Notebooks Behind the Firewall: AI Agents... - Wanjun Gu, University of California, San Francisco

Notebooks Behind the Firewall: AI Agents and Real Patient Data in Jupyter - Wanjun Gu, University of California, San Francisco Biomedical researchers have the same AI agents as everyone else, but can't point them at their actual data. Patient records can't leave the medical center, so the agent never sees them. Institutions already host compliant model inference. The gap sits at the agent layer. This talk covers how we use Biorouter to close that gap at UCSF and connect it to Jupyter. Biorouter is an open-source research agent that routes work across institutionally hosted, local, and commercial models, with the private and public boundary enforced in source, and MCP connectors into where the data lives: a 7-million-patient OMOP electronic health record database and the SPOKE knowledge graph. With the Jupyter integration, researchers keep the notebooks they already have and gain institutionally hosted inference plus clearance for protected health data. I'll demo the integration and walk through one study it enabled: predicting hospitalization in a multiple sclerosis cohort from that database, from plain-English hypothesis to trained model (AUC 0.78). This is infrastructure work as much as research. The pattern applies across genomics, clinical research, and other HIPAA-governed biomedical work.