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Identifying mortality factors from Machine Learning using Shapley values - a case of COVID19.

ABSTRACT: In this paper we apply a series of Machine Learning models to a recently published unique dataset on the mortality of COVID19 patients. We use a dataset consisting of blood samples of 375 patients admitted to a hospital in the region of Wuhan, China. There are 201 patients who survived hospitalisation and 174 patients who died whilst in hospital. The focus of the paper is not only on seeing which Machine Learning model is able to obtain the absolute highest accuracy but more on the interpretation of what the Machine Learning models provides. We find that age, days in hospital, Lymphocyte and Neutrophils are important and robust predictors when predicting a patients mortality. Furthermore, the algorithms we use allows us to observe the marginal impact of each variable on a case-by-case patient level, which might help practicioneers to easily detect anomalous patterns. This paper analyses the global and local interpretation of the Machine Learning models on patients with COVID19.

SUBMITTER: Smith M

PROVIDER: S-EPMC7948528 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature

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Identifying mortality factors from Machine Learning using Shapley values - a case of COVID19.

Smith Matthew M Alvarez Francisco F

Expert systems with applications 20210311

In this paper we apply a series of Machine Learning models to a recently published unique dataset on the mortality of COVID19 patients. We use a dataset consisting of blood samples of 375 patients admitted to a hospital in the region of Wuhan, China. There are 201 patients who survived hospitalisation and 174 patients who died whilst in hospital. The focus of the paper is not only on seeing which Machine Learning model is able to obtain the absolute highest accuracy but more on the interpretatio ...[more]

PMID: 33723478

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Project description:AimRacial disparities in opioid use disorder (OUD) management exist, however, and there is limited research on factors that influence opioid cessation in different population groups.MethodsWe employed multiple machine learning prediction algorithms least absolute shrinkage and selection operator, random forest, deep neural network, and support vector machine to assess factors associated with ceasing opioid use in a sample of 1,192 African Americans (AAs) and 2,557 individuals of European ancestry (EAs) who met Diagnostic and Statistical Manual of Mental Disorders, 5th Edition criteria for OUD. Values for nearly 4,000 variables reflecting demographics, alcohol and other drug use, general health, non-drug use behaviors, and diagnoses for other psychiatric disorders, were obtained for each participant from the Semi-Structured Assessment for Drug Dependence and Alcoholism, a detailed semi-structured interview.ResultsSupport vector machine models performed marginally better on average than other machine learning methods with maximum prediction accuracies of 75.4% in AAs and 79.4% in EAs. Subsequent stepwise regression considered the 83 most highly ranked variables across all methods and models and identified less recent cocaine use (AAs: odds ratio (OR) = 1.82, P = 9.19 × 10-5; EAs: OR = 1.91, P = 3.30 × 10-15), shorter duration of opioid use (AAs: OR = 0.55, P = 5.78 × 10-6; EAs: OR = 0.69, P = 3.01 × 10-7), and older age (AAs: OR = 2.44, P = 1.41 × 10-12; EAs: OR = 2.00, P = 5.74 × 10-9) as the strongest independent predictors of opioid cessation in both AAs and EAs. Attending self-help groups for OUD was also an independent predictor (P < 0.05) in both population groups, while less gambling severity (OR = 0.80, P = 3.32 × 10-2) was specific to AAs and post-traumatic stress disorder recovery (OR = 1.93, P = 7.88 × 10-5), recent antisocial behaviors (OR = 0.64, P = 2.69 × 10-3), and atheism (OR = 1.45, P = 1.34 × 10-2) were specific to EAs. Factors related to drug use comprised about half of the significant independent predictors in both AAs and EAs, with other predictors related to non-drug use behaviors, psychiatric disorders, overall health, and demographics.ConclusionsThese proof-of-concept findings provide avenues for hypothesis-driven analysis, and will lead to further research on strategies to improve OUD management in EAs and AAs.

Project description:BackgroundPrevious predictive models using logistic regression for stillbirth do not leverage the advanced and nuanced techniques involved in sophisticated machine learning methods, such as modeling nonlinear relationships between outcomes.ObjectiveThis study aimed to create and refine machine learning models for predicting stillbirth using data available before viability (22-24 weeks) and throughout pregnancy, as well as demographic, medical, and prenatal visit data, including ultrasound and fetal genetics.Study designThis is a secondary analysis of the Stillbirth Collaborative Research Network, which included data from pregnancies resulting in stillborn and live-born infants delivered at 59 hospitals in 5 diverse regions across the United States from 2006 to 2009. The primary aim was the creation of a model for predicting stillbirth using data available before viability. Secondary aims included refining models with variables available throughout pregnancy and determining variable importance.ResultsAmong 3000 live births and 982 stillbirths, 101 variables of interest were identified. Of the models incorporating data available before viability, the random forests model had 85.1% accuracy (area under the curve) and high sensitivity (88.6%), specificity (85.3%), positive predictive value (85.3%), and negative predictive value (84.8%). A random forests model using data collected throughout pregnancy resulted in accuracy of 85.0%; this model had 92.2% sensitivity, 77.9% specificity, 84.7% positive predictive value, and 88.3% negative predictive value. Important variables in the previability model included previous stillbirth, minority race, gestational age at the earliest prenatal visit and ultrasound, and second-trimester serum screening.ConclusionApplying advanced machine learning techniques to a comprehensive database of stillbirths and live births with unique and clinically relevant variables resulted in an algorithm that could accurately identify 85% of pregnancies that would result in stillbirth, before they reached viability. Once validated in representative databases reflective of the US birthing population and then prospectively, these models may provide effective risk stratification and clinical decision-making support to better identify and monitor those at risk of stillbirth.

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Identifying mortality factors from Machine Learning using Shapley values - a case of COVID19.

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Identifying mortality factors from Machine Learning using Shapley values - a case of COVID19.

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