A machine learning model for predicting deterioration of COVID-19 inpatients.
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ABSTRACT:
SUBMITTER: Noy O
PROVIDER: S-EPMC8850417 | biostudies-literature | 2022 Feb
REPOSITORIES: biostudies-literature
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A machine learning model for predicting deterioration of COVID-19 inpatients.
Noy Omer O Coster Dan D Metzger Maya M Atar Itai I Shenhar-Tsarfaty Shani S Berliner Shlomo S Rahav Galia G Rogowski Ori O Shamir Ron R
Scientific reports 20220216 1
The COVID-19 pandemic has been spreading worldwide since December 2019, presenting an urgent threat to global health. Due to the limited understanding of disease progression and of the risk factors for the disease, it is a clinical challenge to predict which hospitalized patients will deteriorate. Moreover, several studies suggested that taking early measures for treating patients at risk of deterioration could prevent or lessen condition worsening and the need for mechanical ventilation. We dev ...[more]
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Project description:BackgroundDiscover possible Drug Target Interactions (DTIs) is a decisive step in the detection of the effects of drugs as well as drug repositioning. There is a strong incentive to develop effective computational methods that can effectively predict potential DTIs, as traditional DTI laboratory experiments are expensive, time-consuming, and labor-intensive. Some technologies have been developed for this purpose, however large numbers of interactions have not yet been detected, the accuracy of their prediction still low, and protein sequences and structured data are rarely used together in the prediction process.MethodsThis paper presents DTIs prediction model that takes advantage of the special capacity of the structured form of proteins and drugs. Our model obtains features from protein amino-acid sequences using physical and chemical properties, and from drugs smiles (Simplified Molecular Input Line Entry System) strings using encoding techniques. Comparing the proposed model with different existing methods under K-fold cross validation, empirical results show that our model based on ensemble learning algorithms for DTI prediction provide more accurate results from both structures and features data.ResultsThe proposed model is applied on two datasets:Benchmark (feature only) datasets and DrugBank (Structure data) datasets. Experimental results obtained by Light-Boost and ExtraTree using structures and feature data results in 98 % accuracy and 0.97 f-score comparing to 94 % and 0.92 achieved by the existing methods. Moreover, our model can successfully predict more yet undiscovered interactions, and hence can be used as a practical tool to drug repositioning. A case study of applying our prediction model on the proteins that are known to be affected by Corona viruses in order to predict the possible interactions among these proteins and existing drugs is performed. Also, our model is applied on Covid-19 related drugs announced on DrugBank. The results show that some drugs like DB00691 and DB05203 are predicted with 100 % accuracy to interact with ACE2 protein. This protein is a self-membrane protein that enables Covid-19 infection. Hence, our model can be used as an effective tool in drug reposition to predict possible drug treatments for Covid-19.
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Project description:Introduction. The risk of infectious disease transmission, including COVID-19, is disproportionately high in correctional facilities due to close living conditions, relatively low levels of vaccination, and reduced access to testing and treatment. While much progress has been made on describing and mitigating COVID-19 and other infectious disease risk in jails and prisons, there are open questions about which data can best predict future outbreaks. Methods. We used facility data and demographic and health data collected from 24 prison facilities in the Pennsylvania Department of Corrections from March 2020 to May 2021 to determine which sources of data best predict a coming COVID-19 outbreak in a prison facility. We used machine learning methods to cluster the prisons into groups based on similar facility-level characteristics, including size, rurality, and demographics of incarcerated people. We developed logistic regression classification models to predict for each cluster, before and after vaccine availability, whether there would be no cases, an outbreak defined as 2 or more cases, or a large outbreak, defined as 10 or more cases in the next 1, 2, and 3 d. We compared these predictions to data on outbreaks that occurred. Results. Facilities were divided into 8 clusters of sizes varying from 1 to 7 facilities per cluster. We trained 60 logistic regressions; 20 had test sets with between 35% and 65% of days with outbreaks detected. Of these, 8 logistic regressions correctly predicted the occurrence of an outbreak more than 55% of the time. The most common predictive feature was incident cases among the incarcerated population from 2 to 32 d prior. Other predictive features included the number of tests administered from 1 to 33 d prior, total population, test positivity rate, and county deaths, hospitalizations, and incident cases. Cumulative cases, vaccination rates, and race, ethnicity, or age statistics for incarcerated populations were generally not predictive. Conclusions. County-level measures of COVID-19, facility population, and test positivity rate appear as potential promising predictors of COVID-19 outbreaks in correctional facilities, suggesting that correctional facilities should monitor community transmission in addition to facility transmission to inform future outbreak response decisions. These efforts should not be limited to COVID-19 but should include any large-scale infectious disease outbreak that may involve institution-community transmission.HighlightsThe risk of infectious disease transmission, including COVID-19, is disproportionately high in correctional facilities.We used machine learning methods with data collected from 24 prison facilities in the Pennsylvania Department of Corrections to determine which sources of data best predict a coming COVID-19 outbreak in a prison facility.Key predictors included county-level measures of COVID-19, facility population, and the test positivity rate in a facility.Fortifying correctional facilities with the ability to monitor local community rates of infection (e.g., though improved interagency collaboration and data sharing) along with continued testing of incarcerated people and staff can help correctional facilities better predict-and respond to-future infectious disease outbreaks.
