Disentangled and Self-Explainable Node Representation Learning
Abstract
Node embeddings are low-dimensional vectors that capture node properties, typically learned through unsupervised structural similarity objectives or supervised tasks. While recent efforts have focused on post-hoc explanations for graph models, intrinsic interpretability in unsupervised node embeddings remains largely underexplored. To bridge this gap, we introduce DiSeNE (Disentangled and Self-Explainable Node Embedding), a framework that learns self-explainable node representations in an unsupervised fashion. By leveraging disentangled representation learning, DiSeNE ensures that each embedding dimension corresponds to a distinct topological substructure of the graph, thus offering clear, dimension-wise interpretability. We introduce new objective functions grounded in principled desiderata, jointly optimizing for structural fidelity, disentanglement, and human interpretability. Additionally, we propose several new metrics to evaluate representation quality and human interpretability. Extensive experiments on multiple benchmark datasets demonstrate that DiSeNE not only preserves the underlying graph structure but also provides transparent, human-understandable explanations for each embedding dimension.
Benchmark Results
Tested on 1 dataset 2 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
PPI
Global leaderboard →Default metric is F1. The paper reports 9 values on F1 , 9 values on Topological Alignment and 2 values on Overlap Consistency .
| # | Model | F1 ↑ default | Topological Alignment ↑ | Overlap Consistency ↑ | Paper |
|---|---|---|---|---|---|
| 1 | GAMLP(JK) | 0.9982
±
0.0001 | — | — | Topological Alignment
— Overlap Consistency
— |
| 2 | GraphCON-GCN | 0.9960 | — | — | Topological Alignment
— Overlap Consistency
— |
| 3 | GCNII | 0.9953
±
0.0001 | — | — | Topological Alignment
— Overlap Consistency
— |
| 21 | GCN | 0.9850 | — | — | Topological Alignment
— Overlap Consistency
— |
| 85 | DiSe-GAE | 0.9370
±
0.0010 | 0.5150
±
0.0010 | 0.9370
±
0.0010 | Topological Alignment
0.5150
±
0.0010 Overlap Consistency
0.9370
±
0.0010 |
| 86 | DiSe-FCAE | 0.9340
±
0.0030 | 0.4840
±
0.0010 | 0.9340
±
0.0030 | Topological Alignment
0.4840
±
0.0010 Overlap Consistency
0.9340
±
0.0030 |
| 94 | DW+Dine | 0.8550
±
0.0160 | 0.5690
±
0.0220 | — | Topological Alignment
0.5690
±
0.0220 Overlap Consistency
— |
| 101 | GraphSAGE | 0.7860 best reported | 0.3060
±
0.0050 | — | Topological Alignment
0.3060
±
0.0050 Overlap Consistency
— best at pub: Optimization-Induced Graph Implicit Nonlinear Diffusion (ICML 2022) |
| 146 | GAE+Dine | 0.6460
±
0.0030 | 0.4840
±
0.0070 | — | Topological Alignment
0.4840
±
0.0070 Overlap Consistency
— |
| 164 | DeepWalk | 0.5290 best reported | 0.2810
±
0.0020 | — | Topological Alignment
0.2810
±
0.0020 Overlap Consistency
— best at pub: Sub-graph Contrast for Scalable Self-Supervised Graph Representation Learning (2020) |
| 173 | MLP | 0.4620 | — | — | Topological Alignment
— Overlap Consistency
— |
| 174 | GraphAE | 0.4520
±
0.0080 | 0.2630
±
0.0030 | — | Topological Alignment
0.2630
±
0.0030 Overlap Consistency
— |
| 180 | InfWalk | 0.1340
±
0.0020 | 0.3120
±
0.0020 | — | Topological Alignment
0.3120
±
0.0020 Overlap Consistency
— |
| 181 | DGLFRM | 0.1020
±
0.0020 | 0.5150
±
0.0080 | — | Topological Alignment
0.5150
±
0.0080 Overlap Consistency
— |
