Nationwide EHR-Based Chronic Rhinosinusitis Prediction Using Demographic-Stratified Models
Authors: Sicong Chang, Yidan Shen, Justina Varghese, Akshay R Prabhakar, Sebastian Guadarrama-Sistos-Vazquez, Jiefu Chen, Masayoshi Takashima, Omar G. Ahmed, +2 more
Abstract
Chronic rhinosinusitis (CRS) is a common heterogeneous inflammatory disorder that causes substantial morbidity and healthcare costs. CRS is difficult to identify early from routine encounters, as symptom presentations overlap with common conditions such as allergic rhinitis, and heterogeneous phenotypes further obscure risk patterns. Prior predictive studies often rely on single-institutional cohorts , which reduce population-level generalizability. To overcome this, we leveraged nationwide longitudinal EHR data from the \textit{All of Us} Research Program to predict CRS diagnosis using two years of pre-diagnostic history. To address extreme feature sparsity and dimensionality in coded EHR data, we implemented a hybrid feature-selection pipeline that combines prevalence-based statistical screening with model-based importance ranking, compressing approximately 110,000 candidate codes into 100 interpretable features. To capture demographic heterogeneity, we trained demographic stratified models across six adult sex and life-stage subgroups with subgroup-specific hyperparameter tuning. Our framework achieved an overall AUC of 0.8461, improving discrimination by 0.0168 over the best baseline. These results demonstrate that routinely collected EHR data may support population-representative CRS risk stratification and inform earlier triage and referral prioritization in primary care.
Emergency triage requires reliable decisions within a short time period. However, the available electronic health record (EHR) data, including structured data and clinical text, are often incomplete, unreliable, and inconsistent. This makes machine learning (ML)-based triage prediction more challenging, as existing ML models typically rely on complete and reliable EHR data to accurately predict patients' acuity levels. To address this, we propose confidence- and reliability-aware selective triage (CRS-Triage) to predict patients' acuity levels with a confidence score. By comparing the confidence score with a predefined threshold, CRS-Triage can selectively determine whether the model should make the decision or defer the case. Specifically, CRS-Triage separately evaluates the reliability of structured data and clinical text and then jointly considers the consistency between the two modalities to estimate the confidence of each prediction. Moreover, to reduce the risk of missing high-acuity patients, namely under-triage, CRS-Triage prefers to assign patients slightly higher acuity levels, namely over-triage, by penalizing under-triage errors. Experiments on the MIMIC-IV-ED dataset show that CRS-Triage achieves strong predictive performance. It also provides a better risk-coverage trade-off and remains reliable when the available EHR data are incomplete, degraded, or inconsistent across modalities.
We evaluated whether a glaucoma risk assessment (GRA) model trained on All of Us national data can identify patients at high probability of glaucoma using only systemic electronic health records (EHR) at an independent institution. In this cross-sectional study, 20,636 Stanford patients seen from November 2013 to January 2024 were included (15% with glaucoma). A pretrained GRA model was fine-tuned on the Stanford cohort and tested on a held-out set using demographics, systemic diagnoses, medications, laboratory results, and physical examination measurements as inputs. The best model achieved AUROC 0.883 and PPV 0.657. Calibration was consistent with clinical risk: the highest prediction decile showed the greatest glaucoma diagnosis rate (65.7%) and treatment rate (57.0%). Performance improved with more trainable layers up to 15 and with additional data. An EHR-only GRA model may enable scalable and accessible pre-screening without specialized imaging.
In routine care, individuals identified a priori as high-risk are usually tested for conditions more frequently. Protected attributes, such as sex or ethnicity may also determine testing frequency. Such heterogeneous detection rates across a population induce label error. This causes systematic model error for specific groups and biases performance metrics during validation. This paper proposes a method to correct for such bias in prediction models due to differential diagnostic delay. We use a causal inference framework to define our target estimand: an individual's diagnosis probability in a counterfactual scenario where their diagnosis rate matches that of a reference group. We model the longitudinal process as a hidden Markov model, in which confirmatory test results are emissions from a latent progressive disease stage. We validate our approach in simulated data and apply it to a case study of chronic kidney disease prediction using electronic health records. In simulations, our method reduces prediction bias and improves calibration-in-the-large, correcting the Observed:Expected ratio in the underdiagnosed group from 1.34 (standard deviation: 0.09) in a model developed without any correction for underdiagnosis bias to 1.02 (0.09). Violations of assumptions in the simulation affected the estimation of model parameters, but the proposed approach nonetheless remained better calibrated than the standard model. In the clinical case study, we identify diabetes as the main driver of observability, with an odds ratio of 10.36 (95% confidence interval, 9.80 - 11.02) in 6-month urine albumin-creatinine ratio testing rate. Using our approach to predict the counterfactual diagnostic rate in patients without diabetes, we improved the Observed:Expected ratio of a developed clinical prediction model from 1.55 (1.51 - 1.59) to 1.01 (0.98 - 1.04).
Jose Benitez-Aurioles, Ricardo Silva, Brian McMillan +1