Timothy Keyes

Nigam H. Shah, Nerissa Ambers, Abby Pandya et al.

While large language models (LLMs) can support clinical documentation needs, standalone tools struggle with "workflow friction" from manual data entry. We developed ChatEHR, a system that enables the use of LLMs with the entire patient timeline spanning several years. ChatEHR enables automations - which are static combinations of prompts and data that perform a fixed task - and interactive use in the electronic health record (EHR) via a user interface (UI). The resulting ability to sift through patient medical records for diverse use-cases such as pre-visit chart review, screening for transfer eligibility, monitoring for surgical site infections, and chart abstraction, redefines LLM use as an institutional capability. This system, accessible after user-training, enables continuous monitoring and evaluation of LLM use. In 1.5 years, we built 7 automations and 1075 users have trained to become routine users of the UI, engaging in 23,000 sessions in the first 3 months of launch. For automations, being model-agnostic and accessing multiple types of data was essential for matching specific clinical or administrative tasks with the most appropriate LLM. Benchmark-based evaluations proved insufficient for monitoring and evaluation of the UI, requiring new methods to monitor performance. Generation of summaries was the most frequent task in the UI, with an estimated 0.73 hallucinations and 1.60 inaccuracies per generation. The resulting mix of cost savings, time savings, and revenue growth required a value assessment framework to prioritize work as well as quantify the impact of using LLMs. Initial estimates are $6M savings in the first year of use, without quantifying the benefit of the better care offered. Such a "build-from-within" strategy provides an opportunity for health systems to maintain agency via a vendor-agnostic, internally governed LLM platform.

Tim Ellis-Caleo, Timothy Keyes, Nerissa Ambers et al.

Tumor boards are multidisciplinary conferences dedicated to producing actionable patient care recommendations with live review of primary radiology and pathology data. Succinct patient case summaries are needed to drive efficient and accurate case discussions. We developed a manual AI-based workflow to generate patient summaries to display live at the Stanford Thoracic Tumor board. To improve on this manually intensive process, we developed several automated AI chart summarization methods and evaluated them against physician gold standard summaries and fact-based scoring rubrics. We report these comparative evaluations as well as our deployment of the final state automated AI chart summarization tool along with post-deployment monitoring. We also validate the use of an LLM as a judge evaluation strategy for fact-based scoring. This work is an example of integrating AI-based workflows into routine clinical practice.

Timothy Keyes, Alison Callahan, Abby S. Pandya et al.

Post-deployment monitoring of artificial intelligence (AI) systems in health care is essential to ensure their safety, quality, and sustained benefit-and to support governance decisions about which systems to update, modify, or decommission. Motivated by these needs, we developed a framework for monitoring deployed AI systems grounded in the mandate to take specific actions when they fail to behave as intended. This framework, which is now actively used at Stanford Health Care, is organized around three complementary principles: system integrity, performance, and impact. System integrity monitoring focuses on maximizing system uptime, detecting runtime errors, and identifying when changes to the surrounding IT ecosystem have unintended effects. Performance monitoring focuses on maintaining accurate system behavior in the face of changing health care practices (and thus input data) over time. Impact monitoring assesses whether a deployed system continues to have value in the form of benefit to clinicians and patients. Drawing on examples of deployed AI systems at our academic medical center, we provide practical guidance for creating monitoring plans based on these principles that specify which metrics to measure, when those metrics should be reviewed, who is responsible for acting when metrics change, and what concrete follow-up actions should be taken-for both traditional and generative AI. We also discuss challenges to implementing this framework, including the effort and cost of monitoring for health systems with limited resources and the difficulty of incorporating data-driven monitoring practices into complex organizations where conflicting priorities and definitions of success often coexist. This framework offers a practical template and starting point for health systems seeking to ensure that AI deployments remain safe and effective over time.

Jane Wang, Timothy Keyes, April S Liang et al.

