Noise-Resilient Unsupervised Graph Representation Learning via Multi-Hop Feature Quality Estimation

Shiyuan Li, Yixin Liu, Qingfeng Chen, Geoffrey I. Webb, Shirui Pan

Main figure for Noise-Resilient Unsupervised Graph Representation Learning via Multi-Hop Feature Quality Estimation

Abstract

Unsupervised graph representation learning (UGRL) based on graph neural networks (GNNs), has received increasing attention owing to its efficacy in handling graph-structured data. However, existing UGRL methods ideally assume that the node features are noise-free, which makes them fail to distinguish between useful information and noise when applied to real data with noisy features, thus affecting the quality of learned representations. This urges us to take node noisy features into account in real-world UGRL. With empirical analysis, we reveal that feature propagation, the essential operation in GNNs, acts as a ``double-edged sword'' in handling noisy features - it can both denoise and diffuse noise, leading to varying feature quality across nodes, even within the same node at different hops. Building on this insight, we propose a novel UGRL method based on ulti-hop feature uality stimation (MQE for short). Unlike most UGRL models that directly utilize propagation-based GNNs to generate representations, our approach aims to learn representations through estimating the quality of propagated features at different hops. Specifically, we introduce a Gaussian model that utilizes a learnable ``meta-representation'' as a condition to estimate the expectation and variance of multi-hop propagated features via neural networks. In this way, the ``meta representation'' captures the semantic and structural information underlying multiple propagated features but is naturally less susceptible to interference by noise, thereby serving as high-quality node representations beneficial for downstream tasks. Extensive experiments on multiple real-world datasets demonstrate that MQE in learning reliable node representations in scenarios with diverse types of feature noise.

Proposed method: MQE

Benchmark Results

Tested on 2 datasets 1 baseline value reported too low

Tables show presented results in global context (best 3 papers + GCN + MLP).

Classic

#ModelAccuracy ↑Paper
1
LGTL
0.9518 ±0.0011
2
MixHop (LO)
0.9513 ±0.0038
3
GraphSAGE (LO)
0.9511 ±0.0036
18
GCN
0.9296 ±0.0015
171
MQE
0.8773 ±0.0019
This paper
187
MaskGAE
actual #187 vs paper #187
0.8748 ±0.0020
actual #187 vs paper #187
paper 0.8748 ±0.0020
194
GRACE
actual #194 vs paper #228 34 places worse
0.8730 ±0.0010
best reported
actual #194 vs paper #228 34 places worse
paper 0.8610 ±0.0028
paper 0.8610 ±0.0028 Δ at pub 0.0120
204
DGI
actual #204 vs paper #204
0.8708 ±0.0017
actual #204 vs paper #204
paper 0.8708 ±0.0017

Improvement within reported uncertainty; not highlighted.

paper 0.8708 ±0.0017 Δ at pub 0.0005
208
COSTA
actual #208 vs paper #208
0.8698 ±0.0033
actual #208 vs paper #208
paper 0.8698 ±0.0033
paper 0.8698 ±0.0033 Δ at pub 0.0658
210
MLP
0.8690 ±0.0074
232
GraphMAE
actual #232 vs paper #232
0.8594 ±0.0016
actual #232 vs paper #232
paper 0.8594 ±0.0016
#ModelAccuracy ↑Paper
1
GraphTARIF
0.9703 ±0.0019
2
GAT
0.9669 ±0.0014
3
GAT+T
0.9660 ±0.0007
7
SAGE
0.9643 ±0.0027
77
MQE
0.9449 ±0.0017
This paper
161
MaskGAE
actual #161 vs paper #161
0.9342 ±0.0026
actual #161 vs paper #161
paper 0.9342 ±0.0026
paper 0.9342 ±0.0026 Δ at pub 0.0187
164
GraphMAE
actual #164 vs paper #184 20 places worse
0.9341 ±0.0010
best reported
actual #164 vs paper #184 20 places worse
paper 0.9327 ±0.0031

Difference within reported uncertainty; not counted as underperformance.

paper 0.9327 ±0.0031 Δ at pub 0.0014
203
GRACE
actual #203 vs paper #268 65 places worse
0.9313 ±0.0017
best reported
actual #203 vs paper #268 65 places worse
paper 0.9262 ±0.0023
paper 0.9262 ±0.0023 Δ at pub 0.0018 Δ today 0.0051
213
DGI
actual #213 vs paper #213
0.9309 ±0.0008
actual #213 vs paper #213
paper 0.9309 ±0.0008
paper 0.9309 ±0.0008 Δ at pub 0.0109
263
COSTA
actual #263 vs paper #263
0.9267 ±0.0016
actual #263 vs paper #263
paper 0.9267 ±0.0016

Improvement within reported uncertainty; not highlighted.

paper 0.9267 ±0.0016 Δ at pub 0.0011
390
MLP
0.9128 ±0.0063
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 Best today — OK at publication; today's leaderboard best is elsewhere