EXPOSE: Explainable and Domain-Robust Embeddings from Pathology Vision Foundation Models using Sparse Autoencoders

Abstract

Vision Foundation Models (VFMs) are widely used in computational pathology but remain sensitive to domain shifts arising from variations in staining, tissue preparation, and scanner hardware. A key limitation is that VFM embeddings entangle biological with domain-specific information, hindering cross-domain generalization. We propose Explainable Probing of Cross-Domain Sparse Embeddings (EXPOSE), a framework that uses Sparse Autoencoders (SAEs) as an explainable bottleneck to identify and suppress domain-specific components in VFM embeddings. We train a sparse representation of VFM features, use a linear classifier to identify domain-specific latent dimensions, and mask these features prior to downstream relapse prediction without retraining the backbone model. Experiments on a large prostate cancer dataset with multiple acquisition domains show that SAE features capture both domain- and task-specific information, which are partially disentangled in the latent space. Removing domain-specific features improves cross-domain performance and increases embedding robustness as measured by the Domain Robustness Index (DoRI). Code is available at https://github.com/imsb-uke/expose .