# Inter-Rater Uncertainty Quantification in Medical Image Segmentation via Rater-Specific Bayesian Neural Networks

arXiv: https://arxiv.org/abs/2306.16556 · HTML: https://mlsanity.com/paper/2306.16556/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 28 of its 36 references that are in the map.
- First posted on arXiv 28 Jun 2023.

## Builds on (most cited first, 28 of 28)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Dropout as a Bayesian Approximation: Representing Model Uncertainty in Deep Learning](https://mlsanity.com/paper/1506.02142/) (2015)
- [Auto-Encoding Variational Bayes](https://mlsanity.com/paper/1312.6114/) (2013)
- [What Uncertainties Do We Need in Bayesian Deep Learning for Computer Vision?](https://mlsanity.com/paper/1703.04977/) (2017)
- [Attention U-Net: Learning Where to Look for the Pancreas](https://mlsanity.com/paper/1804.03999/) (2018)
- [Weight Uncertainty in Neural Networks](https://mlsanity.com/paper/1505.05424/) (2015)
- [Identifying the Best Machine Learning Algorithms for Brain Tumor Segmentation, Progression Assessment, and Overall Survival Prediction in the BRATS Challenge](https://mlsanity.com/paper/1811.02629/) (2018)
- [The Liver Tumor Segmentation Benchmark (LiTS)](https://mlsanity.com/paper/1901.04056/) (2019)
- [A large annotated medical image dataset for the development and evaluation of segmentation algorithms](https://mlsanity.com/paper/1902.09063/) (2019)
- [A Probabilistic U-Net for Segmentation of Ambiguous Images](https://mlsanity.com/paper/1806.05034/) (2018)
- [Aleatoric uncertainty estimation with test-time augmentation for medical image segmentation with convolutional neural networks](https://mlsanity.com/paper/1807.07356/) (2018)
- [Exploring Uncertainty Measures in Deep Networks for Multiple Sclerosis Lesion Detection and Segmentation](https://mlsanity.com/paper/1808.01200/) (2018)
- [PHiSeg: Capturing Uncertainty in Medical Image Segmentation](https://mlsanity.com/paper/1906.04045/) (2019)
- [Stochastic Segmentation Networks: Modelling Spatially Correlated Aleatoric Uncertainty](https://mlsanity.com/paper/2006.06015/) (2020)
- [A Hierarchical Probabilistic U-Net for Modeling Multi-Scale Ambiguities](https://mlsanity.com/paper/1905.13077/) (2019)
- [Disentangling Human Error from the Ground Truth in Segmentation of Medical Images](https://mlsanity.com/paper/2007.15963/) (2020)
- [Exploiting Epistemic Uncertainty of Anatomy Segmentation for Anomaly Detection in Retinal OCT](https://mlsanity.com/paper/1905.12806/) (2019)
- [Is MC Dropout Bayesian?](https://mlsanity.com/paper/2110.04286/) (2021)
- [Bayesian Image Quality Transfer with CNNs: Exploring Uncertainty in dMRI Super-Resolution](https://mlsanity.com/paper/1705.00664/) (2017)
- [Automated Muscle Segmentation from Clinical CT using Bayesian U-Net for Personalized Musculoskeletal Modeling](https://mlsanity.com/paper/1907.08915/) (2019)
- [Inherent Brain Segmentation Quality Control from Fully ConvNet Monte Carlo Sampling](https://mlsanity.com/paper/1804.07046/) (2018)
- [Efficient Bayesian Uncertainty Estimation for nnU-Net](https://mlsanity.com/paper/2212.06278/) (2022)
- [Let's agree to disagree: learning highly debatable multirater labelling](https://mlsanity.com/paper/1909.01891/) (2019)
- [U2-Net: A Bayesian U-Net model with epistemic uncertainty feedback for photoreceptor layer segmentation in pathological OCT scans](https://mlsanity.com/paper/1901.07929/) (2019)
- [Effect of latent space distribution on the segmentation of images with multiple annotations](https://mlsanity.com/paper/2304.13476/) (2023)
- [RevPHiSeg: A Memory-Efficient Neural Network for Uncertainty Quantification in Medical Image Segmentation](https://mlsanity.com/paper/2008.06999/) (2020)

## Built on by (most cited first, 3 of 3)

- [Tyche: Stochastic In-Context Learning for Medical Image Segmentation](https://mlsanity.com/paper/2401.13650/) (2024)
- [A Review of Bayesian Uncertainty Quantification in Deep Probabilistic Image Segmentation](https://mlsanity.com/paper/2411.16370/) (2024)
- [Harmonized Feature Conditioning and Frequency-Prompt Personalization for Multi-Rater Medical Segmentation](https://mlsanity.com/paper/2605.08210/) (2026)

## Abstract (arXiv)

Automated medical image segmentation inherently involves a certain degree of uncertainty. One key factor contributing to this uncertainty is the ambiguity that can arise in determining the boundaries of a target region of interest, primarily due to variations in image appearance. On top of this, even among experts in the field, different opinions can emerge regarding the precise definition of specific anatomical structures. This work specifically addresses the modeling of segmentation uncertainty, known as inter-rater uncertainty. Its primary objective is to explore and analyze the variability in segmentation outcomes that can occur when multiple experts in medical imaging interpret and annotate the same images. We introduce a novel Bayesian neural network-based architecture to estimate inter-rater uncertainty in medical image segmentation. Our approach has three key advancements. Firstly, we introduce a one-encoder-multi-decoder architecture specifically tailored for uncertainty estimation, enabling us to capture the rater-specific representation of each expert involved. Secondly, we propose Bayesian modeling for the new architecture, allowing efficient capture of the inter-rater distribution, particularly in scenarios with limited annotations. Lastly, we enhance the rater-specific representation by integrating an attention module into each decoder. This module facilitates focused and refined segmentation results for each rater. We conduct extensive evaluations using synthetic and real-world datasets to validate our technical innovations rigorously. Our method surpasses existing baseline methods in five out of seven diverse tasks on the publicly available QUBIQ dataset, considering two evaluation metrics encompassing different uncertainty aspects. Our codes, models, and the new dataset are available through our GitHub repository: https://github.com/HaoWang420/bOEMD-net .