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Chen M, Qian Q, Pan X, Li T. An investigation into the impact of temporality on COVID-19 infection and mortality predictions: new perspective based on Shapley Values. BMC Med Res Methodol 2025; 25:111. [PMID: 40275181 PMCID: PMC12020040 DOI: 10.1186/s12874-025-02572-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 04/16/2025] [Indexed: 04/26/2025] Open
Abstract
INTRODUCTION Machine learning models have been employed to predict COVID-19 infections and mortality, but many models were built on training and testing sets from different periods. The purpose of this study is to investigate the impact of temporality, i.e., the temporal gap between training and testing sets, on model performances for predicting COVID-19 infections and mortality. Furthermore, this study seeks to understand the causes of the impact of temporality. METHODS This study used a COVID-19 surveillance dataset collected from Brazil in year 2020, 2021 and 2022, and built prediction models for COVID-19 infections and mortality using random forest and logistic regression, with 20 model features. Models were trained and tested based on data from different years and the same year as well, to examine the impact of temporality. To further explain the impact of temporality and its driving factors, Shapley values are employed to quantify individual contributions to model predictions. RESULTS For the infection model, we found that the temporal gap had a negative impact on prediction accuracy. On average, the loss in accuracy was 0.0256 for logistic regression and 0.0436 for random forest when there was a temporal gap between the training and testing sets. For the mortality model, the loss in accuracy was 0.0144 for logistic regression and 0.0098 for random forest, which means the impact of temporality was not as strong as in the infection model. Shapley values uncovered the reason behind such differences between the infection and mortality models. CONCLUSIONS Our study confirmed the negative impact of temporality on model performance for predicting COVID-19 infections, but it did not find such negative impact of temporality for predicting COVID-19 mortality. Shapley value revealed that there was a fixed set of four features that made predominant contributions for the mortality model across data in three years (2020-2022), while for the infection model there was no such fixed set of features across different years.
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Affiliation(s)
- Mingming Chen
- Academy of Pharmacy, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou, 215123, Jiangsu, P.R. China
- Institute of Population Health, Faculty of Health & Life Sciences Waterhouse Building, University of Liverpool, Liverpool, England
| | - Qihang Qian
- School of Computer Science and Technology, Zhejiang University of Technology, No. 18 Chaowang Road, Hangzhou, Zhejiang, 310014, P.R. China
| | - Xiang Pan
- School of Computer Science and Technology, Zhejiang University of Technology, No. 18 Chaowang Road, Hangzhou, Zhejiang, 310014, P.R. China
| | - Tenglong Li
- Academy of Pharmacy, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou, 215123, Jiangsu, P.R. China.
- Institute of Population Health, Faculty of Health & Life Sciences Waterhouse Building, University of Liverpool, Liverpool, England.
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2
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Alzahrani SI, Yafooz WMS, Aljamaan IA, Alwaleedi A, Al-Hariri M, Saleh G. AI-driven health analysis for emerging respiratory diseases: A case study of Yemen patients using COVID-19 data. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2025; 22:554-584. [PMID: 40083282 DOI: 10.3934/mbe.2025021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/16/2025]
Abstract
In low-income and resource-limited countries, distinguishing COVID-19 from other respiratory diseases is challenging due to similar symptoms and the prevalence of comorbidities. In Yemen, acute comorbidities further complicate the differentiation between COVID-19 and other infectious diseases. We explored the use of AI-powered predictive models and classifiers to enhance healthcare preparedness by forecasting respiratory disease trends using COVID-19 data. We developed mathematical models based on autoregressive (AR), moving average (MA), ARMA, and machine and deep learning algorithms to predict daily confirmed deaths. Statistical models were trained on 80% of the data and tested on the remaining 20%, with predicted results compared to actual values. The ARMA model demonstrated promising performance. Additionally, eight machine learning (ML) classifiers and deep learning (DL) models were utilized to identify COVID-19 severity indicators. Among the ML classifiers, the Decision Tree (DT) achieved the highest accuracy at 74.70%, followed closely by Random Forest (RF) at 74.66%. DL models showed comparable accuracy scores, around 70%. In terms of AUC-ROC, the kernel Support Vector Machine (SVM) outperformed others, achieving 71% accuracy, with precision, recall, F-measure, and area under the curve values of 0.7, 0.75, 0.59, and 0.72, respectively. These findings underscore the potential of AI-driven health analysis to optimize resource allocation and enhance forecasting for respiratory diseases.
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Affiliation(s)
- Saleh I Alzahrani
- Biomedical Engineering Department, College of Engineering, Imam Abdulrahman Bin Faisal University, PO box 1982, Dammam 31451, Saudi Arabia
| | - Wael M S Yafooz
- Computer Science Department, Taibah University, Saudi Arabia
| | - Ibrahim A Aljamaan
- Biomedical Engineering Department, College of Engineering, Imam Abdulrahman Bin Faisal University, PO box 1982, Dammam 31451, Saudi Arabia
| | - Ali Alwaleedi
- Department of Epidemiology and Public Health, College of Medicine, Aden University, Aden, Yemen
| | - Mohammed Al-Hariri
- Department of Physiology, College of Medicine, Imam Abdulrahman Bin Faisal University, PO box 1982, Dammam 31451, Saudi Arabia
| | - Gameel Saleh
- Biomedical Engineering Department, College of Engineering, Imam Abdulrahman Bin Faisal University, PO box 1982, Dammam 31451, Saudi Arabia
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3
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Rachmadi MF, Valdés-Hernández MDC, Makin S, Wardlaw J, Skibbe H. Prediction of white matter hyperintensities evolution one-year post-stroke from a single-point brain MRI and stroke lesions information. Sci Rep 2025; 15:1208. [PMID: 39774013 PMCID: PMC11706948 DOI: 10.1038/s41598-024-83128-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/11/2024] [Indexed: 01/11/2025] Open
Abstract
Predicting the evolution of white matter hyperintensities (WMH), a common feature in brain magnetic resonance imaging (MRI) scans of older adults (i.e., whether WMH will grow, remain stable, or shrink with time) is important for personalised therapeutic interventions. However, this task is difficult mainly due to the myriad of vascular risk factors and comorbidities that influence it, and the low specificity and sensitivity of the image intensities and textures alone for predicting WMH evolution. Given the predominantly vascular nature of WMH, in this study, we evaluate the impact of incorporating stroke lesion information to a probabilistic deep learning model to predict the evolution of WMH 1-year after the baseline image acquisition, taken soon after a mild stroke event, using T2-FLAIR brain MRI. The Probabilistic U-Net was chosen for this study due to its capability of simulating and quantifying the uncertainties involved in the prediction of WMH evolution. We propose to use an additional loss called volume loss to train our model, and incorporate stroke lesions information, an influential factor in WMH evolution. Our experiments showed that jointly segmenting the disease evolution map (DEM) of WMH and stroke lesions, improved the accuracy of the DEM representing WMH evolution. The combination of introducing the volume loss and joint segmentation of DEM of WMH and stroke lesions outperformed other model configurations with mean volumetric absolute error of 0.0092 ml (down from 1.7739 ml) and 0.47% improvement on average Dice similarity coefficient in shrinking, growing and stable WMH.
