A Multimodal Foundation Model of Spatial Transcriptomics and Histology for Biological Discovery and Clinical Prediction

Spatial transcriptomics (ST) enables gene expression mapping within anatomical context but remains costly and low-throughput. Hematoxylin and eosin (H\&E) staining offers rich morphology yet lacks molecular resolution. We present \textbf{\ours} (\textbf{S}patial \textbf{T}ranscriptomics and hist\textbf{O}logy \textbf{R}epresentation \textbf{M}odel), a foundation model trained on 1.2 million spatially resolved transcriptomic profiles with matched histology across 18 organs. Using a hierarchical architecture integrating morphological features, gene expression, and spatial context, STORM bridges imaging and omics through robust molecular--morphological representations. STORM enhances spatial domain discovery, producing biologically coherent tissue maps, and outperforms existing methods in predicting spatial gene expression from H\&E images across 11 tumor types. The model is platform-agnostic, performing consistently across Visium, Xenium, Visium HD, and CosMx. Applied to 23 independent cohorts comprising 7,245 patients, STORM significantly improves immunotherapy response prediction and prognostication over established biomarkers, providing a scalable framework for spatially informed discovery and clinical precision medicine.

Lightweight Mobile Automated Assistant-to-physician for Global Lower-resource Areas

Importance: Lower-resource areas in Africa and Asia face a unique set of healthcare challenges: the dual high burden of communicable and non-communicable diseases; a paucity of highly trained primary healthcare providers in both rural and densely populated urban areas; and a lack of reliable, inexpensive internet connections. Objective: To address these challenges, we designed an artificial intelligence assistant to help primary healthcare providers in lower-resource areas document demographic and medical sign/symptom data and to record and share diagnostic data in real-time with a centralized database. Design: We trained our system using multiple data sets, including US-based electronic medical records (EMRs) and open-source medical literature and developed an adaptive, general medical assistant system based on machine learning algorithms. Main outcomes and Measure: The application collects basic information from patients and provides primary care providers with diagnoses and prescriptions suggestions. The application is unique from existing systems in that it covers a wide range of common diseases, signs, and medication typical in lower-resource countries; the application works with or without an active internet connection. Results: We have built and implemented an adaptive learning system that assists trained primary care professionals by means of an Android smartphone application, which interacts with a central database and collects real-time data. The application has been tested by dozens of primary care providers. Conclusions and Relevance: Our application would provide primary healthcare providers in lower-resource areas with a tool that enables faster and more accurate documentation of medical encounters. This application could be leveraged to automatically populate local or national EMR systems.