Faculty Bibliography

The COVID-19 pandemic has challenged front-line clinical decision-making, leading to numerous published prognostic tools. However, few models have been prospectively validated and none report implementation in practice. Here, we use 3345 retrospective and 474 prospective hospitalizations to develop and validate a parsimonious model to identify patients with favorable outcomes within 96 h of a prediction, based on real-time lab values, vital signs, and oxygen support variables. In retrospective and prospective validation, the model achieves high average precision (88.6% 95% CI: [88.4-88.7] and 90.8% [90.8-90.8]) and discrimination (95.1% [95.1-95.2] and 86.8% [86.8-86.9]) respectively. We implemented and integrated the model into the EHR, achieving a positive predictive value of 93.3% with 41% sensitivity. Preliminary results suggest clinicians are adopting these scores into their clinical workflows.

During the COVID-19 pandemic, rapid and accurate triage of patients at the emergency department is critical to inform decision-making. We propose a data-driven approach for automatic prediction of deterioration risk using a deep neural network that learns from chest X-ray images, and a gradient boosting model that learns from routine clinical variables. Our AI prognosis system, trained using data from 3,661 patients, achieves an AUC of 0.786 (95% CI: 0.742-0.827) when predicting deterioration within 96 hours. The deep neural network extracts informative areas of chest X-ray images to assist clinicians in interpreting the predictions, and performs comparably to two radiologists in a reader study. In order to verify performance in a real clinical setting, we silently deployed a preliminary version of the deep neural network at NYU Langone Health during the first wave of the pandemic, which produced accurate predictions in real-time. In summary, our findings demonstrate the potential of the proposed system for assisting front-line physicians in the triage of COVID-19 patients.

BACKGROUND:Because of the strong link between childhood obesity and adulthood obesity comorbidities, and the difficulty in decreasing body mass index (BMI) later in life, effective strategies are needed to address this condition in early childhood. The ability to predict obesity before age five could be a useful tool, allowing prevention strategies to focus on high risk children. The few existing prediction models for obesity in childhood have primarily employed data from longitudinal cohort studies, relying on difficult to collect data that are not readily available to all practitioners. Instead, we utilized real-world unaugmented electronic health record (EHR) data from the first two years of life to predict obesity status at age five, an approach not yet taken in pediatric obesity research. METHODS AND FINDINGS/RESULTS:We trained a variety of machine learning algorithms to perform both binary classification and regression. Following previous studies demonstrating different obesity determinants for boys and girls, we similarly developed separate models for both groups. In each of the separate models for boys and girls we found that weight for length z-score, BMI between 19 and 24 months, and the last BMI measure recorded before age two were the most important features for prediction. The best performing models were able to predict obesity with an Area Under the Receiver Operator Characteristic Curve (AUC) of 81.7% for girls and 76.1% for boys. CONCLUSIONS:We were able to predict obesity at age five using EHR data with an AUC comparable to cohort-based studies, reducing the need for investment in additional data collection. Our results suggest that machine learning approaches for predicting future childhood obesity using EHR data could improve the ability of clinicians and researchers to drive future policy, intervention design, and the decision-making process in a clinical setting.

Visual inspection of histopathology slides is one of the main methods used by pathologists to assess the stage, type and subtype of lung tumors. Adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC) are the most prevalent subtypes of lung cancer, and their distinction requires visual inspection by an experienced pathologist. In this study, we trained a deep convolutional neural network (inception v3) on whole-slide images obtained from The Cancer Genome Atlas to accurately and automatically classify them into LUAD, LUSC or normal lung tissue. The performance of our method is comparable to that of pathologists, with an average area under the curve (AUC) of 0.97. Our model was validated on independent datasets of frozen tissues, formalin-fixed paraffin-embedded tissues and biopsies. Furthermore, we trained the network to predict the ten most commonly mutated genes in LUAD. We found that six of them-STK11, EGFR, FAT1, SETBP1, KRAS and TP53-can be predicted from pathology images, with AUCs from 0.733 to 0.856 as measured on a held-out population. These findings suggest that deep-learning models can assist pathologists in the detection of cancer subtype or gene mutations. Our approach can be applied to any cancer type, and the code is available at https://github.com/ncoudray/DeepPATH .