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Affiliation(s)
- Muhammad Febrian Rachmadi
- RIKEN Center for Brain Science, Brain Image Analysis Unit, Wako-shi, 351-0106, Japan.
- Faculty of Computer Science, Universitas Indonesia, Depok, 16424, Indonesia.
| | | | - Stephen Makin
- Centre for Rural Health, University of Aberdeen, Inverness, IV2 3JH, UK
| | - Joanna Wardlaw
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - Henrik Skibbe
- RIKEN Center for Brain Science, Brain Image Analysis Unit, Wako-shi, 351-0106, Japan
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4
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Dhakal S, Yin A, Escarra-Senmarti M, Demko ZO, Pisanic N, Johnston TS, Trejo-Zambrano MI, Kruczynski K, Lee JS, Hardick JP, Shea P, Shapiro JR, Park HS, Parish MA, Caputo C, Ganesan A, Mullapudi SK, Gould SJ, Betenbaugh MJ, Pekosz A, Heaney CD, Antar AAR, Manabe YC, Cox AL, Karaba AH, Andrade F, Zeger SL, Klein SL. Application of machine learning algorithms to identify serological predictors of COVID-19 severity and outcomes. COMMUNICATIONS MEDICINE 2024; 4:249. [PMID: 39592832 PMCID: PMC11599591 DOI: 10.1038/s43856-024-00658-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 10/29/2024] [Indexed: 11/28/2024] Open
Abstract
BACKGROUND Critically ill hospitalized patients with COVID-19 have greater antibody titers than those with mild to moderate illness, but their association with recovery or death from COVID-19 has not been characterized. METHODS In a cohort study of 178 COVID-19 patients, 73 non-hospitalized and 105 hospitalized patients, mucosal swabs and plasma samples were collected at hospital enrollment and up to 3 months post-enrollment (MPE) to measure virus RNA, cytokines/chemokines, binding antibodies, ACE2 binding inhibition, and Fc effector antibody responses against SARS-CoV-2. The association of demographic variables and more than 20 serological antibody measures with intubation or death due to COVID-19 was determined using machine learning algorithms. RESULTS Predictive models reveal that IgG binding and ACE2 binding inhibition responses at 1 MPE are positively and anti-Spike antibody-mediated complement activation at enrollment is negatively associated with an increased probability of intubation or death from COVID-19 within 3 MPE. CONCLUSIONS At enrollment, serological antibody measures are more predictive than demographic variables of subsequent intubation or death among hospitalized COVID-19 patients.
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Affiliation(s)
- Santosh Dhakal
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Anna Yin
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Zoe O Demko
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Nora Pisanic
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Trevor S Johnston
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Kate Kruczynski
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - John S Lee
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Justin P Hardick
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Patrick Shea
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Janna R Shapiro
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Han-Sol Park
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Maclaine A Parish
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Christopher Caputo
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Abhinaya Ganesan
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Sarika K Mullapudi
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Stephen J Gould
- Department of Biological Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Advanced Mammalian Biomanufacturing Innovation Center, Johns Hopkins University, Baltimore, MD, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Christopher D Heaney
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Annukka A R Antar
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Yukari C Manabe
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Andrea L Cox
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Andrew H Karaba
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Felipe Andrade
- Division of Rheumatology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Scott L Zeger
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Sabra L Klein
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA.
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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5
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Lin L, Spreng RL, Seaton KE, Dennison SM, Dahora LC, Schuster DJ, Sawant S, Gilbert PB, Fong Y, Kisalu N, Pollard AJ, Tomaras GD, Li J. GeM-LR: Discovering predictive biomarkers for small datasets in vaccine studies. PLoS Comput Biol 2024; 20:e1012581. [PMID: 39541411 PMCID: PMC11594404 DOI: 10.1371/journal.pcbi.1012581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 11/26/2024] [Accepted: 10/23/2024] [Indexed: 11/16/2024] Open
Abstract
Despite significant progress in vaccine research, the level of protection provided by vaccination can vary significantly across individuals. As a result, understanding immunologic variation across individuals in response to vaccination is important for developing next-generation efficacious vaccines. Accurate outcome prediction and identification of predictive biomarkers would represent a significant step towards this goal. Moreover, in early phase vaccine clinical trials, small datasets are prevalent, raising the need and challenge of building a robust and explainable prediction model that can reveal heterogeneity in small datasets. We propose a new model named Generative Mixture of Logistic Regression (GeM-LR), which combines characteristics of both a generative and a discriminative model. In addition, we propose a set of model selection strategies to enhance the robustness and interpretability of the model. GeM-LR extends a linear classifier to a non-linear classifier without losing interpretability and empowers the notion of predictive clustering for characterizing data heterogeneity in connection with the outcome variable. We demonstrate the strengths and utility of GeM-LR by applying it to data from several studies. GeM-LR achieves better prediction results than other popular methods while providing interpretations at different levels.
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Affiliation(s)
- Lin Lin
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, United States of America
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, United States of America
| | - Rachel L. Spreng
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Kelly E. Seaton
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, United States of America
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - S. Moses Dennison
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, United States of America
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - Lindsay C. Dahora
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, United States of America
| | - Daniel J. Schuster
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, United States of America
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, United States of America
| | - Sheetal Sawant
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, United States of America
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - Peter B. Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Youyi Fong
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Neville Kisalu
- Center for Vaccine Innovation and Access, PATH, Washington, DC, United States of America
| | - Andrew J. Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Georgia D. Tomaras
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, United States of America
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America
| | - Jia Li
- Department of Statistics, The Pennsylvania State University, Pennsylvania, United States of America
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6
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Diakou I, Iliopoulos E, Papakonstantinou E, Dragoumani K, Yapijakis C, Iliopoulos C, Spandidos DA, Chrousos GP, Eliopoulos E, Vlachakis D. Multi‑label classification of biomedical data. MEDICINE INTERNATIONAL 2024; 4:68. [PMID: 39301328 PMCID: PMC11411592 DOI: 10.3892/mi.2024.192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 08/30/2024] [Indexed: 09/22/2024]
Abstract
Biomedical datasets constitute a rich source of information, containing multivariate data collected during medical practice. In spite of inherent challenges, such as missing or imbalanced data, these types of datasets are increasingly utilized as a basis for the construction of predictive machine-learning models. The prediction of disease outcomes and complications could inform the process of decision-making in the hospital setting and ensure the best possible patient management according to the patient's features. Multi-label classification algorithms, which are trained to assign a set of labels to input samples, can efficiently tackle outcome prediction tasks. Myocardial infarction (MI) represents a widespread health risk, accounting for a significant portion of heart disease-related mortality. Moreover, the danger of potential complications occurring in patients with MI during their period of hospitalization underlines the need for systems to efficiently assess the risks of patients with MI. In order to demonstrate the critical role of applying machine-learning methods in medical challenges, in the present study, a set of multi-label classifiers was evaluated on a public dataset of MI-related complications to predict the outcomes of hospitalized patients with MI, based on a set of input patient features. Such methods can be scaled through the use of larger datasets of patient records, along with fine-tuning for specific patient sub-groups or patient populations in specific regions, to increase the performance of these approaches. Overall, a prediction system based on classifiers trained on patient records may assist healthcare professionals in providing personalized care and efficient monitoring of high-risk patient subgroups.
