Comparing Natural Language Processing and Structured Medical Data to Develop a Computable Phenotype for Patients Hospitalized Due to COVID-19: Retrospective Analysis

Background: Throughout the COVID-19 pandemic, many hospitals conducted routine testing of hospitalized patients for SARS-CoV-2 infection upon admission. Some of these patients are admitted for reasons unrelated to COVID-19 and incidentally test positive for the virus. Because COVID-19-related hospitalizations have become a critical public health indicator, it is important to identify patients who are hospitalized because of COVID-19 as opposed to those who are admitted for other indications.

Objective: We compared the performance of different computable phenotype definitions for COVID-19 hospitalizations that use different types of data from electronic health records (EHRs), including structured EHR data elements, clinical notes, or a combination of both data types.

Methods: We conducted a retrospective data analysis, using clinician chart review-based validation at a large academic medical center. We reviewed and analyzed the charts of 586 hospitalized individuals who tested positive for SARS-CoV-2 in January 2022. We used LASSO (least absolute shrinkage and selection operator) regression and random forests to fit classification algorithms that incorporated structured EHR data elements, clinical notes, or a combination of structured data and clinical notes. We used natural language processing to incorporate data from clinical notes. The performance of each model was evaluated based on the area under the receiver operator characteristic curve (AUROC) and an associated decision rule based on sensitivity and positive predictive value. We also identified top words and clinical indicators of COVID-19-specific hospitalization and assessed the impact of different phenotyping strategies on estimated hospital outcome metrics.

Results: Based on a chart review, 38.2% (224/586) of patients were determined to have been hospitalized for reasons other than COVID-19, despite having tested positive for SARS-CoV-2. A computable phenotype that used clinical notes had significantly better discrimination than one that used structured EHR data elements (AUROC: 0.894 vs 0.841; P<.001) and performed similarly to a model that combined clinical notes with structured data elements (AUROC: 0.894 vs 0.893; P=.91). Assessments of hospital outcome metrics significantly differed based on whether the population included all hospitalized patients who tested positive for SARS-CoV-2 or those who were determined to have been hospitalized due to COVID-19.

Conclusions: These findings highlight the importance of cause-specific phenotyping for COVID-19 hospitalizations. More generally, this work demonstrates the utility of natural language processing approaches for deriving information related to patient hospitalizations in cases where there may be multiple conditions that could serve as the primary indication for hospitalization.