We present a new approach to population health, in which data-driven predictive models are learned for outcomes such as type 2 diabetes. Our approach enables risk assessment from readily available electronic claims data on large populations, without additional screening cost. Proposed model uncovers early and late-stage risk factors. Using administrative claims, pharmacy records, healthcare utilization, and laboratory results of 4.1 million individuals between 2005 and 2009, an initial set of 42,000 variables were derived that together describe the full health status and history of every individual. Machine learning was then used to methodically enhance predictive variable set and fit models predicting onset of type 2 diabetes in 2009-2011, 2010-2012, and 2011-2013. We compared the enhanced model with a parsimonious model consisting of known diabetes risk factors in a real-world environment, where missing values are common and prevalent. Furthermore, we analyzed novel and known risk factors emerging from the model at different age groups at different stages before the onset. Parsimonious model using 21 classic diabetes risk factors resulted in area under ROC curve (AUC) of 0.75 for diabetes prediction within a 2-year window following the baseline. The enhanced model increased the AUC to 0.80, with about 900 variables selected as predictive (p < 0.0001 for differences between AUCs). Similar improvements were observed for models predicting diabetes onset 1-3 years and 2-4 years after baseline. The enhanced model improved positive predictive value by at least 50% and identified novel surrogate risk factors for type 2 diabetes, such as chronic liver disease (odds ratio [OR] 3.71), high alanine aminotransferase (OR 2.26), esophageal reflux (OR 1.85), and history of acute bronchitis (OR 1.45). Liver risk factors emerge later in the process of diabetes development compared with obesity-related factors such as hypertension and high hemoglobin A1c. In conclusion, population-level risk prediction for type 2 diabetes using readily available administrative data is feasible and has better prediction performance than classical diabetes risk prediction algorithms on very large populations with missing data. The new model enables intervention allocation at national scale quickly and accurately and recovers potentially novel risk factors at different stages before the disease onset.

IMPORTANCE/UNASSIGNED:Pancreatic ductal adenocarcinoma (PDAC) is a leading cause of cancer deaths in the US. Although early detection improves survival, the rarity of the disease has rendered population screening a difficult approach. OBJECTIVE/UNASSIGNED:To develop and validate a parsimonious, interpretable, and generalizable model predicting incident PDAC-termed PRIME (PDAC Risk Model for Earlier Detection)-using routinely available electronic health record (EHR) data. DESIGN, SETTING, AND PARTICIPANTS/UNASSIGNED:This cohort study used the Optum Labs Data Warehouse, a longitudinal, deidentified US EHR and claims database. Adults 40 years or older with an outpatient clinical encounter between 2016 and 2018 were included. Participants from 23 health systems (n = 4 859 833) comprised the training cohort; 31 additional systems (n = 5 619 091) served as validation. International validation was conducted in the UK Biobank (n = 498 754). Data analysis occurred July 2025 to January 2026. EXPOSURES/UNASSIGNED:Demographics, diagnosis codes, and routinely measured laboratory values were evaluated. Elastic-net regularization with 10-fold cross-validation selected the predictor set. MAIN OUTCOMES AND MEASURES/UNASSIGNED:Incident PDAC was identified by International Classification of Diseases, Ninth and Tenth Revisions (ICD-9/10) codes. Model performance was assessed using time-dependent area under the curve (AUC) and calibration metrics. RESULTS/UNASSIGNED:Overall, the study included more than 11 million adults (2.1% Asian individuals, 8.4% Black individuals, 4.3% Hispanic/Latino individuals, 82.7% White individuals, and 2.4% other race/ethnicity by EHR reporting). In the training cohort (mean [SD] age, 60.4 [11] years), 14 405 individuals were diagnosed with PDAC (incidence 55 per 100 000 person-years) over a mean (SD) of 5.4 (2.5) years; in the validation cohort, 11 693 individuals were diagnosed with PDAC (54 per 100 000 person-years) over a mean (SD) of 3.9 (2.5) years. PRIME retained 19 predictors including history of pancreatitis, gastrointestinal disorders, prior cancers, type 2 diabetes, elevated aspartate aminotransferase levels, smoking, non-type-O blood, and male sex. Discrimination was strong at the 36-month time horizon (AUC = 0.75 in both the training and validation cohorts) with good calibration. In the validation cohort, patients in the top 1% of predicted risk had substantially higher PDAC risk (HR, 7.63; 95% CI, 6.85-8.49) compared with average-risk patients. In the UK Biobank, PRIME achieved a 36-month AUC of 0.71 with good calibration. CONCLUSIONS AND RELEVANCE/UNASSIGNED:In this validation cohort study, PRIME was a transparent EHR-based model that effectively stratified PDAC risk across diverse US health systems and generalized internationally. Prospective studies should evaluate for EHR-guided PDAC case-finding and integration with blood-based early-detection assays.