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Affiliation(s)
- Io Diakou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Eddie Iliopoulos
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Eleni Papakonstantinou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
- University Research Institute of Maternal and Child Health and Precision Medicine, National and Kapodistrian University of Athens, 'Aghia Sophia' Children's Hospital, 11527 Athens, Greece
| | - Konstantina Dragoumani
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Christos Yapijakis
- University Research Institute of Maternal and Child Health and Precision Medicine, National and Kapodistrian University of Athens, 'Aghia Sophia' Children's Hospital, 11527 Athens, Greece
| | - Costas Iliopoulos
- School of Informatics, Faculty of Natural and Mathematical Sciences, King's College London, London WC2R 2LS, UK
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - George P Chrousos
- University Research Institute of Maternal and Child Health and Precision Medicine, National and Kapodistrian University of Athens, 'Aghia Sophia' Children's Hospital, 11527 Athens, Greece
| | - Elias Eliopoulos
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
- University Research Institute of Maternal and Child Health and Precision Medicine, National and Kapodistrian University of Athens, 'Aghia Sophia' Children's Hospital, 11527 Athens, Greece
- School of Informatics, Faculty of Natural and Mathematical Sciences, King's College London, London WC2R 2LS, UK
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7
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Haber R, Ghezzawi M, Puzantian H, Haber M, Saad S, Ghandour Y, El Bachour J, Yazbeck A, Hassanieh G, Mehdi C, Ismail D, Abi-Kharma E, El-Zein O, Khamis A, Chakhtoura M, Mantzoros C. Mortality risk in patients with obesity and COVID-19 infection: a systematic review and meta-analysis. Metabolism 2024; 155:155812. [PMID: 38360130 DOI: 10.1016/j.metabol.2024.155812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 01/13/2024] [Accepted: 01/29/2024] [Indexed: 02/17/2024]
Abstract
Obesity is a risk factor for severe respiratory diseases, including COVID-19 infection. Meta-analyses on mortality risk were inconsistent. We systematically searched 3 databases (Medline, Embase, CINAHL) and assessed the quality of studies using the Newcastle-Ottawa tool (CRD42020220140). We included 199 studies from US and Europe, with a mean age of participants 41.8-78.2 years, and a variable prevalence of metabolic co-morbidities of 20-80 %. Exceptionally, one third of the studies had a low prevalence of obesity of <20 %. Compared to patients with normal weight, those with obesity had a 34 % relative increase in the odds of mortality (p-value 0.002), with a dose-dependent relationship. Subgroup analyses showed an interaction with the country income. There was a high heterogeneity in the results, explained by clinical and methodologic variability across studies. We identified one trial only comparing mortality rate in vaccinated compared to unvaccinated patients with obesity; there was a trend for a lower mortality in the former group. Mortality risk in COVID-19 infection increases in parallel to an increase in BMI. BMI should be included in the predictive models and stratification scores used when considering mortality as an outcome in patients with COVID-19 infections. Furthermore, patients with obesity might need to be prioritized for COVID-19 vaccination.
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Affiliation(s)
- Rachelle Haber
- Department of Internal Medicine, Division of Endocrinology, American University of Beirut Medical Center, Beirut, Lebanon
| | - Malak Ghezzawi
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Houry Puzantian
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon; Hariri School of Nursing, American University of Beirut, Beirut, Lebanon.
| | - Marc Haber
- Faculty of Health Sciences, American University of Beirut, Beirut, Lebanon
| | - Sacha Saad
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Yara Ghandour
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | | | - Anthony Yazbeck
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | | | - Celine Mehdi
- Faculty of Arts and Sciences, American University of Beirut, Beirut, Lebanon
| | - Dima Ismail
- Faculty of Arts and Sciences, American University of Beirut, Beirut, Lebanon
| | - Elias Abi-Kharma
- Department of Internal Medicine, Division of Endocrinology, American University of Beirut Medical Center, Beirut, Lebanon
| | - Ola El-Zein
- Saab Medical Library, American University of Beirut, Beirut, Lebanon
| | - Assem Khamis
- Hull York Medical School, University of Hull, York, United Kingdom
| | - Marlene Chakhtoura
- Department of Internal Medicine, Division of Endocrinology, American University of Beirut Medical Center, Beirut, Lebanon.
| | - Christos Mantzoros
- Beth Israel Deaconess Medical Center and Boston VA Healthcare System, Harvard Medical School, Boston, MA, USA
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8
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Lourenço AA, Amaral PHR, Paim AAO, Marques-Ferreira G, Gomes-de-Pontes L, da Mata CPSM, da Fonseca FG, Pérez JCG, Coelho-dos-Reis JGA. Algorithms for predicting COVID outcome using ready-to-use laboratorial and clinical data. Front Public Health 2024; 12:1347334. [PMID: 38807995 PMCID: PMC11130428 DOI: 10.3389/fpubh.2024.1347334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/30/2024] [Indexed: 05/30/2024] Open
Abstract
The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging crisis affecting the public health system. The clinical features of COVID-19 can range from an asymptomatic state to acute respiratory syndrome and multiple organ dysfunction. Although some hematological and biochemical parameters are altered during moderate and severe COVID-19, there is still a lack of tools to combine these parameters to predict the clinical outcome of a patient with COVID-19. Thus, this study aimed at employing hematological and biochemical parameters of patients diagnosed with COVID-19 in order to build machine learning algorithms for predicting COVID mortality or survival. Patients included in the study had a diagnosis of SARS-CoV-2 infection confirmed by RT-PCR and biochemical and hematological measurements were performed in three different time points upon hospital admission. Among the parameters evaluated, the ones that stand out the most are the important features of the T1 time point (urea, lymphocytes, glucose, basophils and age), which could be possible biomarkers for the severity of COVID-19 patients. This study shows that urea is the parameter that best classifies patient severity and rises over time, making it a crucial analyte to be used in machine learning algorithms to predict patient outcome. In this study optimal and medically interpretable machine learning algorithms for outcome prediction are presented for each time point. It was found that urea is the most paramount variable for outcome prediction over all three time points. However, the order of importance of other variables changes for each time point, demonstrating the importance of a dynamic approach for an effective patient's outcome prediction. All in all, the use of machine learning algorithms can be a defining tool for laboratory monitoring and clinical outcome prediction, which may bring benefits to public health in future pandemics with newly emerging and reemerging SARS-CoV-2 variants of concern.
