Abstract
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.
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The authors gratefully acknowledge TU Delft AI Initiative for financial support.
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Zhao, Y., Yang, C., Schweidtmann, A., Tao, Q. (2022). Efficient Bayesian Uncertainty Estimation for nnU-Net. In: Wang, L., Dou, Q., Fletcher, P.T., Speidel, S., Li, S. (eds) Medical Image Computing and Computer Assisted Intervention – MICCAI 2022. MICCAI 2022. Lecture Notes in Computer Science, vol 13438. Springer, Cham. https://doi.org/10.1007/978-3-031-16452-1_51
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