Jason Hom

Justin Xu, Zhihong Chen, Andrew Johnston et al. · oxford, stanford

Recent developments in natural language generation have tremendous implications for healthcare. For instance, state-of-the-art systems could automate the generation of sections in clinical reports to alleviate physician workload and streamline hospital documentation. To explore these applications, we present a shared task consisting of two subtasks: (1) Radiology Report Generation (RRG24) and (2) Discharge Summary Generation ("Discharge Me!"). RRG24 involves generating the 'Findings' and 'Impression' sections of radiology reports given chest X-rays. "Discharge Me!" involves generating the 'Brief Hospital Course' and 'Discharge Instructions' sections of discharge summaries for patients admitted through the emergency department. "Discharge Me!" submissions were subsequently reviewed by a team of clinicians. Both tasks emphasize the goal of reducing clinician burnout and repetitive workloads by generating documentation. We received 201 submissions from across 8 teams for RRG24, and 211 submissions from across 16 teams for "Discharge Me!".

Dave Van Veen, Cara Van Uden, Louis Blankemeier et al.

Analyzing vast textual data and summarizing key information from electronic health records imposes a substantial burden on how clinicians allocate their time. Although large language models (LLMs) have shown promise in natural language processing (NLP), their effectiveness on a diverse range of clinical summarization tasks remains unproven. In this study, we apply adaptation methods to eight LLMs, spanning four distinct clinical summarization tasks: radiology reports, patient questions, progress notes, and doctor-patient dialogue. Quantitative assessments with syntactic, semantic, and conceptual NLP metrics reveal trade-offs between models and adaptation methods. A clinical reader study with ten physicians evaluates summary completeness, correctness, and conciseness; in a majority of cases, summaries from our best adapted LLMs are either equivalent (45%) or superior (36%) compared to summaries from medical experts. The ensuing safety analysis highlights challenges faced by both LLMs and medical experts, as we connect errors to potential medical harm and categorize types of fabricated information. Our research provides evidence of LLMs outperforming medical experts in clinical text summarization across multiple tasks. This suggests that integrating LLMs into clinical workflows could alleviate documentation burden, allowing clinicians to focus more on patient care.

Eric Wu, Kevin Wu, Jason Hom et al.

Large language models (LLMs) are increasingly central to clinician workflows, spanning clinical decision support, medical education, and patient communication. However, current evaluation methods for medical LLMs rely heavily on static, templated benchmarks that fail to capture the complexity and dynamics of real-world clinical practice, creating a dissonance between benchmark performance and clinical utility. To address these limitations, we present MedArena, an interactive evaluation platform that enables clinicians to directly test and compare leading LLMs using their own medical queries. Given a clinician-provided query, MedArena presents responses from two randomly selected models and asks the user to select the preferred response. Out of 1571 preferences collected across 12 LLMs up to November 1, 2025, Gemini 2.0 Flash Thinking, Gemini 2.5 Pro, and GPT-4o were the top three models by Bradley-Terry rating. Only one-third of clinician-submitted questions resembled factual recall tasks (e.g., MedQA), whereas the majority addressed topics such as treatment selection, clinical documentation, or patient communication, with ~20% involving multi-turn conversations. Additionally, clinicians cited depth and detail and clarity of presentation more often than raw factual accuracy when explaining their preferences, highlighting the importance of readability and clinical nuance. We also confirm that the model rankings remain stable even after controlling for style-related factors like response length and formatting. By grounding evaluation in real-world clinical questions and preferences, MedArena offers a scalable platform for measuring and improving the utility and efficacy of medical LLMs.

Asad Aali, Dave Van Veen, Yamin Ishraq Arefeen et al.

Brief hospital course (BHC) summaries are clinical documents that summarize a patient's hospital stay. While large language models (LLMs) depict remarkable capabilities in automating real-world tasks, their capabilities for healthcare applications such as synthesizing BHCs from clinical notes have not been shown. We introduce a novel pre-processed dataset, the MIMIC-IV-BHC, encapsulating clinical note and brief hospital course (BHC) pairs to adapt LLMs for BHC synthesis. Furthermore, we introduce a benchmark of the summarization performance of two general-purpose LLMs and three healthcare-adapted LLMs. Using clinical notes as input, we apply prompting-based (using in-context learning) and fine-tuning-based adaptation strategies to three open-source LLMs (Clinical-T5-Large, Llama2-13B, FLAN-UL2) and two proprietary LLMs (GPT-3.5, GPT-4). We evaluate these LLMs across multiple context-length inputs using natural language similarity metrics. We further conduct a clinical study with five clinicians, comparing clinician-written and LLM-generated BHCs across 30 samples, focusing on their potential to enhance clinical decision-making through improved summary quality. We observe that the Llama2-13B fine-tuned LLM outperforms other domain-adapted models given quantitative evaluation metrics of BLEU and BERT-Score. GPT-4 with in-context learning shows more robustness to increasing context lengths of clinical note inputs than fine-tuned Llama2-13B. Despite comparable quantitative metrics, the reader study depicts a significant preference for summaries generated by GPT-4 with in-context learning compared to both Llama2-13B fine-tuned summaries and the original summaries, highlighting the need for qualitative clinical evaluation.

