Predictive Model for Extended-Spectrum β-Lactamase–Producing Bacterial Infections Using Natural Language Processing Technique and Open Data in Intensive Care Unit Environment: Retrospective Observational Study (Preprint)

Abstract

Machine learning has advanced medical event prediction, mostly using private data. The public MIMIC-3 (Medical Information Mart for Intensive Care III) data set, which contains detailed data on over 40,000 intensive care unit patients, stands out as it can help develop better models including structured and textual data.

This study aimed to build and test a machine learning model using the MIMIC-3 data set to determine the effectiveness of information extracted from electronic medical record text using a named entity recognition, specifically QuickUMLS, for predicting important medical events. Using the prediction of extended-spectrum β-lactamase (ESBL)–producing bacterial infections as an example, this study shows how open data sources and simple technology can be useful for making clinically meaningful predictions.

The MIMIC-3 data set, including demographics, vital signs, laboratory results, and textual data, such as discharge summaries, was used. This study specifically targeted patients diagnosed with <i>Klebsiella pneumoniae</i> or <i>Escherichia coli</i> infection. Predictions were based on ESBL-producing bacterial standards and the minimum inhibitory concentration criteria. Both the structured data and extracted patient histories were used as predictors. In total, 2 models, an L1-regularized logistic regression model and a LightGBM model, were evaluated using the receiver operating characteristic area under the curve (ROC-AUC) and the precision-recall curve area under the curve (PR-AUC).

Of 46,520 MIMIC-3 patients, 4046 were identified with bacterial cultures, indicating the presence of <i>K pneumoniae</i> or <i>E coli</i>. After excluding patients who lacked discharge summary text, 3614 patients remained. The L1-penalized model, with variables from only the structured data, displayed a ROC-AUC of 0.646 and a PR-AUC of 0.307. The LightGBM model, combining structured and textual data, achieved a ROC-AUC of 0.707 and a PR-AUC of 0.369. Key contributors to the LightGBM model included patient age, duration since hospital admission, and specific medical history such as diabetes. The structured data-based model showed improved performance compared to the reference models. Performance was further improved when textual medical history was included. Compared to other models predicting drug-resistant bacteria, the results of this study ranked in the middle. Some misidentifications, potentially due to the limitations of QuickUMLS, may have affected the accuracy of the model.

This study successfully developed a predictive model for ESBL-producing bacterial infections using the MIMIC-3 data set, yielding results consistent with existing literature. This model stands out for its transparency and reliance on open data and open-named entity recognition technology. The performance of the model was enhanced using textual information. With advancements in natural language processing tools such as BERT and GPT, the extraction of medical data from text holds substantial potential for future model optimization.