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Affiliation(s)
- Alice Aparecida Lourenço
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Adriana Alves Oliveira Paim
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Geovane Marques-Ferreira
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Leticia Gomes-de-Pontes
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Flávio Guimarães da Fonseca
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- CT Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Juan Carlos González Pérez
- Departamento de Física, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Jordana Grazziela Alves Coelho-dos-Reis
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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9
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Klein S, Dhakal S, Yin A, Escarra-Senmarti M, Demko Z, Pisanic N, Johnston T, Trejo-Zambrano M, Kruczynski K, Lee J, Hardick J, Shea P, Shapiro J, Park HS, Parish M, Caputo C, Ganesan A, Mullapudi S, Gould S, Betenbaugh M, Pekosz A, Heaney CD, Antar A, Manabe Y, Cox A, Karaba A, Andrade F, Zeger S. Application of machine learning models to identify serological predictors of COVID-19 severity and outcomes. RESEARCH SQUARE 2023:rs.3.rs-3463155. [PMID: 38014049 PMCID: PMC10680931 DOI: 10.21203/rs.3.rs-3463155/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Critically ill people with COVID-19 have greater antibody titers than those with mild to moderate illness, but their association with recovery or death from COVID-19 has not been characterized. In 178 COVID-19 patients, 73 non-hospitalized and 105 hospitalized patients, mucosal swabs and plasma samples were collected at hospital enrollment and up to 3 months post-enrollment (MPE) to measure virus RNA, cytokines/chemokines, binding antibodies, ACE2 binding inhibition, and Fc effector antibody responses against SARS-CoV-2. The association of demographic variables and >20 serological antibody measures with intubation or death due to COVID-19 was determined using machine learning algorithms. Predictive models revealed that IgG binding and ACE2 binding inhibition responses at 1 MPE were positively and C1q complement activity at enrollment was negatively associated with an increased probability of intubation or death from COVID-19 within 3 MPE. Serological antibody measures were more predictive than demographic variables of intubation or death among COVID-19 patients.
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Affiliation(s)
- Sabra Klein
- Johns Hopkins Bloomberg School of Public Health
| | | | - Anna Yin
- Johns Hopkins Bloomberg School of Public Health
| | | | | | | | | | | | | | - John Lee
- Johns Hopkins Bloomberg School of Public Health
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Yukari Manabe
- Division of Infectious Diseases, Department of Medicine, The Johns Hopkins School of Medicine
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10
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Liu L, Song W, Patil N, Sainlaire M, Jasuja R, Dykes PC. Predicting COVID-19 severity: Challenges in reproducibility and deployment of machine learning methods. Int J Med Inform 2023; 179:105210. [PMID: 37769368 DOI: 10.1016/j.ijmedinf.2023.105210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/30/2023]
Abstract
The increasing use of electronic health records (EHR) based computable phenotypes in clinical research is providing new opportunities for development of data-driven medical applications. Adopted widely in the United States and globally, EHRs facilitate systematic collection of patients' longitudinal information, which serves as one of the important foundations for artificial intelligence applications in medicine. Harmonization of input variables and outcome definitions is critically important for wider clinical applicability of artificial intelligence (AI) methodologies. In this review, we focused on Coronavirus Disease 2019 (COVID-19) severity machine learning prediction models and explored the pipeline for standardizing future disease severity model development using EHR information. We identified 2,967 studies published between 01/01/2020 and 02/15/2022 and selected 135 independent studies that had built machine learning prediction models to predict severity related outcomes of COVID-19 patients based on EHR data for the final review. These 135 studies spanning across 27 counties covered a broad range of severity related prediction outcomes. We observed substantial inconsistency in COVID-19 severity phenotype definitions among models in these studies. Moreover, there was a gap between the outcome of these models and clinician-recognized clinical concepts. Accordingly, we recommend that robust clinical input metrics, with outcome definitions which eliminate ambiguity in interpretation, to reduce algorithmic bias, mitigate model brittleness and improve generalizability of a universal model for COVID-19 severity. This framework can potentially be extended to broader clinical application.
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Affiliation(s)
- Luwei Liu
- Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA
| | - Wenyu Song
- Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Namrata Patil
- Department of Surgery, Brigham & Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | | | - Ravi Jasuja
- Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
| | - Patricia C Dykes
- Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
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11
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Shakibfar S, Nyberg F, Li H, Zhao J, Nordeng HME, Sandve GKF, Pavlovic M, Hajiebrahimi M, Andersen M, Sessa M. Artificial intelligence-driven prediction of COVID-19-related hospitalization and death: a systematic review. Front Public Health 2023; 11:1183725. [PMID: 37408750 PMCID: PMC10319067 DOI: 10.3389/fpubh.2023.1183725] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/31/2023] [Indexed: 07/07/2023] Open
Abstract
Aim To perform a systematic review on the use of Artificial Intelligence (AI) techniques for predicting COVID-19 hospitalization and mortality using primary and secondary data sources. Study eligibility criteria Cohort, clinical trials, meta-analyses, and observational studies investigating COVID-19 hospitalization or mortality using artificial intelligence techniques were eligible. Articles without a full text available in the English language were excluded. Data sources Articles recorded in Ovid MEDLINE from 01/01/2019 to 22/08/2022 were screened. Data extraction We extracted information on data sources, AI models, and epidemiological aspects of retrieved studies. Bias assessment A bias assessment of AI models was done using PROBAST. Participants Patients tested positive for COVID-19. Results We included 39 studies related to AI-based prediction of hospitalization and death related to COVID-19. The articles were published in the period 2019-2022, and mostly used Random Forest as the model with the best performance. AI models were trained using cohorts of individuals sampled from populations of European and non-European countries, mostly with cohort sample size <5,000. Data collection generally included information on demographics, clinical records, laboratory results, and pharmacological treatments (i.e., high-dimensional datasets). In most studies, the models were internally validated with cross-validation, but the majority of studies lacked external validation and calibration. Covariates were not prioritized using ensemble approaches in most of the studies, however, models still showed moderately good performances with Area under the Receiver operating characteristic Curve (AUC) values >0.7. According to the assessment with PROBAST, all models had a high risk of bias and/or concern regarding applicability. Conclusions A broad range of AI techniques have been used to predict COVID-19 hospitalization and mortality. The studies reported good prediction performance of AI models, however, high risk of bias and/or concern regarding applicability were detected.