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.

Asad Aali, Andrew Johnston, Louis Blankemeier et al.

Abdominal computed tomography (CT) scans are frequently performed in clinical settings. Opportunistic CT involves repurposing routine CT images to extract diagnostic information and is an emerging tool for detecting underdiagnosed conditions such as sarcopenia, hepatic steatosis, and ascites. This study utilizes deep learning methods to promote accurate diagnosis and clinical documentation. We analyze 2,674 inpatient CT scans to identify discrepancies between imaging phenotypes (characteristics derived from opportunistic CT scans) and their corresponding documentation in radiology reports and ICD coding. Through our analysis, we find that only 0.5%, 3.2%, and 30.7% of scans diagnosed with sarcopenia, hepatic steatosis, and ascites (respectively) through either opportunistic imaging or radiology reports were ICD-coded. Our findings demonstrate opportunistic CT's potential to enhance diagnostic precision and accuracy of risk adjustment models, offering advancements in precision medicine.

April S. Liang, Fatemeh Amrollahi, Yixing Jiang et al.

Repetitive laboratory testing unlikely to yield clinically useful information is a common practice that burdens patients and increases healthcare costs. Education and feedback interventions have limited success, while general test ordering restrictions and electronic alerts impede appropriate clinical care. We introduce and evaluate SmartAlert, a machine learning (ML)-driven clinical decision support (CDS) system integrated into the electronic health record that predicts stable laboratory results to reduce unnecessary repeat testing. This case study describes the implementation process, challenges, and lessons learned from deploying SmartAlert targeting complete blood count (CBC) utilization in a randomized controlled pilot across 9270 admissions in eight acute care units across two hospitals between August 15, 2024, and March 15, 2025. Results show significant decrease in number of CBC results within 52 hours of SmartAlert display (1.54 vs 1.82, p <0.01) without adverse effect on secondary safety outcomes, representing a 15% relative reduction in repetitive testing. Implementation lessons learned include interpretation of probabilistic model predictions in clinical contexts, stakeholder engagement to define acceptable model behavior, governance processes for deploying a complex model in a clinical environment, user interface design considerations, alignment with clinical operational priorities, and the value of qualitative feedback from end users. In conclusion, a machine learning-driven CDS system backed by a deliberate implementation and governance process can provide precision guidance on inpatient laboratory testing to safely reduce unnecessary repetitive testing.

Adrit Rao, Malte Jensen, Andrea T. Fisher et al.

Artificial intelligence allows automatic extraction of imaging biomarkers from already-acquired radiologic images. This paradigm of opportunistic imaging adds value to medical imaging without additional imaging costs or patient radiation exposure. However, many open-source image analysis solutions lack rigorous validation while commercial solutions lack transparency, leading to unexpected failures when deployed. Here, we report development and validation for two of the first fully open-sourced, FDA-510(k)-cleared deep learning pipelines to mitigate both challenges: Abdominal Aortic Quantification (AAQ) and Bone Mineral Density (BMD) estimation are both offered within the Comp2Comp package for opportunistic analysis of computed tomography scans. AAQ segments the abdominal aorta to assess aneurysm size; BMD segments vertebral bodies to estimate trabecular bone density and osteoporosis risk. AAQ-derived maximal aortic diameters were compared against radiologist ground-truth measurements on 258 patient scans enriched for abdominal aortic aneurysms from four external institutions. BMD binary classifications (low vs. normal bone density) were compared against concurrent DXA scan ground truths obtained on 371 patient scans from four external institutions. AAQ had an overall mean absolute error of 1.57 mm (95% CI 1.38-1.80 mm). BMD had a sensitivity of 81.0% (95% CI 74.0-86.8%) and specificity of 78.4% (95% CI 72.3-83.7%). Comp2Comp AAQ and BMD demonstrated sufficient accuracy for clinical use. Open-sourcing these algorithms improves transparency of typically opaque FDA clearance processes, allows hospitals to test the algorithms before cumbersome clinical pilots, and provides researchers with best-in-class methods.

