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bioRxiv · 10.1101/2020.04.24.058982

Leveraging UMLS-driven NLP to enhance identification of influenza predictors derived from electronic medical record data

Stephens, K. A.·Au, M. A.·Yetisgen, M.·Lutz, B.·Suchsland, M. Z.·Ebell, M. H.·Thompson, M.
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Abstract

ObjectiveMultiple clinical prediction rules have been developed, but lack validation. This study aims to identify a set of prediction algorithms for influenza, based on electronic health record (EHR) structured data and clinical notes derived data using Unified Medical Language System (UMLS) driven natural language processing (NLP). Materials and MethodsData were extracted from an enterprise-wide data warehouse for all patients who tested positive for influenza and were seen in ambulatory care between 2009 and 2019 (N = 7,278). A text processing pipeline was used to analyze chart notes for UMLS terms for symptoms of interest to improve data quality completeness. Three models, which step up complexity of the dataset and predictors, were tested with least absolute shrinkage and selection operator (LASSO)-selected parameters to identify predictors for influenza. Receiver operating characteristic (ROC) curves compared test accuracy across the three models. ResultsThree models identified 7, 8, and 10 predictors, and the most complex model performed best. The addition of the UMLS-driven NLP symptoms data improved data quality (false negatives) and increased the number of significant predictors. NLP also increased the strength of the models, as did the addition of two-way predictor interactions. DiscussionThe EHR is a feasible source for offering rapidly accessible datasets for influenza related prediction research that was used to produce a prediction model for influenza. Combining data collected in routine care with data science methods improved a prediction model for influenza, and in the future, could be used to drive diagnostics at the point of care.

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Stephens, K. A., Au, M. A., Yetisgen, M., Lutz, B., Suchsland, M. Z., Ebell, M. H., Thompson, M.. 2020-04-25. Leveraging UMLS-driven NLP to enhance identification of influenza predictors derived from electronic medical record data. https://doi.org/10.1101/2020.04.24.058982

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