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Affiliation(s)
- Saeed Shakibfar
- Pharmacovigilance Research Center, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Fredrik Nyberg
- School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Huiqi Li
- School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jing Zhao
- Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- UiORealArt Convergence Environment, University of Oslo, Oslo, Norway
| | - Hedvig Marie Egeland Nordeng
- Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- UiORealArt Convergence Environment, University of Oslo, Oslo, Norway
| | - Geir Kjetil Ferkingstad Sandve
- UiORealArt Convergence Environment, University of Oslo, Oslo, Norway
- Department of Informatics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Milena Pavlovic
- UiORealArt Convergence Environment, University of Oslo, Oslo, Norway
- Department of Informatics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | | | - Morten Andersen
- Pharmacovigilance Research Center, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Maurizio Sessa
- Pharmacovigilance Research Center, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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12
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Abbasi Habashi S, Koyuncu M, Alizadehsani R. A Survey of COVID-19 Diagnosis Using Routine Blood Tests with the Aid of Artificial Intelligence Techniques. Diagnostics (Basel) 2023; 13:1749. [PMID: 37238232 PMCID: PMC10217633 DOI: 10.3390/diagnostics13101749] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/19/2023] [Accepted: 04/29/2023] [Indexed: 05/28/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), causing a disease called COVID-19, is a class of acute respiratory syndrome that has considerably affected the global economy and healthcare system. This virus is diagnosed using a traditional technique known as the Reverse Transcription Polymerase Chain Reaction (RT-PCR) test. However, RT-PCR customarily outputs a lot of false-negative and incorrect results. Current works indicate that COVID-19 can also be diagnosed using imaging resolutions, including CT scans, X-rays, and blood tests. Nevertheless, X-rays and CT scans cannot always be used for patient screening because of high costs, radiation doses, and an insufficient number of devices. Therefore, there is a requirement for a less expensive and faster diagnostic model to recognize the positive and negative cases of COVID-19. Blood tests are easily performed and cost less than RT-PCR and imaging tests. Since biochemical parameters in routine blood tests vary during the COVID-19 infection, they may supply physicians with exact information about the diagnosis of COVID-19. This study reviewed some newly emerging artificial intelligence (AI)-based methods to diagnose COVID-19 using routine blood tests. We gathered information about research resources and inspected 92 articles that were carefully chosen from a variety of publishers, such as IEEE, Springer, Elsevier, and MDPI. Then, these 92 studies are classified into two tables which contain articles that use machine Learning and deep Learning models to diagnose COVID-19 while using routine blood test datasets. In these studies, for diagnosing COVID-19, Random Forest and logistic regression are the most widely used machine learning methods and the most widely used performance metrics are accuracy, sensitivity, specificity, and AUC. Finally, we conclude by discussing and analyzing these studies which use machine learning and deep learning models and routine blood test datasets for COVID-19 detection. This survey can be the starting point for a novice-/beginner-level researcher to perform on COVID-19 classification.
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Affiliation(s)
| | - Murat Koyuncu
- Department of Information Systems Engineering, Atilim University, 06830 Ankara, Turkey;
| | - Roohallah Alizadehsani
- Institute for Intelligent Systems Research and Innovation (IISRI), Deakin University, Waurn Ponds, Geelong, VIC 3216, Australia
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13
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Martinez G, Garduno A, Mahmud-Al-Rafat A, Ostadgavahi AT, Avery A, de Avila e Silva S, Cusack R, Cameron C, Cameron M, Martin-Loeches I, Kelvin D. An artificial neural network classification method employing longitudinally monitored immune biomarkers to predict the clinical outcome of critically ill COVID-19 patients. PeerJ 2022; 10:e14487. [PMID: 36530391 PMCID: PMC9753745 DOI: 10.7717/peerj.14487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/08/2022] [Indexed: 12/14/2022] Open
Abstract
Background The severe form of COVID-19 can cause a dysregulated host immune syndrome that might lead patients to death. To understand the underlying immune mechanisms that contribute to COVID-19 disease we have examined 28 different biomarkers in two cohorts of COVID-19 patients, aiming to systematically capture, quantify, and algorithmize how immune signals might be associated to the clinical outcome of COVID-19 patients. Methods The longitudinal concentration of 28 biomarkers of 95 COVID-19 patients was measured. We performed a dimensionality reduction analysis to determine meaningful biomarkers for explaining the data variability. The biomarkers were used as input of artificial neural network, random forest, classification and regression trees, k-nearest neighbors and support vector machines. Two different clinical cohorts were used to grant validity to the findings. Results We benchmarked the classification capacity of two COVID-19 clinicals studies with different models and found that artificial neural networks was the best classifier. From it, we could employ different sets of biomarkers to predict the clinical outcome of COVID-19 patients. First, all the biomarkers available yielded a satisfactory classification. Next, we assessed the prediction capacity of each protein separated. With a reduced set of biomarkers, our model presented 94% accuracy, 96.6% precision, 91.6% recall, and 95% of specificity upon the testing data. We used the same model to predict 83% and 87% (recovered and deceased) of unseen data, granting validity to the results obtained. Conclusions In this work, using state-of-the-art computational techniques, we systematically identified an optimal set of biomarkers that are related to a prediction capacity of COVID-19 patients. The screening of such biomarkers might assist in understanding the underlying immune response towards inflammatory diseases.
