TMLR 2024

Disentangled and Self-Explainable Node Representation Learning

Simone Piaggesi, A. Panisson, Megha Khosla

Main figure for 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 .

#ModelF1 ↑ defaultTopological 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
——
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
This paper
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
This paper
94
DW+Dine
0.8550 ± 0.0160
0.5690 ± 0.0220
—
Topological Alignment 0.5690 ± 0.0220
Overlap Consistency —
This paper
101
GraphSAGE
0.7860
best reported
0.3060 ± 0.0050
—
Topological Alignment 0.3060 ± 0.0050
Overlap Consistency —
paper 0.0970 ±0.0400
paper 0.0970 ±0.0400 Δ at pub 0.6890
146
GAE+Dine
0.6460 ± 0.0030
0.4840 ± 0.0070
—
Topological Alignment 0.4840 ± 0.0070
Overlap Consistency —
This paper
164
DeepWalk
0.5290
best reported
0.2810 ± 0.0020
—
Topological Alignment 0.2810 ± 0.0020
Overlap Consistency —
paper 0.0150 ±0.0030
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 —
This paper
180
InfWalk
0.1340 ± 0.0020
0.3120 ± 0.0020
—
Topological Alignment 0.3120 ± 0.0020
Overlap Consistency —
This paper
181
DGLFRM
0.1020 ± 0.0020
0.5150 ± 0.0080
—
Topological Alignment 0.5150 ± 0.0080
Overlap Consistency —
This paper
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)