Surgical co-management (SCM) is an evidence-based model in which hospitalists jointly manage medically complex perioperative patients alongside surgical teams. Despite its clinical and financial value, SCM is limited by the need to manually identify eligible patients. To determine whether SCM triage can be automated, we conducted a prospective, unblinded study at Stanford Health Care in which an LLM-based, electronic health record (EHR)-integrated triage tool (SCM Navigator) provided SCM recommendations followed by physician review. Using pre-operative documentation, structured data, and clinical criteria for perioperative morbidity, SCM Navigator categorized patients as appropriate, not appropriate, or possibly appropriate for SCM. Faculty indicated their clinical judgment and provided free-text feedback when they disagreed. Sensitivity, specificity, positive predictive value, and negative predictive value were measured using physician determinations as a reference. Free-text reasons were thematically categorized, and manual chart review was conducted on all false-negative cases and 30 randomly selected cases from the largest false-positive category. Since deployment, 6,193 cases have been triaged, of which 1,582 (23%) were recommended for hospitalist consultation. SCM Navigator displayed high sensitivity (0.94, 95% CI 0.91-0.96) and moderate specificity (0.74, 95% CI 0.71-0.77). Post-hoc chart review suggested most discrepancies reflect modifiable gaps in clinical criteria, institutional workflow, or physician practice variability rather than LLM misclassification, which accounted for 2 of 19 (11%) false-negative cases. These findings demonstrate that an LLM-powered, EHR-integrated, human-in-the-loop AI system can accurately and safely triage surgical patients for SCM, and that AI-enabled screening tools can augment and potentially automate time-intensive clinical workflows.

Chukwuebuka Anyaegbuna, Eduardo Juan Perez Guerrero, Jerry Liu et al.

Language barriers affect 27.3 million U.S. residents with non-English language preference, yet professional medical translation remains costly and often unavailable. We evaluated four frontier large language models (GPT-5.1, Claude Opus 4.5, Gemini 3 Pro, Kimi K2) translating 22 medical documents into 8 languages spanning high-resource (Spanish, Chinese, Russian, Vietnamese), medium-resource (Korean, Arabic), and low-resource (Tagalog, Haitian Creole) categories using a five-layer validation framework. Across 704 translation pairs, all models achieved high semantic preservation (LaBSE greater than 0.92), with no significant difference between high- and low-resource languages (p = 0.066). Cross-model back-translation confirmed results were not driven by same-model circularity (delta = -0.0009). Inter-model concordance across four independently trained models was high (LaBSE: 0.946), and lexical borrowing analysis showed no correlation between English term retention and fidelity scores in low-resource languages (rho = +0.018, p = 0.82). These converging results suggest frontier LLMs preserve medical meaning across resource levels, with implications for language access in healthcare.

François Grolleau, Emily Alsentzer, Timothy Keyes et al.

Evaluating factual accuracy in Large Language Model (LLM)-generated clinical text is a critical barrier to adoption, as expert review is unscalable for the continuous quality assurance these systems require. We address this challenge with two complementary contributions. First, we introduce MedFactEval, a framework for scalable, fact-grounded evaluation where clinicians define high-salience key facts and an "LLM Jury"--a multi-LLM majority vote--assesses their inclusion in generated summaries. Second, we present MedAgentBrief, a model-agnostic, multi-step workflow designed to generate high-quality, factual discharge summaries. To validate our evaluation framework, we established a gold-standard reference using a seven-physician majority vote on clinician-defined key facts from inpatient cases. The MedFactEval LLM Jury achieved almost perfect agreement with this panel (Cohen's kappa=81%), a performance statistically non-inferior to that of a single human expert (kappa=67%, P < 0.001). Our work provides both a robust evaluation framework (MedFactEval) and a high-performing generation workflow (MedAgentBrief), offering a comprehensive approach to advance the responsible deployment of generative AI in clinical workflows.

Erin Craig, Timothy Keyes, Jolanda Sarno et al.

Single-cell datasets often lack individual cell labels, making it challenging to identify cells associated with disease. To address this, we introduce Mixture Modeling for Multiple Instance Learning (MMIL), an expectation maximization method that enables the training and calibration of cell-level classifiers using patient-level labels. Our approach can be used to train e.g. lasso logistic regression models, gradient boosted trees, and neural networks. When applied to clinically-annotated, primary patient samples in Acute Myeloid Leukemia (AML) and Acute Lymphoblastic Leukemia (ALL), our method accurately identifies cancer cells, generalizes across tissues and treatment timepoints, and selects biologically relevant features. In addition, MMIL is capable of incorporating cell labels into model training when they are known, providing a powerful framework for leveraging both labeled and unlabeled data simultaneously. Mixture Modeling for MIL offers a novel approach for cell classification, with significant potential to advance disease understanding and management, especially in scenarios with unknown gold-standard labels and high dimensionality.