Efficient Bayesian Uncertainty Estimation for nnU-Net

Yidong Zhao, Changchun Yang, Artur Schweidtmann, Qian Tao*

*Corresponding author for this work

Research output: Chapter in Book/Conference proceedings/Edited volumeConference contributionScientificpeer-review


The self-configuring nnU-Net has achieved leading performance in a large range of medical image segmentation challenges. It is widely considered as the model of choice and a strong baseline for medical image segmentation. However, despite its extraordinary performance, nnU-Net does not supply a measure of uncertainty to indicate its possible failure. This can be problematic for large-scale image segmentation applications, where data are heterogeneous and nnU-Net may fail without notice. In this work, we introduce a novel method to estimate nnU-Net uncertainty for medical image segmentation. We propose a highly effective scheme for posterior sampling of weight space for Bayesian uncertainty estimation. Different from previous baseline methods such as Monte Carlo Dropout and mean-field Bayesian Neural Networks, our proposed method does not require a variational architecture and keeps the original nnU-Net architecture intact, thereby preserving its excellent performance and ease of use. Additionally, we boost the segmentation performance over the original nnU-Net via marginalizing multi-modal posterior models. We applied our method on the public ACDC and M &M datasets of cardiac MRI and demonstrated improved uncertainty estimation over a range of baseline methods. The proposed method further strengthens nnU-Net for medical image segmentation in terms of both segmentation accuracy and quality control.

Original languageEnglish
Title of host publicationMedical Image Computing and Computer Assisted Intervention – MICCAI 2022 - 25th International Conference, Proceedings
EditorsLinwei Wang, Qi Dou, P. Thomas Fletcher, Stefanie Speidel, Shuo Li
ISBN (Electronic)978-3-031-16452-1
ISBN (Print)978-3-031-16451-4
Publication statusPublished - 2022
Event25th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2022 - Singapore, Singapore
Duration: 18 Sep 202222 Sep 2022

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume13438 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference25th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2022

Bibliographical note

Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care
Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.


  • nnU-Net
  • Stochastic gradient descent
  • Uncertainty estimation
  • Variational inference


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