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Affiliation(s)
- Gustavo Martinez
- Immunology, Shantou University, Shantou, GD, China,Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Alexis Garduno
- Department of Clinical Medicine, University of Dublin, Trinity College, Dublin, Ireland
| | | | | | - Ann Avery
- Division of Infectious Diseases, MetroHealth Medical Center, Cleveland, OH, United States of America
| | - Scheila de Avila e Silva
- Department of Biotechnology, Universidade de Caxias do Sul, Caxias do Sul, Rio Grande do Sul, Brazil
| | - Rachael Cusack
- Department of Clinical Medicine, University of Dublin, Trinity College, Dublin, Ireland
| | - Cheryl Cameron
- Department of Nutrition, Case Western Reserve University, Cleveland, OH, United States of America
| | - Mark Cameron
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States of America
| | | | - David Kelvin
- Immunology, Shantou University, Shantou, GD, China,Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
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14
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Passarelli-Araujo H, Passarelli-Araujo H, Urbano MR, Pescim RR. Machine learning and comorbidity network analysis for hospitalized patients with COVID-19 in a city in Southern Brazil. SMART HEALTH (AMSTERDAM, NETHERLANDS) 2022; 26:100323. [PMID: 36159078 PMCID: PMC9485420 DOI: 10.1016/j.smhl.2022.100323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 07/17/2022] [Accepted: 09/13/2022] [Indexed: 12/18/2022]
Abstract
The large amount of data generated during the COVID-19 pandemic requires advanced tools for the long-term prediction of risk factors associated with COVID-19 mortality with higher accuracy. Machine learning (ML) methods directly address this topic and are essential tools to guide public health interventions. Here, we used ML to investigate the importance of demographic and clinical variables on COVID-19 mortality. We also analyzed how comorbidity networks are structured according to age groups. We conducted a retrospective study of COVID-19 mortality with hospitalized patients from Londrina, Parana, Brazil, registered in the database for severe acute respiratory infections (SIVEP-Gripe), from January 2021 to February 2022. We tested four ML models to predict the COVID-19 outcome: Logistic Regression, Support Vector Machine, Random Forest, and XGBoost. We also constructed a comorbidity network to investigate the impact of co-occurring comorbidities on COVID-19 mortality. Our study comprised 8358 hospitalized patients, of whom 2792 (33.40%) died. The XGBoost model achieved excellent performance (ROC-AUC = 0.90). Both permutation method and SHAP values highlighted the importance of age, ventilatory support status, and intensive care unit admission as key features in predicting COVID-19 outcomes. The comorbidity networks for old deceased patients are denser than those for young patients. In addition, the co-occurrence of heart disease and diabetes may be the most important combination to predict COVID-19 mortality, regardless of age and sex. This work presents a valuable combination of machine learning and comorbidity network analysis to predict COVID-19 outcomes. Reliable evidence on this topic is crucial for guiding the post-pandemic response and assisting in COVID-19 care planning and provision.
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Key Words
- AUC-ROC, Area under the Receiver-Operating Characteristic curve
- COVID-19, Coronavirus disease 2019
- Co-occurrence analysis
- Epidemiology
- ICU, Intensive Care Unit
- MCC, Matthew's Correlation Coefficient
- ML, Machine learning
- Network density
- OR, Odds ratio
- PCA, Principal Component Analysis
- Risk-factors
- SARS-CoV-2
- SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2
- SHAP, Shapley Additive exPlanations
- SIVEP-Gripe, Sistema de Informação de Vigilância Epidemiológica da Gripe
- SVM, Support Vector Machine
- XGBoost, Extreme Gradient Boosting
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Affiliation(s)
- Hemanoel Passarelli-Araujo
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Hisrael Passarelli-Araujo
- Departamento de Demografia, Faculdade de Ciências Econômicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Mariana R Urbano
- Departamento de Estatística, Universidade Estadual de Londrina, Londrina, PR, Brazil
| | - Rodrigo R Pescim
- Departamento de Estatística, Universidade Estadual de Londrina, Londrina, PR, Brazil
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15
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Lodato I, Iyer AV, To IZ, Lai ZY, Chan HSY, Leung WSW, Tang THC, Cheung VKL, Wu TC, Ng GWY. Prognostic Model of COVID-19 Severity and Survival among Hospitalized Patients Using Machine Learning Techniques. Diagnostics (Basel) 2022; 12:2728. [PMID: 36359571 PMCID: PMC9689804 DOI: 10.3390/diagnostics12112728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/25/2022] [Accepted: 11/03/2022] [Indexed: 08/22/2023] Open
Abstract
We conducted a statistical study and developed a machine learning model to triage COVID-19 patients affected during the height of the COVID-19 pandemic in Hong Kong based on their medical records and test results (features) collected during their hospitalization. The correlation between the values of these features is studied against discharge status and disease severity as a preliminary step to identify those features with a more pronounced effect on the patient outcome. Once identified, they constitute the inputs of four machine learning models, Decision Tree, Random Forest, Gradient and RUSBoosting, which predict both the Mortality and Severity associated with the disease. We test the accuracy of the models when the number of input features is varied, demonstrating their stability; i.e., the models are already highly predictive when run over a core set of (6) features. We show that Random Forest and Gradient Boosting classifiers are highly accurate in predicting patients' Mortality (average accuracy ∼99%) as well as categorize patients (average accuracy ∼91%) into four distinct risk classes (Severity of COVID-19 infection). Our methodical and broad approach combines statistical insights with various machine learning models, which paves the way forward in the AI-assisted triage and prognosis of COVID-19 cases, which is potentially generalizable to other seasonal flus.
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Affiliation(s)
- Ivano Lodato
- Allos Limited, 1 Hok Cheung Street, Kowloon, Hong Kong, China
| | - Aditya Varna Iyer
- Allos Limited, 1 Hok Cheung Street, Kowloon, Hong Kong, China
- Department of Physics, University of Oxford, Oxford OX1 3PJ, UK
| | | | - Zhong-Yuan Lai
- Allos Limited, 1 Hok Cheung Street, Kowloon, Hong Kong, China
- Department of Physics, Fudan University, Shanghai 200433, China
| | - Helen Shuk-Ying Chan
- Division of Infectious Diseases, Department of Medicine, Queen Elizabeth Hospital, Hong Kong, China
| | - Winnie Suk-Wai Leung
- Division of Integrative Systems and Design, Hong Kong University of Science and Technology, Hong Kong, China
| | - Tommy Hing-Cheung Tang
- Division of Infectious Diseases, Department of Medicine, Queen Elizabeth Hospital, Hong Kong, China
| | - Victor Kai-Lam Cheung
- Multi-Disciplinary Simulation and Skills Centre, Queen Elizabeth Hospital, Hong Kong, China
| | - Tak-Chiu Wu
- Division of Infectious Diseases, Department of Medicine, Queen Elizabeth Hospital, Hong Kong, China
| | - George Wing-Yiu Ng
- Intensive Care Unit, Department of Medicine, Queen Elizabeth Hospital, Hong Kong, China
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16
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Giotta M, Trerotoli P, Palmieri VO, Passerini F, Portincasa P, Dargenio I, Mokhtari J, Montagna MT, De Vito D. Application of a Decision Tree Model to Predict the Outcome of Non-Intensive Inpatients Hospitalized for COVID-19. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:13016. [PMID: 36293594 PMCID: PMC9602523 DOI: 10.3390/ijerph192013016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 05/05/2023]
Abstract
Many studies have identified predictors of outcomes for inpatients with coronavirus disease 2019 (COVID-19), especially in intensive care units. However, most retrospective studies applied regression methods to evaluate the risk of death or worsening health. Recently, new studies have based their conclusions on retrospective studies by applying machine learning methods. This study applied a machine learning method based on decision tree methods to define predictors of outcomes in an internal medicine unit with a prospective study design. The main result was that the first variable to evaluate prediction was the international normalized ratio, a measure related to prothrombin time, followed by immunoglobulin M response. The model allowed the threshold determination for each continuous blood or haematological parameter and drew a path toward the outcome. The model's performance (accuracy, 75.93%; sensitivity, 99.61%; and specificity, 23.43%) was validated with a k-fold repeated cross-validation. The results suggest that a machine learning approach could help clinicians to obtain information that could be useful as an alert for disease progression in patients with COVID-19. Further research should explore the acceptability of these results to physicians in current practice and analyze the impact of machine learning-guided decisions on patient outcomes.
