MAE-UNETR++: Masked Autoencoder Pretraining for 3-D Lung Nodule Segmentation

Abstract

Voxel-level annotation for volumetric medical imaging is expensive and difficult to scale, which makes training highcapacity 3-D segmentation models challenging in practice. Transfer learning (TL) from large public datasets is a common remedy, but it can under-perform when the source domain differs from the target anatomy and acquisition characteristics, as is often the case for pulmonary nodules. In this work, we propose a masked autoencoder (MAE) pretraining-based approach to break the data efficiency wall of domain difference and present a focused empirical study of domain-specific self-supervised learning (SSL) for 3-D lung nodule segmentation. We evaluate two experimental settings: first, Masked Autoencoder (MAE) pretraining versus random initialization across representative baselines; second, MAE versus Decathlon TL for UNETR++ while testing whether MAE-based pretraining also benefits a CNN baseline (V-Net). MAE pretraining on target-domain CT volumes achieves a Dice Similarity Coefficient (DSC) of 0.307, outperforming random initialization (0.136) and Decathlon weights (0.257). In addition, MAE improves the stability of V-Net in a "low-data" regime (i.e., with "insufficiently labeled" data), increasing DSC from 0.010 to0.071. Overall, these results suggest that MAE-based pretraining can provide a practical and robust initialization strategy for volumetric segmentation when labeled data are limited.