MeDUET: Disentangled Unified Pretraining for 3D Medical Image Synthesis and Analysis

Abstract

Self-supervised learning (SSL) and diffusion models have advanced representation learning and image synthesis. However, in 3D medical imaging, they remain separate: diffusion for synthesis, SSL for analysis. Unifying 3D medical image synthesis and analysis is intuitive yet challenging, as multi-center datasets exhibit dominant style shifts, while downstream tasks rely on anatomy, and site-specific style co-varies with anatomy across slices, making factors unreliable without explicit constraints. In this paper, we propose MeDUET, a 3D Medical image Disentangled UnifiEd PreTraining framework that performs SSL in the Variational Autoencoder (VAE) latent space which explicitly disentangles domain-invariant content from domain-specific style. The token demixing mechanism serves to turn disentanglement from a modeling assumption into an empirically identifiable property. Two novel proxy tasks, Mixed-Factor Token Distillation (MFTD) and Swap-invariance Quadruplet Contrast (SiQC), are devised to synergistically enhance disentanglement. Once pretrained, MeDUET is capable of (i) delivering higher fidelity, faster convergence, and improved controllability for synthesis, and (ii) demonstrating strong domain generalization and notable label efficiency for analysis across diverse medical benchmarks. In summary, MeDUET converts multi-source heterogeneity from an obstacle into a learning signal, enabling unified pretraining for 3D medical image synthesis and analysis. The code is available at https://github.com/JK-Liu7/MeDUET .