Phenotyping hypotensive patients in critical care using hospital discharge summaries

Among critically-ill patients, hypotension represents a failure in compensatory mechanisms and may lead to organ hypoperfusion and failure. In this work, we adopt a datadriven approach for phenotype discovery and visualization of patient similarity and cohort structure in the intensive care unit (ICU). We used Hierarchical Dirichlet Process (HDP) as a non-parametric topic modeling technique to automatically learn a d-dimensional feature representation of patients that captures the latent 'topic' structure of diseases, symptoms, medications, and findings documented in hospital discharge summaries. We then used the t-Distributed Stochastic Neighbor Embedding (t-SNE) algorithm to convert the d-dimensional latent structure learned from HDP into a matrix of pairwise similarities for visualizing patient similarity and cohort structure. Using discharge summaries of a large patient cohort from the MIMIC II database, we evaluated the clinical utility of the discovered topic structure in phenotyping critically-ill patients who experienced hypotensive episodes. Our results indicate that the approach is able to reveal clinically interpretable clustering structure within our cohort and may potentially provide valuable insights to better understand the association between disease phenotypes and outcomes.National Institutes of Health (U.S.) (Grant R01-EB017205)National Institutes of Health (U.S.) (Grant R01-EB001659)National Institutes of Health (U.S.) (Grant R01GM104987

A framework for applying natural language processing in digital health interventions

BACKGROUND: Digital health interventions (DHIs) are poised to reduce target symptoms in a scalable, affordable, and empirically supported way. DHIs that involve coaching or clinical support often collect text data from 2 sources: (1) open correspondence between users and the trained practitioners supporting them through a messaging system and (2) text data recorded during the intervention by users, such as diary entries. Natural language processing (NLP) offers methods for analyzing text, augmenting the understanding of intervention effects, and informing therapeutic decision making. OBJECTIVE: This study aimed to present a technical framework that supports the automated analysis of both types of text data often present in DHIs. This framework generates text features and helps to build statistical models to predict target variables, including user engagement, symptom change, and therapeutic outcomes. METHODS: We first discussed various NLP techniques and demonstrated how they are implemented in the presented framework. We then applied the framework in a case study of the Healthy Body Image Program, a Web-based intervention trial for eating disorders (EDs). A total of 372 participants who screened positive for an ED received a DHI aimed at reducing ED psychopathology (including binge eating and purging behaviors) and improving body image. These users generated 37,228 intervention text snippets and exchanged 4285 user-coach messages, which were analyzed using the proposed model. RESULTS: We applied the framework to predict binge eating behavior, resulting in an area under the curve between 0.57 (when applied to new users) and 0.72 (when applied to new symptom reports of known users). In addition, initial evidence indicated that specific text features predicted the therapeutic outcome of reducing ED symptoms. CONCLUSIONS: The case study demonstrates the usefulness of a structured approach to text data analytics. NLP techniques improve the prediction of symptom changes in DHIs. We present a technical framework that can be easily applied in other clinical trials and clinical presentations and encourage other groups to apply the framework in similar contexts

Diagnostic and prognostic prediction models in ventilator-associated pneumonia: Systematic review and meta-analysis of prediction modelling studies

Machine learning; Mechanical ventilation; Prognostic modelAprenentatge automàtic; Ventilació mecànica; Model pronòsticAprendizaje automático; Ventilacion mecanica; Modelo pronósticoPurpose Existing expert systems have not improved the diagnostic accuracy of ventilator-associated pneumonia (VAP). The aim of this systematic literature review was to review and summarize state-of-the-art prediction models detecting or predicting VAP from exhaled breath, patient reports and demographic and clinical characteristics. Methods Both diagnostic and prognostic prediction models were searched from a representative list of multidisciplinary databases. An extensive list of validated search terms was added to the search to cover papers failing to mention predictive research in their title or abstract. Two authors independently selected studies, while three authors extracted data using predefined criteria and data extraction forms. The Prediction Model Risk of Bias Assessment Tool was used to assess both the risk of bias and the applicability of the prediction modelling studies. Technology readiness was also assessed. Results Out of 2052 identified studies, 20 were included. Fourteen (70%) studies reported the predictive performance of diagnostic models to detect VAP from exhaled human breath with a high degree of sensitivity and a moderate specificity. In addition, the majority of them were validated on a realistic dataset. The rest of the studies reported the predictive performance of diagnostic and prognostic prediction models to detect VAP from unstructured narratives [2 (10%)] as well as baseline demographics and clinical characteristics [4 (20%)]. All studies, however, had either a high or unclear risk of bias without significant improvements in applicability. Conclusions The development and deployment of prediction modelling studies are limited in VAP and related outcomes. More computational, translational, and clinical research is needed to bring these tools from the bench to the bedside.The project is supported by the Academy of Finland (project number 326291) and the University of Oulu

Barriers and facilitators perceived by physicians when using prediction models in practice

Objectives Prediction models may facilitate risk-based management of health care conditions. In a large cluster-randomized trial, presenting calculated risks of postoperative nausea and vomiting (PONV) to physicians (assistive approach) increased risk-based management of PONV. This increase did not improve patient outcome - that is, PONV incidence. This prompted us to explore how prediction tools guide the decision-making process of physicians. Study Design and Setting Using mixed methods, we interviewed eight physicians to understand how predicted risks were perceived by the physicians and how they influenced decision making. Subsequently, all 57 physicians of the trial were surveyed for how the presented risks influenced their perceptions. Results Although the prediction tool made physicians more aware of PONV prevention, the physicians reported three barriers to use predicted risks in their decision making. PONV was not considered an outcome of utmost importance; decision making on PONV prophylaxis was mostly intuitive rather than risk based; prediction models do not weigh benefits and risks of prophylactic drugs. Conclusion Combining probabilistic output of the model with their clinical experience may be difficult for physicians, especially when their decision-making process is mostly intuitive. Adding recommendations to predicted risks (directive approach) was considered an important step to facilitate the uptake of a prediction tool

Learning Better Clinical Risk Models.

Risk models are used to estimate a patient’s risk of suffering particular outcomes throughout clinical practice. These models are important for matching patients to the appropriate level of treatment, for effective allocation of resources, and for fairly evaluating the performance of healthcare providers. The application and development of methods from the field of machine learning has the potential to improve patient outcomes and reduce healthcare spending with more accurate estimates of patient risk. This dissertation addresses several limitations of currently used clinical risk models, through the identification of novel risk factors and through the training of more effective models. As wearable monitors become more effective and less costly, the previously untapped predictive information in a patient’s physiology over time has the potential to greatly improve clinical practice. However translating these technological advances into real-world clinical impacts will require computational methods to identify high-risk structure in the data. This dissertation presents several approaches to learning risk factors from physiological recordings, through the discovery of latent states using topic models, and through the identification of predictive features using convolutional neural networks. We evaluate these approaches on patients from a large clinical trial and find that these methods not only outperform prior approaches to leveraging heart rate for cardiac risk stratification, but that they improve overall prediction of cardiac death when considered alongside standard clinical risk factors. We also demonstrate the utility of this work for learning a richer description of sleep recordings. Additionally, we consider the development of risk models in the presence of missing data, which is ubiquitous in real-world medical settings. We present a novel method for jointly learning risk and imputation models in the presence of missing data, and find significant improvements relative to standard approaches when evaluated on a large national registry of trauma patients.PhDComputer Science and EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/113326/1/alexve_1.pd