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| S-EPMC8851750 | biostudies-literature
Project description:A high-performing interpretable model is proposed to predict the risk of deterioration in coronavirus disease 2019 (COVID-19) patients. The model was developed using a cohort of 3028 patients diagnosed with COVID-19 and exhibiting common clinical symptoms that were internally verified (AUC 0.8517, 95% CI 0.8433, 0.8601). A total of 15 high risk factors for deterioration and their approximate warning ranges were identified. This included prothrombin time (PT), prothrombin activity, lactate dehydrogenase, international normalized ratio, heart rate, body-mass index (BMI), D-dimer, creatine kinase, hematocrit, urine specific gravity, magnesium, globulin, activated partial thromboplastin time, lymphocyte count (L%), and platelet count. Four of these indicators (PT, heart rate, BMI, HCT) and comorbidities were selected for a streamlined combination of indicators to produce faster results. The resulting model showed good predictive performance (AUC 0.7941 95% CI 0.7926, 0.8151). A website for quick pre-screening online was also developed as part of the study.
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Project description:IntroductionThe COVID-19 patients in the convalescent stage noticeably have pulmonary diffusing capacity impairment (PDCI). The pulmonary diffusing capacity is a frequently-used indicator of the COVID-19 survivors' prognosis of pulmonary function, but the current studies focusing on prediction of the pulmonary diffusing capacity of these people are limited. The aim of this study was to develop and validate a machine learning (ML) model for predicting PDCI in the COVID-19 patients using routinely available clinical data, thus assisting the clinical diagnosis.MethodsCollected from a follow-up study from August to September 2021 of 221 hospitalized survivors of COVID-19 18 months after discharge from Wuhan, including the demographic characteristics and clinical examination, the data in this study were randomly separated into a training (80%) data set and a validation (20%) data set. Six popular machine learning models were developed to predict the pulmonary diffusing capacity of patients infected with COVID-19 in the recovery stage. The performance indicators of the model included area under the curve (AUC), Accuracy, Recall, Precision, Positive Predictive Value(PPV), Negative Predictive Value (NPV) and F1. The model with the optimum performance was defined as the optimal model, which was further employed in the interpretability analysis. The MAHAKIL method was utilized to balance the data and optimize the balance of sample distribution, while the RFECV method for feature selection was utilized to select combined features more favorable to machine learning.ResultsA total of 221 COVID-19 survivors were recruited in this study after discharge from hospitals in Wuhan. Of these participants, 117 (52.94%) were female, with a median age of 58.2 years (standard deviation (SD) = 12). After feature selection, 31 of the 37 clinical factors were finally selected for use in constructing the model. Among the six tested ML models, the best performance was accomplished in the XGBoost model, with an AUC of 0.755 and an accuracy of 78.01% after experimental verification. The SHAPELY Additive explanations (SHAP) summary analysis exhibited that hemoglobin (Hb), maximal voluntary ventilation (MVV), severity of illness, platelet (PLT), Uric Acid (UA) and blood urea nitrogen (BUN) were the top six most important factors affecting the XGBoost model decision-making.ConclusionThe XGBoost model reported here showed a good prognostic prediction ability for PDCI of COVID-19 survivors during the recovery period. Among the interpretation methods based on the importance of SHAP values, Hb and MVV contributed the most to the prediction of PDCI outcomes of COVID-19 survivors in the recovery period.
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Project description:Within the UK, COVID-19 has contributed towards over 103,000 deaths. Although multiple risk factors for COVID-19 have been identified, using this data to improve clinical care has proven challenging. The main aim of this study is to develop a reliable, multivariable predictive model for COVID-19 in-patient outcomes, thus enabling risk-stratification and earlier clinical decision-making. Anonymised data consisting of 44 independent predictor variables from 355 adults diagnosed with COVID-19, at a UK hospital, was manually extracted from electronic patient records for retrospective, case-control analysis. Primary outcomes included inpatient mortality, required ventilatory support, and duration of inpatient treatment. Pulmonary embolism sequala was the only secondary outcome. After balancing data, key variables were feature selected for each outcome using random forests. Predictive models were then learned and constructed using Bayesian networks. The proposed probabilistic models were able to predict, using feature selected risk factors, the probability of the mentioned outcomes. Overall, our findings demonstrate reliable, multivariable, quantitative predictive models for four outcomes, which utilise readily available clinical information for COVID-19 adult inpatients. Further research is required to externally validate our models and demonstrate their utility as risk stratification and clinical decision-making tools.
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