 0.9101 0.0132 | 0.5426 0.0116 | 0.6629 0.0072 |
| MVGRL | 0.7455 0.0063 | 0.7310 0.0073 | 0.6094 0.0120 | 0.6101 0.0110 | 0.9105 0.0032 | 0.9098 0.0032 | 0.5102 0.0210 | 0.6438 0.0167 |
| Syn1 | IMDB | ACM | Freebase | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Macro | Micro | Macro | Micro | Macro | Micro | Macro | Micro | |||
| ✓ | ✗ | ✗ | 0.7450 0.0520 | 0.7500 0.0447 | 0.6145 0.0196 | 0.6187 0.0180 | 0.8658 0.0142 | 0.8651 0.0142 | 0.5760 0.0187 | 0.6607 0.0136 |
| ✓ | ✓ | ✗ | 0.7673 0.1500 | 0.7700 0.1503 | 0.6599 0.0244 | 0.6617 0.0233 | 0.9152 0.0106 | 0.9147 0.0106 | 0.5807 0.0188 | 0.6615 0.0109 |
| ✓ | ✗ | ✓ | 0.7844 0.0477 | 0.7800 0.0510 | 0.6576 0.0125 | 0.6580 0.0109 | 0.9169 0.0100 | 0.9164 0.0101 | 0.6109 0.0101 | 0.6793 0.0035 |
| ✓ | ✓ | ✓ | 0.8178 0.0516 | 0.8200 0.0510 | 0.6667 0.0158 | 0.6682 0.0155 | 0.9287 0.0084 | 0.9283 0.0085 | 0.6224 0.0121 | 0.6887 0.0137 |
| Dataset | Task | #Clusters | Epochs | Learning rates | Loss weights | |||||
|---|---|---|---|---|---|---|---|---|---|---|
| Syn1 | Node classification | |||||||||
| Syn2 | Node clustering | |||||||||
| Syn3 | Node clustering | centers/layer | ||||||||
| Syn4 | Graph classification | classes (or subclasses) |
| Dynamics | Equation |
|---|---|
| Population dynamics | |
| Regulatory dynamics (degree-driven) | |
| Epidemic dynamics | |
| Biochemical dynamics | |
| Mutualistic dynamics | |
| Regulatory dynamics (degree-avert) |
| Parameter | HCP | DBLP | IMDB | ACM | Freebase |
|---|---|---|---|---|---|
| 360 | 7,907 | 3,550 | 3,025 | 3,492 | |
| 2 | 3 | 2 | 2 | 3 | |
| Downstream task | Graph classification | Node classification | Node classification | Node classification | Node classification |
| Number of classes | 3 | 4 | 3 | 3 | 3 |
| 20 | 20 | 20 | 20 | 30 | |
| 0.6 | 0.6 | 0.6 | 0.6 | 0.6 |
| Without augmentation | With augmentation | |||
|---|---|---|---|---|
| Dataset | Macro F1 | Micro F1 | Macro F1 | Micro F1 |
| IMDB | ||||
| ACM | ||||
| DBLP | ||||
| Freebase | ||||
| First synthetic data | ||||
Graph Representation Learning
Graph representation learning develops methods for encoding nodes, edges, and whole graphs for prediction, comparison, and transfer.
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