# Delving into Instance-Dependent Label Noise in Graph Data: A Comprehensive Study and Benchmark

arXiv: https://arxiv.org/abs/2506.12468 · HTML: https://mlsanity.com/paper/2506.12468/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- Builds on 38 of its 72 references that are in the map.
- First posted on arXiv 14 Jun 2025.

## Builds on (most cited first, 30 of 38)

- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [On Calibration of Modern Neural Networks](https://mlsanity.com/paper/1706.04599/) (2017)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [Co-teaching: Robust Training of Deep Neural Networks with Extremely Noisy Labels](https://mlsanity.com/paper/1804.06872/) (2018)
- [Pitfalls of Graph Neural Network Evaluation](https://mlsanity.com/paper/1811.05868/) (2018)
- [ChatGPT Outperforms Crowd-Workers for Text-Annotation Tasks](https://mlsanity.com/paper/2303.15056/) (2023)
- [Geom-GCN: Geometric Graph Convolutional Networks](https://mlsanity.com/paper/2002.05287/) (2020)
- [DivideMix: Learning with Noisy Labels as Semi-supervised Learning](https://mlsanity.com/paper/2002.07394/) (2020)
- [Making Deep Neural Networks Robust to Label Noise: a Loss Correction Approach](https://mlsanity.com/paper/1609.03683/) (2016)
- [Cluster-GCN: An Efficient Algorithm for Training Deep and Large Graph Convolutional Networks](https://mlsanity.com/paper/1905.07953/) (2019)
- [Robust Loss Functions under Label Noise for Deep Neural Networks](https://mlsanity.com/paper/1712.09482/) (2017)
- [Diffusion Improves Graph Learning](https://mlsanity.com/paper/1911.05485/) (2019)
- [Deep Gaussian Embedding of Graphs: Unsupervised Inductive Learning via Ranking](https://mlsanity.com/paper/1707.03815/) (2017)
- [Combating noisy labels by agreement: A joint training method with co-regularization](https://mlsanity.com/paper/2003.02752/) (2020)
- [Normalized Loss Functions for Deep Learning with Noisy Labels](https://mlsanity.com/paper/2006.13554/) (2020)
- [Learning with Noisy Labels Revisited: A Study Using Real-World Human Annotations](https://mlsanity.com/paper/2110.12088/) (2021)
- [One for All: Towards Training One Graph Model for All Classification Tasks](https://mlsanity.com/paper/2310.00149/) (2023)
- [Human uncertainty makes classification more robust](https://mlsanity.com/paper/1908.07086/) (2019)
- [Graph Neural Networks for Graphs with Heterophily: A Survey](https://mlsanity.com/paper/2202.07082/) (2022)
- [Learning with Symmetric Label Noise: The Importance of Being Unhinged](https://mlsanity.com/paper/1505.07634/) (2015)
- [Understanding and Improving Early Stopping for Learning with Noisy Labels](https://mlsanity.com/paper/2106.15853/) (2021)
- [NRGNN: Learning a Label Noise-Resistant Graph Neural Network on Sparsely and Noisily Labeled Graphs](https://mlsanity.com/paper/2106.04714/) (2021)
- [Can LLMs Replace Manual Annotation of Software Engineering Artifacts?](https://mlsanity.com/paper/2408.05534/) (2024)
- [Learning Graph Neural Networks with Noisy Labels](https://mlsanity.com/paper/1905.01591/) (2019)
- [Robust Training of Graph Neural Networks via Noise Governance](https://mlsanity.com/paper/2211.06614/) (2022)
- [The Effectiveness of LLMs as Annotators: A Comparative Overview and Empirical Analysis of Direct Representation](https://mlsanity.com/paper/2405.01299/) (2024)
- [CLNode: Curriculum Learning for Node Classification](https://mlsanity.com/paper/2206.07258/) (2022)
- [Beyond Real-world Benchmark Datasets: An Empirical Study of Node Classification with GNNs](https://mlsanity.com/paper/2206.09144/) (2022)

## Built on by (most cited first, 4 of 4)

- [Identifying and Correcting Label Noise for Robust GNNs via Influence Contradiction](https://mlsanity.com/paper/2601.17469/) (2026)
- [Structured Exploration and Exploitation of Label Functions for Automated Data Annotation](https://mlsanity.com/paper/2604.08578/) (2026)
- [Where LLM Annotators Fail: Label-Free Learning on Graphs with LLMs](https://mlsanity.com/paper/2605.27913/) (2026)
- [Particle Competition and Cooperation for Robust Graph Convolutional Network Learning Under Label Noise](https://mlsanity.com/paper/2609.22053/) (2026)

## Abstract (arXiv)

Graph Neural Networks (GNNs) have achieved state-of-the-art performance in node classification tasks but struggle with label noise in real-world data. Existing studies on graph learning with label noise commonly rely on class-dependent label noise, overlooking the complexities of instance-dependent noise and falling short of capturing real-world corruption patterns. We introduce BeGIN (Benchmarking for Graphs with Instance-dependent Noise), a new benchmark that provides realistic graph datasets with various noise types and comprehensively evaluates noise-handling strategies across GNN architectures, noisy label detection, and noise-robust learning. To simulate instance-dependent corruptions, BeGIN introduces algorithmic methods and LLM-based simulations. Our experiments reveal the challenges of instance-dependent noise, particularly LLM-based corruption, and underscore the importance of node-specific parameterization to enhance GNN robustness. By comprehensively evaluating noise-handling strategies, BeGIN provides insights into their effectiveness, efficiency, and key performance factors. We expect that BeGIN will serve as a valuable resource for advancing research on label noise in graphs and fostering the development of robust GNN training methods. The code is available at https://github.com/kimsu55/BeGIN.