Background Novel approaches that complement and go beyond evidence-based medicine are required in the domain of chronic diseases, given the growing incidence of such conditions on the worldwide population. A promising avenue is the secondary use of electronic health records (EHRs), where patient data are analyzed to conduct clinical and translational research. Methods based on machine learning to process EHRs are resulting in improved understanding of patient clinical trajectories and chronic disease risk prediction, creating a unique opportunity to derive previously unknown clinical insights. However, a wealth of clinical histories remains locked behind clinical narratives in free-form text. Consequently, unlocking the full potential of EHR data is contingent on the development of natural language processing (NLP) methods to automatically transform clinical text into structured clinical data that can guide clinical decisions and potentially delay or prevent disease onset. Objective The goal of the research was to provide a comprehensive overview of the development and uptake of NLP methods applied to free-text clinical notes related to chronic diseases, including the investigation of challenges faced by NLP methodologies in understanding clinical narratives. Methods Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed and searches were conducted in 5 databases using “clinical notes,” “natural language processing,” and “chronic disease” and their variations as keywords to maximize coverage of the articles. Results Of the 2652 articles considered, 106 met the inclusion criteria. Review of the included papers resulted in identification of 43 chronic diseases, which were then further classified into 10 disease categories using the International Classification of Diseases, 10th Revision . The majority of studies focused on diseases of the circulatory system (n=38) while endocrine and metabolic diseases were fewest (n=14). This was due to the structure of clinical records related to metabolic diseases, which typically contain much more structured data, compared with medical records for diseases of the circulatory system, which focus more on unstructured data and consequently have seen a stronger focus of NLP. The review has shown that there is a significant increase in the use of machine learning methods compared to rule-based approaches; however, deep learning methods remain emergent (n=3). Consequently, the majority of works focus on classification of disease phenotype with only a handful of papers addressing extraction of comorbidities from the free text or integration of clinical notes with structured data. There is a notable use of relatively simple methods, such as shallow classifiers (or combination with rule-based methods), due to the interpretability of predictions, which still represents a significant issue for more complex methods...

Progress of machine learning in critical care has been difficult to track, in part due to absence of public benchmarks. Other fields of research (such as computer vision and natural language processing) have established various competitions and public benchmarks. Recent availability of large clinical datasets has enabled the possibility of establishing public benchmarks. Taking advantage of this opportunity, we propose a public benchmark suite to address four areas of critical care, namely mortality prediction, estimation of length of stay, patient phenotyping and risk of decompensation. We define each task and compare the performance of both clinical models as well as baseline and deep learning models using eICU critical care dataset of around 73,000 patients. This is the first public benchmark on a multicentre critical care dataset, comparing the performance of clinical gold standard with our predictive model. We also investigate the impact of numerical variables as well as handling of categorical variables on each of the defined tasks. The source code, detailing our methods and experiments is publicly available such that anyone can replicate our results and build upon our work.

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Introduction Delirium occurrence is common and preventive strategies are resource intensive. Screening tools can prioritize patients at risk. Using machine learning, we can capture time and treatment effects that pose a challenge to delirium prediction. We aim to develop a delirium prediction model that can be used as a screening tool. Methods From the eICU Collaborative Research Database (eICU-CRD) and the Medical Information Mart for Intensive Care version III (MIMIC-III) database, patients with one or more Confusion Assessment Method-Intensive Care Unit (CAM-ICU) values and intensive care unit (ICU) length of stay greater than 24 h were included in our study. We validated our model using 21 quantitative clinical parameters and assessed performance across a range of observation and prediction windows, using different thresholds and applied interpretation techniques. We evaluate our models based on stratified repeated cross-validation using 3 algorithms, namely Logistic Regression, Random Forest, and Bidirectional Long Short-Term Memory (BiLSTM). BiLSTM represents an evolution from recurrent neural network-based Long Short-Term Memory, and with a backward input, preserves information from both past and future. Model performance is measured using Area Under Receiver Operating Characteristic, Area Under Precision Recall Curve, Recall, Precision (Positive Predictive Value), and Negative Predictive Value metrics. Results We evaluated our results on 16 546 patients (47% female) and 6294 patients (44% female) from eICU-CRD and MIMIC-III databases, respectively. Performance was best in BiLSTM models where, precision and recall changed from 37.52% (95% confidence interval [CI], 36.00%–39.05%) to 17.45 (95% CI, 15.83%–19.08%) and 86.1% (95% CI, 82.49%–89.71%) to 75.58% (95% CI, 68.33%–82.83%), respectively as prediction window increased from 12 to 96 h. After optimizing for higher recall, precision and recall changed from 26.96% (95% CI, 24.99%–28.94%) to 11.34% (95% CI, 10.71%–11.98%) and 93.73% (95% CI, 93.1%–94.37%) to 92.57% (95% CI, 88.19%–96.95%), respectively. Comparable results were obtained in the MIMIC-III cohort. Conclusions Our model performed comparably to contemporary models using fewer variables. Using techniques like sliding windows, modification of threshold to augment recall and feature ranking for interpretability, we addressed shortcomings of current models.