# Beyond Voxel Prediction Uncertainty: Identifying brain lesions you can trust

arXiv: https://arxiv.org/abs/2209.10877 · HTML: https://mlsanity.com/paper/2209.10877/

## Key facts

- Cited by 6 papers in the map (data through 14 Oct 2026).
- Builds on 17 of its 23 references that are in the map.
- First posted on arXiv 22 Sep 2022.

## Builds on (most cited first, 17 of 17)

- [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)
- [Dropout as a Bayesian Approximation: Representing Model Uncertainty in Deep Learning](https://mlsanity.com/paper/1506.02142/) (2015)
- [Simple and Scalable Predictive Uncertainty Estimation using Deep Ensembles](https://mlsanity.com/paper/1612.01474/) (2016)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [Deep Bayesian Active Learning with Image Data](https://mlsanity.com/paper/1703.02910/) (2017)
- [A Review of Uncertainty Quantification in Deep Learning: Techniques, Applications and Challenges](https://mlsanity.com/paper/2011.06225/) (2020)
- [Efficient Object Localization Using Convolutional Networks](https://mlsanity.com/paper/1411.4280/) (2014)
- [Bayesian SegNet: Model Uncertainty in Deep Convolutional Encoder-Decoder Architectures for Scene Understanding](https://mlsanity.com/paper/1511.02680/) (2015)
- [Exploring Uncertainty Measures in Deep Networks for Multiple Sclerosis Lesion Detection and Segmentation](https://mlsanity.com/paper/1808.01200/) (2018)
- [Prediction Error Meta Classification in Semantic Segmentation: Detection via Aggregated Dispersion Measures of Softmax Probabilities](https://mlsanity.com/paper/1811.00648/) (2018)
- [Bayesian QuickNAT: Model Uncertainty in Deep Whole-Brain Segmentation for Structure-wise Quality Control](https://mlsanity.com/paper/1811.09800/) (2018)
- [Towards Characterizing Adversarial Defects of Deep Learning Software from the Lens of Uncertainty](https://mlsanity.com/paper/2004.11573/) (2020)
- [Towards increased trustworthiness of deep learning segmentation methods on cardiac MRI](https://mlsanity.com/paper/1809.10430/) (2018)
- [Applications of Deep Learning Techniques for Automated Multiple Sclerosis Detection Using Magnetic Resonance Imaging: A Review](https://mlsanity.com/paper/2105.04881/) (2021)
- [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)

## Built on by (most cited first, 6 of 6)

- [Trustworthy clinical AI solutions: a unified review of uncertainty quantification in deep learning models for medical image analysis](https://mlsanity.com/paper/2210.03736/) (2022)
- [Novel structural-scale uncertainty measures and error retention curves: application to multiple sclerosis](https://mlsanity.com/paper/2211.04825/) (2022)
- [Structural-Based Uncertainty in Deep Learning Across Anatomical Scales: Analysis in White Matter Lesion Segmentation](https://mlsanity.com/paper/2311.08931/) (2023)
- [Fast refacing of MR images with a generative neural network lowers re-identification risk and preserves volumetric consistency](https://mlsanity.com/paper/2305.16922/) (2023)
- [Interpretability of Uncertainty: Exploring Cortical Lesion Segmentation in Multiple Sclerosis](https://mlsanity.com/paper/2407.05761/) (2024)
- [Explaining Uncertainty in Multiple Sclerosis Cortical Lesion Segmentation Beyond Prediction Errors](https://mlsanity.com/paper/2504.04814/) (2025)

## Abstract (arXiv)

Deep neural networks have become the gold-standard approach for the automated segmentation of 3D medical images. Their full acceptance by clinicians remains however hampered by the lack of intelligible uncertainty assessment of the provided results. Most approaches to quantify their uncertainty, such as the popular Monte Carlo dropout, restrict to some measure of uncertainty in prediction at the voxel level. In addition not to be clearly related to genuine medical uncertainty, this is not clinically satisfying as most objects of interest (e.g. brain lesions) are made of groups of voxels whose overall relevance may not simply reduce to the sum or mean of their individual uncertainties. In this work, we propose to go beyond voxel-wise assessment using an innovative Graph Neural Network approach, trained from the outputs of a Monte Carlo dropout model. This network allows the fusion of three estimators of voxel uncertainty: entropy, variance, and model's confidence; and can be applied to any lesion, regardless of its shape or size. We demonstrate the superiority of our approach for uncertainty estimate on a task of Multiple Sclerosis lesions segmentation.