Asad Aali, Vasiliki Bikia, Maya Varma et al. · stanford

With the growing use of language models (LMs) in clinical environments, there is an immediate need to evaluate the accuracy and safety of LM-generated medical text. Currently, such evaluation relies solely on manual physician review. However, detecting errors in LM-generated text is challenging because 1) manual review is costly and 2) expert-composed reference outputs are often unavailable in real-world settings. While the "LM-as-judge" paradigm (a LM evaluating another LM) offers scalable evaluation, even frontier LMs can miss subtle but clinically significant errors. To address these challenges, we propose MedVAL, a novel, self-supervised, data-efficient distillation method that leverages synthetic data to train evaluator LMs to assess whether LM-generated medical outputs are factually consistent with inputs, without requiring physician labels or reference outputs. To evaluate LM performance, we introduce MedVAL-Bench, a dataset of 840 physician-annotated outputs across 6 diverse medical tasks capturing real-world challenges. Across 10 state-of-the-art LMs spanning open-source and proprietary models, MedVAL distillation significantly improves (p < 0.001) alignment with physicians across seen and unseen tasks, increasing average F1 scores from 66% to 83%. Despite strong baseline performance, MedVAL improves the best-performing proprietary LM (GPT-4o) by 8% without training on physician-labeled data, demonstrating a performance statistically non-inferior to a single human expert (p < 0.001). To support a scalable, risk-aware pathway towards clinical integration, we open-source: 1) Codebase (https://github.com/StanfordMIMI/MedVAL), 2) MedVAL-Bench (https://huggingface.co/datasets/stanfordmimi/MedVAL-Bench), 3) MedVAL-4B (https://huggingface.co/stanfordmimi/MedVAL-4B). Our benchmark provides evidence of LMs approaching expert-level ability in validating AI-generated medical text.

Louis Blankemeier, Ashwin Kumar, Joseph Paul Cohen et al.

The large volume of abdominal computed tomography (CT) scans coupled with the shortage of radiologists have intensified the need for automated medical image analysis tools. Previous state-of-the-art approaches for automated analysis leverage vision-language models (VLMs) that jointly model images and radiology reports. However, current medical VLMs are generally limited to 2D images and short reports. Here to overcome these shortcomings for abdominal CT interpretation, we introduce Merlin, a 3D VLM that learns from volumetric CT scans, electronic health record data and radiology reports. This approach is enabled by a multistage pretraining framework that does not require additional manual annotations. We trained Merlin using a high-quality clinical dataset of paired CT scans (>6 million images from 15,331 CT scans), diagnosis codes (>1.8 million codes) and radiology reports (>6 million tokens). We comprehensively evaluated Merlin on 6 task types and 752 individual tasks that covered diagnostic, prognostic and quality-related tasks. The non-adapted (off-the-shelf) tasks included zero-shot classification of findings (30 findings), phenotype classification (692 phenotypes) and zero-shot cross-modal retrieval (image-to-findings and image-to-impression). The model-adapted tasks included 5-year chronic disease prediction (6 diseases), radiology report generation and 3D semantic segmentation (20 organs). We validated Merlin at scale, with internal testing on 5,137 CT scans and external testing on 44,098 CT scans from 3 independent sites and 2 public datasets. The results demonstrated high generalization across institutions and anatomies. Merlin outperformed 2D VLMs, CT foundation models and off-the-shelf radiology models. We also release our trained models, code, and dataset, available at: https://github.com/StanfordMIMI/Merlin.

Peter G. Brodeur, Thomas A. Buckley, Zahir Kanjee et al.

A seminal paper published by Ledley and Lusted in 1959 introduced complex clinical diagnostic reasoning cases as the gold standard for the evaluation of expert medical computing systems, a standard that has held ever since. Here, we report the results of a physician evaluation of a large language model (LLM) on challenging clinical cases against a baseline of hundreds of physicians. We conduct five experiments to measure clinical reasoning across differential diagnosis generation, display of diagnostic reasoning, triage differential diagnosis, probabilistic reasoning, and management reasoning, all adjudicated by physician experts with validated psychometrics. We then report a real-world study comparing human expert and AI second opinions in randomly-selected patients in the emergency room of a major tertiary academic medical center in Boston, MA. We compared LLMs and board-certified physicians at three predefined diagnostic touchpoints: triage in the emergency room, initial evaluation by a physician, and admission to the hospital or intensive care unit. In all experiments--both vignettes and emergency room second opinions--the LLM displayed superhuman diagnostic and reasoning abilities, as well as continued improvement from prior generations of AI clinical decision support. Our study suggests that LLMs have achieved superhuman performance on general medical diagnostic and management reasoning, fulfilling the vision put forth by Ledley and Lusted, and motivating the urgent need for prospective trials.

David Wu, Fateme Nateghi Haredasht, Saloni Kumar Maharaj et al.

Large language models (LLMs) are routinely used by physicians and patients for medical advice, yet their clinical safety profiles remain poorly characterized. We present NOHARM (Numerous Options Harm Assessment for Risk in Medicine), a benchmark using 100 real primary-care-to-specialist consultation cases to measure harm frequency and severity from LLM-generated medical recommendations. NOHARM covers 10 specialties, with 12,747 expert annotations for 4,249 clinical management options. Across 31 LLMs, severe harm occurs in up to 22.2% (95% CI 21.6-22.8%) of cases, with harms of omission accounting for 76.6% (95% CI 76.4-76.8%) of errors. Safety performance is only moderately correlated (r = 0.61-0.64) with existing AI and medical knowledge benchmarks. The best models outperform generalist physicians on safety (mean difference 9.7%, 95% CI 7.0-12.5%), and a diverse multi-agent approach reduces harm compared to solo models (mean difference 8.0%, 95% CI 4.0-12.1%). Therefore, despite strong performance on existing evaluations, widely used AI models can produce severely harmful medical advice at nontrivial rates, underscoring clinical safety as a distinct performance dimension necessitating explicit measurement.

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.