AI-powered virtual tissues from spatial proteomics for clinical diagnostics and biomedical discovery
This work addresses computational bottlenecks in spatial proteomics for biomedical researchers and clinicians, offering a generalist model for improved diagnostics and discovery.
The paper tackles the challenge of analyzing high-dimensional spatial proteomics data with varying markers and study designs by introducing Virtual Tissues (VirTues), a foundation model framework that operates across molecular, cellular, and tissue scales, demonstrating strong generalization without task-specific fine-tuning and outperforming existing approaches in clinical diagnostics and biological discovery.
Spatial proteomics technologies have transformed our understanding of complex tissue architectures by enabling simultaneous analysis of multiple molecular markers and their spatial organization. The high dimensionality of these data, varying marker combinations across experiments and heterogeneous study designs pose unique challenges for computational analysis. Here, we present Virtual Tissues (VirTues), a foundation model framework for biological tissues that operates across the molecular, cellular and tissue scale. VirTues introduces innovations in transformer architecture design, including a novel tokenization scheme that captures both spatial and marker dimensions, and attention mechanisms that scale to high-dimensional multiplex data while maintaining interpretability. Trained on diverse cancer and non-cancer tissue datasets, VirTues demonstrates strong generalization capabilities without task-specific fine-tuning, enabling cross-study analysis and novel marker integration. As a generalist model, VirTues outperforms existing approaches across clinical diagnostics, biological discovery and patient case retrieval tasks, while providing insights into tissue function and disease mechanisms.