Distributionally Robust Segmentation of Abnormal Fetal Brain 3D MRI

TL;DR

This paper introduces a distributionally robust training method for fetal brain MRI segmentation that improves performance on abnormal cases by reweighting training samples using Distributionally Robust Optimization (DRO).

Contribution

It proposes a novel DRO-based approach to enhance deep learning segmentation robustness for pathological fetal brain MRI cases, addressing hidden stratification.

Findings

Improved segmentation consistency on abnormal fetal brain MRIs.

DRO-based training outperforms standard methods on diverse pathological cases.

Enhanced generalization to unseen abnormal cases.

Abstract

The performance of deep neural networks typically increases with the number of training images. However, not all images have the same importance towards improved performance and robustness. In fetal brain MRI, abnormalities exacerbate the variability of the developing brain anatomy compared to non-pathological cases. A small number of abnormal cases, as is typically available in clinical datasets used for training, are unlikely to fairly represent the rich variability of abnormal developing brains. This leads machine learning systems trained by maximizing the average performance to be biased toward non-pathological cases. This problem was recently referred to as hidden stratification. To be suited for clinical use, automatic segmentation methods need to reliably achieve high-quality segmentation outcomes also for pathological cases. In this paper, we show that the state-of-the-art deep learning pipeline nnU-Net has difficulties to generalize to unseen abnormal cases. To mitigate this problem, we propose to train a deep neural network to minimize a percentile of the distribution of per-volume loss over the dataset. We show that this can be achieved by using Distributionally Robust Optimization (DRO). DRO automatically reweights the training samples with lower performance, encouraging nnU-Net to perform more consistently on all cases. We validated our approach using a dataset of 368 fetal brain T2w MRIs, including 124 MRIs of open spina bifida cases and 51 MRIs of cases with other severe abnormalities of brain development.