Head computed tomography (CT) imaging is a widely used imaging modality with multitudes of medical indications, particularly in assessing pathology of the brain, skull and cerebrovascular system. It is commonly used as the first-line imaging in neurologic emergencies given its rapidity of image acquisition, safety, cost and ubiquity. Deep learning models may facilitate detection of a wide range of diseases. However, the scarcity of high-quality labels and annotations, particularly among less common conditions, substantially hinders the development of powerful models. To address this challenge, we introduce FM-HCT, a Foundation Model for Head CT for generalizable disease detection, trained using self-supervised learning. Our approach pretrains a deep learning model on a large, diverse dataset of 361,663 non-contrast 3D head CT scans without the need for manual annotations, enabling the model to learn robust, generalizable features. Our results demonstrate that the self-supervised foundation model substantially improves performance on downstream diagnostic tasks compared to models trained from scratch and previous 3D CT foundation models trained on scarce annotated datasets.

Accurate disease prognosis is essential for patient care but is often hindered by the scarcity of longitudinal data. This study explores deep learning training strategies that utilize large, accessible diagnostic datasets to pretrain models aimed at predicting future disease progression in knee osteoarthritis (OA), Alzheimer's disease (AD), and breast cancer (BC). While diagnostic pretraining improves prognostic task performance, naive fine-tuning for prognosis can cause 'catastrophic forgetting,' where the model's original diagnostic accuracy degrades, a significant patient safety concern in real-world settings. To address this, we propose a sequential learning strategy with experience replay. We used cohorts with knee radiographs, brain MRIs, and digital mammograms to predict 4-year structural worsening in OA, 2-year cognitive decline in AD, and 5-year cancer diagnosis in BC. Our results showed that diagnostic pretraining on larger datasets improved prognosis model performance compared to standard baselines, boosting both the Area Under the Receiver Operating Characteristic curve (AUROC) (e.g., Knee OA external: 0.770 vs 0.747; Breast Cancer: 0.874 vs 0.848) and the Area Under the Precision-Recall Curve (AUPRC) (e.g., Alzheimer's Disease: 0.752 vs 0.683). Additionally, a sequential learning approach with experience replay achieved prognostic performance comparable to dedicated single-task models (e.g., Breast Cancer AUROC 0.876 vs 0.874) while also preserving diagnostic ability. This method maintained high diagnostic accuracy (e.g., Breast Cancer Balanced Accuracy 50.4% vs 50.9% for a dedicated diagnostic model), unlike simpler multitask methods prone to catastrophic forgetting (e.g., 37.7%). Our findings show that leveraging large diagnostic datasets is a reliable and data-efficient way to enhance prognostic models while maintaining essential diagnostic skills.

Despite rapid advances in artificial intelligence (AI) across sectors, health care remains one of the least transformed domains. This stagnation is not due to lack of data, clinical need, or innovation, but rather to persistent regulatory and economic misalignment. Even AI tools cleared by the U.S. Food and Drug Administration that meet clinical efficacy standards often face major barriers to adoption, largely driven by outdated reimbursement frameworks and fragmented incentives among stakeholders. The result is a systemic failure to deploy technologies that could meaningfully reduce clinician workload, shorten wait times, and improve patient lives. In this article, we examine the reimbursement landscape for health AI, focusing first on tools that fit existing regulatory pathways, outlining payment barriers and proposing policy reforms. These include resolving Current Procedural Terminology adoption bottlenecks, addressing integration overhead, and aligning pricing models with AI cost structures. We then extend the discussion to the emerging domain of generative AI in health care, highlighting the urgent need for prospective regulatory frameworks to ensure patient benefits. (Funded by the National Institutes of Health and the Leukemia and Lymphoma Society.).