Data-Agnostic Augmentations for Unknown Variations: Out-of-Distribution Generalisation in MRI Segmentation

Mei Vaish, Felix Meister, Tobias Heimann, Christoph Brune, Jelmer M. Wolterink

Keywords: MRI, segmentation, data augmentation, generalisation, robustness, deep learning

TL;DR: MixUp and Auxiliary Fourier Augmentation boost robustness and generalization in medical image segmentation models under various distribution shifts, offering a simple, effective solution that is easy to implement within nnU-Net.

Abstract: Medical image segmentation models are often trained on curated datasets, leading to performance degradation when deployed in real-world clinical settings due to mismatches between training and test distributions. While data augmentation techniques are widely used to address these challenges, traditional visually consistent augmentation strategies lack the robustness needed for diverse real-world scenarios. In this work, we systematically evaluate alternative augmentation strategies, focusing on MixUp and Auxiliary Fourier Augmentation. These methods mitigate the effects of multiple variations without explicitly targeting specific sources of distribution shifts. We demonstrate how these techniques significantly improve out-of-distribution generalization and robustness to imaging variations across a wide range of transformations in cardiac cine MRI and prostate MRI segmentation. We quantitatively find that these augmentation methods enhance learned feature representations by promoting separability and compactness. Additionally, we highlight how their integration into nnU-Net training pipelines provides an easy-to-implement, effective solution for enhancing the reliability of medical segmentation models in real-world applications. Our code is available at: https://github.com/MIAGroupUT/augmentations-for-the-unknown.

Primary Subject Area: Segmentation

Secondary Subject Area: Transfer Learning and Domain Adaptation

Paper Type: Validation or Application

Registration Requirement: Yes

Reproducibility: https://github.com/MIAGroupUT/augmentations-for-the-unknown

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Submission Number: 93