Learning General-purpose Biomedical Volume Representations using Randomized Synthesis

Abstract

Current volumetric biomedical foundation models struggle to generalize as public 3D datasets are small and do not cover the broad diversity of medical procedures, conditions, anatomical regions, and imaging protocols. We address this by creating a representation learning method that instead anticipates strong domain shifts at training time itself. We first propose a data engine that synthesizes highly variable training samples that would enable generalization to new biomedical contexts. To then train a single 3D network for any voxel-level task, we develop a contrastive learning method that pretrains the network to be stable against nuisance imaging variation simulated by the data engine, a key inductive bias for generalization. This network's features can be used as robust representations of input images for downstream tasks and its weights provide a strong, _dataset-agnostic_ initialization for finetuning on new datasets. As a result, we set new standards across _both_ multimodality registration and few-shot segmentation, a first for any 3D biomedical vision model, all without (pre-)training on any existing dataset of real images.