Modeling patient tissues at molecular resolution with Eva

Tissue structure is essential to function and homeostasis in all organs, and disruptions to structure usually indicate disease. Modeling relationships between structural, molecular, and clinical aspects of tissues could advance new diagnostics and treatment strategies. Although profiling techniques like spatial proteomics can capture these relationships, the data remain challenging to extract insight from. Here, we present Eva, a foundation model for tissue imaging data that learns multi-scale spatial representations of tissues at the molecular, cellular, and sample level. Eva uses a novel vision transformer architecture and is pre-trained on masked reconstruction of over 40 million matched spatial proteomics and histopathology images. We show that Eva excels at a variety of tasks, including cross-modal inference from H&E to proteomics stains, quality control, data annotation, zero-shot retrieval, survival modeling, and patient stratification. Extensive evaluations on held-out validation data demonstrate the versatility and generalizability of the learned embeddings. We anticipate that Eva will accelerate translational science by bridging basic research and clinical practice.