Predicting severe clinical events by learning about life-saving actions and outcomes using distant supervision.

Medical error is a leading cause of patient death in the United States. Among the different types of medical errors, harm to patients caused by doctors missing early signs of deterioration is especially challenging to address due to the heterogeneity of patients' physiological patterns. In this study, we implemented risk prediction models using the gradient boosted tree method to derive risk estimates for acute onset diseases in the near future. The prediction model uses physiological variables as input signals and the time of the administration of outcome-related interventions and discharge diagnoses as labels. We examine four categories of acute onset illness: acute heart failure (AHF), acute lung injury (ALI), acute kidney injury (AKI), and acute liver failure (ALF). To develop and test the model, we consider data from two sources: 23,578 admissions to the Intensive Care Unit (ICU) from the MIMIC-3 dataset (Beth-Israel Hospital) and 16,612 ICU admissions on hospitals affiliated with our institution (University of Washington Medical Center and Harborview Medical Center, the UW-CDR dataset). We systematically identify outcome-related interventions for each acute organ failure, then use them, along with discharge diagnoses, to label proxy events to train gradient boosted trees. The trained models achieve the highest F1 score with a value of 0.6018 when predicting the need for life-saving interventions for ALI within the next 24 h in the MIMIC-3 dataset while showing a median F1 score of 0.3850 from all acute organ failures in both datasets. The approach also achieves the highest F1 score of 0.6301 when classifying a patient's ALI status at the time of discharge from the MIMIC-3 dataset, with a median F1 score of 0.4307 in both datasets. This study shows the potential for using the time of outcome-related intervention administrations and discharge diagnoses as labels to train supervised machine learning models that predict the risk of acute onset illnesses.

Assertion modeling and its role in clinical phenotype identification.

This paper describes an approach to assertion classification and an empirical study on the impact this task has on phenotype identification, a real world application in the clinical domain. The task of assertion classification is to assign to each medical concept mentioned in a clinical report (e.g., pneumonia, chest pain) a specific assertion category (e.g., present, absent, and possible). To improve the classification of medical assertions, we propose several new features that capture the semantic properties of special cue words highly indicative of a specific assertion category. The results obtained outperform the current state-of-the-art results for this task. Furthermore, we confirm the intuition that assertion classification contributes in significantly improving the results of phenotype identification from free-text clinical records.

Beyond SumBasic: Task-focused summarization with sentence simplification and lexical expansion.

In recent years, there has been increased interest in topic-focused multi-document summarization. In this task, automatic summaries are produced in response to a specific information request, or topic, stated by the user. The system we have designed to accomplish this task comprises four main components: a generic extractive summarization system, a topic-focusing component, sentence simplification, and lexical expansion of topic words. This paper details each of these components, together with experiments designed to quantify their individual contributions. We include an analysis of our results on two large datasets commonly used to evaluate task-focused summarization, the DUC2005 and DUC2006 datasets, using automatic metrics. Additionally, we include an analysis of our results on the DUC2006 task according to human evaluation metrics. In the human evaluation of system summaries compared to human summaries, i.e., the Pyramid method, our system ranked first out of 22 systems in terms of overall mean Pyramid score; and in the human evaluation of summary responsiveness to the topic, our system ranked third out of 35 systems.

On-time clinical phenotype prediction based on narrative reports.

In this paper we describe a natural language processing system which is able to predict whether or not a patient exhibits a specific phenotype using the information extracted from the narrative reports associated with the patient. Furthermore, the phenotypic annotations from our report dataset were performed at the report level which allows us to perform the prediction of the clinical phenotype at any point in time during the patient hospitalization period. Our experiments indicate that an important factor in achieving better results for this problem is to determine how much information to extract from the patient reports in the time interval between the patient admission time and the current prediction time.

Automated tools for phenotype extraction from medical records.

Clinical research studying critical illness phenotypes relies on the identification of clinical syndromes defined by consensus definitions. Historically, identifying phenotypes has required manual chart review, a time and resource intensive process. The overall research goal of C ritical I llness PH enotype E xt R action (deCIPHER) project is to develop automated approaches based on natural language processing and machine learning that accurately identify phenotypes from EMR. We chose pneumonia as our first critical illness phenotype and conducted preliminary experiments to explore the problem space. In this abstract, we outline the tools we built for processing clinical records, present our preliminary findings for pneumonia extraction, and describe future steps.

Assessing pneumonia identification from time-ordered narrative reports.

In this paper, we present a natural language processing system that can be used in hospital surveillance applications with the purpose of identifying patients with pneumonia. For this purpose, we built a sequence of supervised classifiers, where the dataset corresponding to each classifier consists of a restricted set of time-ordered narrative reports. In this way the pneumonia surveillance application will be able to invoke the most suitable classifier for each patient based on the period of time that has elapsed since the patient was admitted into the hospital. Our system achieves significantly better results when compared with a baseline previously proposed for pneumonia identification.

Pneumonia identification using statistical feature selection.

OBJECTIVE: This paper describes a natural language processing system for the task of pneumonia identification. Based on the information extracted from the narrative reports associated with a patient, the task is to identify whether or not the patient is positive for pneumonia. DESIGN: A binary classifier was employed to identify pneumonia from a dataset of multiple types of clinical notes created for 426 patients during their stay in the intensive care unit. For this purpose, three types of features were considered: (1) word n-grams, (2) Unified Medical Language System (UMLS) concepts, and (3) assertion values associated with pneumonia expressions. System performance was greatly increased by a feature selection approach which uses statistical significance testing to rank features based on their association with the two categories of pneumonia identification. RESULTS: Besides testing our system on the entire cohort of 426 patients (unrestricted dataset), we also used a smaller subset of 236 patients (restricted dataset). The performance of the system was compared with the results of a baseline previously proposed for these two datasets. The best results achieved by the system (85.71 and 81.67 F1-measure) are significantly better than the baseline results (50.70 and 49.10 F1-measure) on the restricted and unrestricted datasets, respectively. CONCLUSION: Using a statistical feature selection approach that allows the feature extractor to consider only the most informative features from the feature space significantly improves the performance over a baseline that uses all the features from the same feature space. Extracting the assertion value for pneumonia expressions further improves the system performance.