Unlocking Latent Dimensions: Exploring Representations of Large-Scale X-ray Scattering Data using Variational Autoencoders

Variational autoencoders (VAEs) compress high resolution CT volumes into compact latents while preserving clinically relevant structure. However, training CT-specific VAEs from scratch or heavily fine-tuning them incurs substantial computational and engineering cost, and often degrades under heterogeneous scanners, protocols, and diseases. This paper makes a progressive stride toward training-free medical VAEs by leveraging a critical observation: a single Foundation VAE, pretrained at scale on natural images and videos, can serve as a unified interface for CT Reconstruction, Augmentation, and Generation. With both encoder and decoder frozen, the Foundation VAE reconstructs CT volumes with preserved anatomy while suppressing acquisition noise; training segmentation models on these reconstructions improves surface accuracy by 3.9% NSD on average for pancreatic tumor and lung tumor. Within the same Foundation VAE latent space, a conditional latent diffusion model achieves 3.9% lower average FVD with 36.2% higher CT CLIP score, and improves multi-disease generation faithfulness across 18 types by 2.76% AUC. These results demonstrate Foundation VAEs as a practical interface for scalable CT representation reuse and faithful CT generation. Our code and demo are available at https://github.com/qic999/Foundation-VAE.

Despite their ubiquity, variational autoencoders (VAEs) inherently suffer from posterior collapse, a failure mode in which latent variables are effectively ignored. This failure arises because explicit prior imposition drives optimization toward loss landscape regions corresponding to uninformative latent representations. Here, we introduce Entropic Autoencoders (EAEs), a framework in which reconstruction loss is the only explicit objective, and entropy generates the latent variables' prior implicitly through a free energy-minimizing ensemble of encoders. This ensemble biases learning toward high-volume regions of near-optimal solutions, while decoder updates direct the search trajectories toward informative latent representations. We demonstrate that EAEs mitigate posterior collapse by learning non-Gaussian, multimodal latent distributions that yield diverse, data-consistent generations and preserve different forms of underlying structure in the data. As a proof-of-concept, we show that an EAE captures a superposition of the known low-dimensional dynamics of a reaction-diffusion process. Then, we show that an EAE identifies implicit categorical distinctions in MNIST latent representations, and displays a hierarchical understanding of facial structure on the CelebA dataset, from an "all-human" face to individual-dependent features.

Optical scattering has conventionally been regarded as an impediment in imaging research due to the degradation of image quality during reconstruction. Nevertheless, this study explores two cases in which optical scattering may serve a beneficial role in image reconstruction tasks. We compared the No Scattering MNIST dataset with three Scattering MNIST datasets, each generated under distinct scattering conditions. To assess the information content of the resulting speckle patterns, we employed a Variational Autoencoder (VAE) approach which achieves accuracy comparable to state-of-the-art deep learning approaches, but has an interpretable latent space. We find that scattering can enhance data robustness against spatial pixel loss by effectively distributing information. We also demonstrate that scattering can enable distinctions of focal depth information. We anticipate that these findings will contribute to more efficient imaging techniques, particularly in the presence of obstacles and three-dimensional signals.