General Methods Make Great Domain-specific Foundation Models: A Case-study on Fetal Ultrasound

With access to large-scale, unlabeled medical datasets, researchers are confronted with two questions: Should they attempt to pretrain a custom foundation model on this medical data, or use transfer-learning from an existing generalist model? And, if a custom model is pretrained, are novel methods required? In this paper we explore these questions by conducting a case-study, in which we train a foundation model on a large regional fetal ultrasound dataset of 2M images. By selecting the well-established DINOv2 method for pretraining, we achieve state-of-the-art results on three fetal ultrasound datasets, covering data from different countries, classification, segmentation, and few-shot tasks. We compare against a series of models pretrained on natural images, ultrasound images, and supervised baselines. Our results demonstrate two key insights: (i) Pretraining on custom data is worth it, even if smaller models are trained on less data, as scaling in natural image pretraining does not translate to ultrasound performance. (ii) Well-tuned methods from computer vision are making it feasible to train custom foundation models for a given medical domain, requiring no hyperparameter tuning and little methodological adaptation. Given these findings, we argue that a bias towards methodological innovation should be avoided when developing domain specific foundation models under common computational resource constraints.

AMAES: Augmented Masked Autoencoder Pretraining on Public Brain MRI Data for 3D-Native Segmentation

This study investigates the impact of self-supervised pretraining of 3D semantic segmentation models on a large-scale, domain-specific dataset. We introduce BRAINS-45K, a dataset of 44,756 brain MRI volumes from public sources, the largest public dataset available, and revisit a number of design choices for pretraining modern segmentation architectures by simplifying and optimizing state-of-the-art methods, and combining them with a novel augmentation strategy. The resulting AMAES framework is based on masked-image-modeling and intensity-based augmentation reversal and balances memory usage, runtime, and finetuning performance. Using the popular U-Net and the recent MedNeXt architecture as backbones, we evaluate the effect of pretraining on three challenging downstream tasks, covering single-sequence, low-resource settings, and out-of-domain generalization. The results highlight that pretraining on the proposed dataset with AMAES significantly improves segmentation performance in the majority of evaluated cases, and that it is beneficial to pretrain the model with augmentations, despite pretraing on a large-scale dataset. Code and model checkpoints for reproducing results, as well as the BRAINS-45K dataset are available at \url{https://github.com/asbjrnmunk/amaes}.