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Affiliation(s)
- Massimo Giotta
- School of Specialization in Medical Statistics and Biometry, School of Medicine, University of Bari Aldo Moro, 70121 Bari, Italy
| | - Paolo Trerotoli
- Department of Interdisciplinary Medicine, University of Bari Aldo Moro, 70121 Bari, Italy
| | - Vincenzo Ostilio Palmieri
- Department of Biomedical Science and Human Oncology, University of Bari Aldo Moro, 70121 Bari, Italy
| | - Francesca Passerini
- Department of Biomedical Science and Human Oncology, University of Bari Aldo Moro, 70121 Bari, Italy
| | - Piero Portincasa
- Department of Biomedical Science and Human Oncology, University of Bari Aldo Moro, 70121 Bari, Italy
| | - Ilaria Dargenio
- School of Specialization in Medical Statistics and Biometry, School of Medicine, University of Bari Aldo Moro, 70121 Bari, Italy
| | - Jihad Mokhtari
- Department of Basic Medical Sciences, Neurosciences, and Sense Organs, Medical School, University of Bari Aldo Moro, 70121 Bari, Italy
| | - Maria Teresa Montagna
- Department of Interdisciplinary Medicine, University of Bari Aldo Moro, 70121 Bari, Italy
| | - Danila De Vito
- Department of Basic Medical Sciences, Neurosciences, and Sense Organs, Medical School, University of Bari Aldo Moro, 70121 Bari, Italy
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17
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A Review of the Potential of Artificial Intelligence Approaches to Forecasting COVID-19 Spreading. AI 2022. [DOI: 10.3390/ai3020028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The spread of SARS-CoV-2 can be considered one of the most complicated patterns with a large number of uncertainties and nonlinearities. Therefore, analysis and prediction of the distribution of this virus are one of the most challenging problems, affecting the planning and managing of its impacts. Although different vaccines and drugs have been proved, produced, and distributed one after another, several new fast-spreading SARS-CoV-2 variants have been detected. This is why numerous techniques based on artificial intelligence (AI) have been recently designed or redeveloped to forecast these variants more effectively. The focus of such methods is on deep learning (DL) and machine learning (ML), and they can forecast nonlinear trends in epidemiological issues appropriately. This short review aims to summarize and evaluate the trustworthiness and performance of some important AI-empowered approaches used for the prediction of the spread of COVID-19. Sixty-five preprints, peer-reviewed papers, conference proceedings, and book chapters published in 2020 were reviewed. Our criteria to include or exclude references were the performance of these methods reported in the documents. The results revealed that although methods under discussion in this review have suitable potential to predict the spread of COVID-19, there are still weaknesses and drawbacks that fall in the domain of future research and scientific endeavors.
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18
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Mortality Prediction of COVID-19 Patients Using Radiomic and Neural Network Features Extracted from a Wide Chest X-ray Sample Size: A Robust Approach for Different Medical Imbalanced Scenarios. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12083903] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Aim: The aim of this study was to develop robust prognostic models for mortality prediction of COVID-19 patients, applicable to different sets of real scenarios, using radiomic and neural network features extracted from chest X-rays (CXRs) with a certified and commercially available software. Methods: 1816 patients from 5 different hospitals in the Province of Reggio Emilia were included in the study. Overall, 201 radiomic features and 16 neural network features were extracted from each COVID-19 patient’s radiography. The initial dataset was balanced to train the classifiers with the same number of dead and survived patients, randomly selected. The pipeline had three main parts: balancing procedure; three-step feature selection; and mortality prediction with radiomic features through three machine learning (ML) classification models: AdaBoost (ADA), Quadratic Discriminant Analysis (QDA) and Random Forest (RF). Five evaluation metrics were computed on the test samples. The performance for death prediction was validated on both a balanced dataset (Case 1) and an imbalanced dataset (Case 2). Results: accuracy (ACC), area under the ROC-curve (AUC) and sensitivity (SENS) for the best classifier were, respectively, 0.72 ± 0.01, 0.82 ± 0.02 and 0.84 ± 0.04 for Case 1 and 0.70 ± 0.04, 0.79 ± 0.03 and 0.76 ± 0.06 for Case 2. These results show that the prediction of COVID-19 mortality is robust in a different set of scenarios. Conclusions: Our large and varied dataset made it possible to train ML algorithms to predict COVID-19 mortality using radiomic and neural network features of CXRs.
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19
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Cau R, Faa G, Nardi V, Balestrieri A, Puig J, Suri JS, SanFilippo R, Saba L. Long-COVID diagnosis: From diagnostic to advanced AI-driven models. Eur J Radiol 2022; 148:110164. [PMID: 35114535 PMCID: PMC8791239 DOI: 10.1016/j.ejrad.2022.110164] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 12/19/2022]
Abstract
SARS-COV 2 is recognized to be responsible for a multi-organ syndrome. In most patients, symptoms are mild. However, in certain subjects, COVID-19 tends to progress more severely. Most of the patients infected with SARS-COV2 fully recovered within some weeks. In a considerable number of patients, like many other viral infections, various long-lasting symptoms have been described, now defined as "long COVID-19 syndrome". Given the high number of contagious over the world, it is necessary to understand and comprehend this emerging pathology to enable early diagnosis and improve patents outcomes. In this scenario, AI-based models can be applied in long-COVID-19 patients to assist clinicians and at the same time, to reduce the considerable impact on the care and rehabilitation unit. The purpose of this manuscript is to review different aspects of long-COVID-19 syndrome from clinical presentation to diagnosis, highlighting the considerable impact that AI can have.
