A Field Guide to Deploying AI Agents in Clinical Practice

Jack Gallifant; Katherine C. Kellogg; Matt Butler; Amanda Centi; Shan Chen; Patrick F. Doyle; Sayon Dutta; Joyce Guo; Matthew J. Hadfield; Esther H. Kim; David E. Kozono; Hugo JWL Aerts; Adam B. Landman; Raymond H. Mak; Rebecca G. Mishuris; Tanna L. Nelson; Guergana K. Savova; Elad Sharon; Benjamin C. Silverman; Umit Topaloglu; Jeremy L. Warner; Danielle S. Bitterman

arXiv · 2509.26153

A Field Guide to Deploying AI Agents in Clinical Practice

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Abstract

Large language models (LLMs) integrated into agent-driven workflows hold immense promise for healthcare, yet a significant gap exists between their potential and practical implementation within clinical settings. To address this, we present a practitioner-oriented field manual for deploying generative agents that use electronic health record (EHR) data. This guide is informed by our experience deploying the "irAE-Agent", an automated system to detect immune-related adverse events from clinical notes at Mass General Brigham, and by structured interviews with 21 clinicians, engineers, and informatics leaders involved in the project. Our analysis reveals a critical misalignment in clinical AI development: less than 20% of our effort was dedicated to prompt engineering and model development, while over 80% was consumed by the sociotechnical work of implementation. We distill this effort into five "heavy lifts": data integration, model validation, ensuring economic value, managing system drift, and governance. By providing actionable solutions for each of these challenges, this field manual shifts the focus from algorithmic development to the essential infrastructure and implementation work required to bridge the "valley of death" and successfully translate generative AI from pilot projects into routine clinical care.

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Jack Gallifant, Katherine C. Kellogg, Matt Butler, Amanda Centi, Shan Chen, Patrick F. Doyle, Sayon Dutta, Joyce Guo, Matthew J. Hadfield, Esther H. Kim, David E. Kozono, Hugo JWL Aerts, Adam B. Landman, Raymond H. Mak, Rebecca G. Mishuris, Tanna L. Nelson, Guergana K. Savova, Elad Sharon, Benjamin C. Silverman, Umit Topaloglu, Jeremy L. Warner, Danielle S. Bitterman. 2025-09-30. A Field Guide to Deploying AI Agents in Clinical Practice. https://arxiv.org/abs/2509.26153

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