Impact of Different Approaches to Preparing Notes for Analysis With Natural Language Processing on the Performance of Prediction Models in Intensive Care

• Main Authors: Malini Mahendra, MD, Yanting Luo, MS, Hunter Mills, MS, Gundolf Schenk, PhD, Atul J. Butte, MD, PhD, R. Adams Dudley, MD, MBA
• Format: Article
• Language: English
• Published: Wolters Kluwer 2021-06-01
• Series: Critical Care Explorations
• Online Access: http://journals.lww.com/10.1097/CCE.0000000000000450

OBJECTIVES:. To evaluate whether different approaches in note text preparation (known as preprocessing) can impact machine learning model performance in the case of mortality prediction ICU. DESIGN:. Clinical note text was used to build machine learning models for adults admitted to the ICU. Preprocessing strategies studied were none (raw text), cleaning text, stemming, term frequency-inverse document frequency vectorization, and creation of n-grams. Model performance was assessed by the area under the receiver operating characteristic curve. Models were trained and internally validated on University of California San Francisco data using 10-fold cross validation. These models were then externally validated on Beth Israel Deaconess Medical Center data. SETTING:. ICUs at University of California San Francisco and Beth Israel Deaconess Medical Center. SUBJECTS:. Ten thousand patients in the University of California San Francisco training and internal testing dataset and 27,058 patients in the external validation dataset, Beth Israel Deaconess Medical Center. INTERVENTIONS:. None. MEASUREMENTS AND MAIN RESULTS:. Mortality rate at Beth Israel Deaconess Medical Center and University of California San Francisco was 10.9% and 7.4%, respectively. Data are presented as area under the receiver operating characteristic curve (95% CI) for models validated at University of California San Francisco and area under the receiver operating characteristic curve for models validated at Beth Israel Deaconess Medical Center. Models built and trained on University of California San Francisco data for the prediction of inhospital mortality improved from the raw note text model (AUROC, 0.84; CI, 0.80–0.89) to the term frequency-inverse document frequency model (AUROC, 0.89; CI, 0.85–0.94). When applying the models developed at University of California San Francisco to Beth Israel Deaconess Medical Center data, there was a similar increase in model performance from raw note text (area under the receiver operating characteristic curve at Beth Israel Deaconess Medical Center: 0.72) to the term frequency-inverse document frequency model (area under the receiver operating characteristic curve at Beth Israel Deaconess Medical Center: 0.83). CONCLUSIONS:. Differences in preprocessing strategies for note text impacted model discrimination. Completing a preprocessing pathway including cleaning, stemming, and term frequency-inverse document frequency vectorization resulted in the preprocessing strategy with the greatest improvement in model performance. Further study is needed, with particular emphasis on how to manage author implicit bias present in note text, before natural language processing algorithms are implemented in the clinical setting.