Moving Biosurveillance Beyond Coded Data Using AI for Symptom Detection From Physician Notes: Retrospective Cohort Study (Preprint)
Authors: McMurry Andrew J , Zipursky Amy R , Geva Alon , Olson Karen L , Jones James R , Ignatov Vladimir , Miller Timothy A , Mandl Kenneth D 
Published: April 2024

BACKGROUND

Real-time surveillance of emerging infectious diseases necessitates a dynamically evolving, computable case definition, which frequently incorporates symptom-related criteria. For symptom detection, both population health monitoring platforms and research initiatives primarily depend on structured data extracted from electronic health records.

OBJECTIVE

This study sought to validate and test an artificial intelligence (AI)–based natural language processing (NLP) pipeline for detecting COVID-19 symptoms from physician notes in pediatric patients. We specifically study patients presenting to the emergency department (ED) who can be sentinel cases in an outbreak.

METHODS

Subjects in this retrospective cohort study are patients who are 21 years of age and younger, who presented to a pediatric ED at a large academic children’s hospital between March 1, 2020, and May 31, 2022. The ED notes for all patients were processed with an NLP pipeline tuned to detect the mention of 11 COVID-19 symptoms based on Centers for Disease Control and Prevention (CDC) criteria. For a gold standard, 3 subject matter experts labeled 226 ED notes and had strong agreement (<i>F</i><sub>1</sub>-score=0.986; positive predictive value [PPV]=0.972; and sensitivity=1.0). <i>F</i><sub>1</sub>-score, PPV, and sensitivity were used to compare the performance of both NLP and the <i>International Classification of Diseases, 10th Revision</i> (ICD-10) coding to the gold standard chart review. As a formative use case, variations in symptom patterns were measured across SARS-CoV-2 variant eras.

RESULTS

There were 85,678 ED encounters during the study period, including 4% (n=3420) with patients with COVID-19. NLP was more accurate at identifying encounters with patients that had any of the COVID-19 symptoms (<i>F</i><sub>1</sub>-score=0.796) than ICD-10 codes (<i>F</i><sub>1</sub>-score =0.451). NLP accuracy was higher for positive symptoms (sensitivity=0.930) than ICD-10 (sensitivity=0.300). However, ICD-10 accuracy was higher for negative symptoms (specificity=0.994) than NLP (specificity=0.917). Congestion or runny nose showed the highest accuracy difference (NLP: <i>F</i><sub>1</sub>-score=0.828 and ICD-10: <i>F</i><sub>1</sub>-score=0.042). For encounters with patients with COVID-19, prevalence estimates of each NLP symptom differed across variant eras. Patients with COVID-19 were more likely to have each NLP symptom detected than patients without this disease. Effect sizes (odds ratios) varied across pandemic eras.

CONCLUSIONS

This study establishes the value of AI-based NLP as a highly effective tool for real-time COVID-19 symptom detection in pediatric patients, outperforming traditional ICD-10 methods. It also reveals the evolving nature of symptom prevalence across different virus variants, underscoring the need for dynamic, technology-driven approaches in infectious disease surveillance.