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.
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
| # | Model | Accuracy ↑ | 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 | 0.8748
±0.0020 | |
| 194 | GRACE | 0.8730
±0.0010 best reported | best at pub: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) |
| 204 | DGI | 0.8708
±0.0017 | prev best: Node Representation Learning in Graph via Node-to-Neighbourhood Mutual Information Maximization (2022) Improvement within reported uncertainty; not highlighted. |
| 208 | COSTA | 0.8698
±0.0033 | prev best: HomoGCL: Rethinking Homophily in Graph Contrastive Learning (KDD 2023) |
| 210 | MLP | 0.8690
±0.0074 | |
| 232 | GraphMAE | 0.8594
±0.0016 |
| # | Model | Accuracy ↑ | 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 | 0.9342
±0.0026 | prev best: Leveraging Label Non-Uniformity for Node Classification in Graph Neural Networks (ICML 2023) |
| 164 | GraphMAE | 0.9341
±0.0010 best reported | best at pub: Rethinking and Simplifying Bootstrapped Graph Latents (2023) Difference within reported uncertainty; not counted as underperformance. |
| 203 | GRACE | 0.9313
±0.0017 best reported | best at pub: Learning Graph Augmentations to Learn Graph Representations (2022) best today: Learn Beneficial Noise as Graph Augmentation (ICML 2025) |
| 213 | DGI | 0.9309
±0.0008 | prev best: Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-training Tasks (ICLR 2024) |
| 263 | COSTA | 0.9267
±0.0016 | prev best: Graph Soft-Contrastive Learning via Neighborhood Ranking (2022) Improvement within reported uncertainty; not highlighted. |
| 390 | MLP | 0.9128
±0.0063 |