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Affiliation(s)
- Riccardo Cau
- Department of Radiology, Azienda Ospedaliero Universitaria (A.O.U.), di Cagliari - Polo di Monserrato, s.s. 554 Monserrato, Cagliari 09045, Italy
| | - Gavino Faa
- Department of Pathology, Azienda Ospedaliero Universitaria (A.O.U.), di Cagliari, Italy
| | - Valentina Nardi
- Department of Cardiovascular Medicine Mayo Clinic, Rochester, MN, USA
| | - Antonella Balestrieri
- Department of Radiology, Azienda Ospedaliero Universitaria (A.O.U.), di Cagliari - Polo di Monserrato, s.s. 554 Monserrato, Cagliari 09045, Italy
| | - Josep Puig
- Department of Radiology (IDI), Hospital Universitari de Girona, Girona, Spain
| | - Jasjit S Suri
- Stroke Diagnosis and Monitoring Division, Atheropoint LLC, Roseville, CA, USA
| | - Roberto SanFilippo
- Department of Vascular Surgery, Azienda Ospedaliero Universitaria (A.O.U.), di Cagliari - Polo di Monserrato, s.s. 554 Monserrato, Cagliari 09045, Italy
| | - Luca Saba
- Department of Radiology, Azienda Ospedaliero Universitaria (A.O.U.), di Cagliari - Polo di Monserrato, s.s. 554 Monserrato, Cagliari 09045, Italy.
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Kalezhi J, Chibuluma M, Chembe C, Chama V, Lungo F, Kunda D. Modelling Covid-19 infections in Zambia using data mining techniques. RESULTS IN ENGINEERING 2022; 13:100363. [PMID: 35317385 PMCID: PMC8813672 DOI: 10.1016/j.rineng.2022.100363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/08/2022] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
The outbreak of Covid-19 pandemic has been declared a global health crisis by the World Health Organization since its emergence. Several researchers have proposed a number of techniques to understand how the pandemic affects the populations. Reported among these techniques are data mining models which have been successfully applied in a wide range of situations before the advent of Covid-19 pandemic. In this work, the researchers have applied a number of existing data mining methods (classifiers) available in the Waikato Environment for Knowledge Analysis (WEKA) machine learning library. WEKA was used to gain a better understanding on how the epidemic spread within Zambia. The classifiers used are J48 decision tree, Multilayer Perceptron and Naïve Bayes among others. The predictions of these techniques are compared against simpler classifiers and those reported in related works.
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Affiliation(s)
- Josephat Kalezhi
- Department of Computer Engineering, Copperbelt University, Kitwe, Zambia
| | - Mathews Chibuluma
- Department of Information Technology/Systems, Copperbelt University, Kitwe, Zambia
| | | | - Victoria Chama
- Department of Computer Science and Information Technology, Mulungushi University, Kabwe, Zambia
| | - Francis Lungo
- School of Social Sciences, Mulungushi University, Kabwe, Zambia
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21
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Empirical Study on Classifiers for Earlier Prediction of COVID-19 Infection Cure and Death Rate in the Indian States. Healthcare (Basel) 2022; 10:healthcare10010085. [PMID: 35052249 PMCID: PMC8775063 DOI: 10.3390/healthcare10010085] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 12/11/2021] [Accepted: 12/29/2021] [Indexed: 02/04/2023] Open
Abstract
Machine Learning methods can play a key role in predicting the spread of respiratory infection with the help of predictive analytics. Machine Learning techniques help mine data to better estimate and predict the COVID-19 infection status. A Fine-tuned Ensemble Classification approach for predicting the death and cure rates of patients from infection using Machine Learning techniques has been proposed for different states of India. The proposed classification model is applied to the recent COVID-19 dataset for India, and a performance evaluation of various state-of-the-art classifiers to the proposed model is performed. The classifiers forecasted the patients’ infection status in different regions to better plan resources and response care systems. The appropriate classification of the output class based on the extracted input features is essential to achieve accurate results of classifiers. The experimental outcome exhibits that the proposed Hybrid Model reached a maximum F1-score of 94% compared to Ensembles and other classifiers like Support Vector Machine, Decision Trees, and Gaussian Naïve Bayes on a dataset of 5004 instances through 10-fold cross-validation for predicting the right class. The feasibility of automated prediction for COVID-19 infection cure and death rates in the Indian states was demonstrated.
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22
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Early Stage Identification of COVID-19 Patients in Mexico Using Machine Learning: A Case Study for the Tijuana General Hospital. INFORMATION 2021. [DOI: 10.3390/info12120490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: The current pandemic caused by SARS-CoV-2 is an acute illness of global concern. SARS-CoV-2 is an infectious disease caused by a recently discovered coronavirus. Most people who get sick from COVID-19 experience either mild, moderate, or severe symptoms. In order to help make quick decisions regarding treatment and isolation needs, it is useful to determine which significant variables indicate infection cases in the population served by the Tijuana General Hospital (Hospital General de Tijuana). An Artificial Intelligence (Machine Learning) mathematical model was developed in order to identify early-stage significant variables in COVID-19 patients. Methods: The individual characteristics of the study subjects included age, gender, age group, symptoms, comorbidities, diagnosis, and outcomes. A mathematical model that uses supervised learning algorithms, allowing the identification of the significant variables that predict the diagnosis of COVID-19 with high precision, was developed. Results: Automatic algorithms were used to analyze the data: for Systolic Arterial Hypertension (SAH), the Logistic Regression algorithm showed results of 91.0% in area under ROC (AUC), 80% accuracy (CA), 80% F1 and 80% Recall, and 80.1% precision for the selected variables, while for Diabetes Mellitus (DM) with the Logistic Regression algorithm it obtained 91.2% AUC, 89.2% accuracy, 88.8% F1, 89.7% precision, and 89.2% recall for the selected variables. The neural network algorithm showed better results for patients with Obesity, obtaining 83.4% AUC, 91.4% accuracy, 89.9% F1, 90.6% precision, and 91.4% recall. Conclusions: Statistical analyses revealed that the significant predictive symptoms in patients with SAH, DM, and Obesity were more substantial in fatigue and myalgias/arthralgias. In contrast, the third dominant symptom in people with SAH and DM was odynophagia.
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Quiroz-Juárez MA, Torres-Gómez A, Hoyo-Ulloa I, León-Montiel RDJ, U’Ren AB. Identification of high-risk COVID-19 patients using machine learning. PLoS One 2021; 16:e0257234. [PMID: 34543294 PMCID: PMC8452016 DOI: 10.1371/journal.pone.0257234] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 08/26/2021] [Indexed: 12/21/2022] Open
Abstract
The current COVID-19 public health crisis, caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), has produced a devastating toll both in terms of human life loss and economic disruption. In this paper we present a machine-learning algorithm capable of identifying whether a given patient (actually infected or suspected to be infected) is more likely to survive than to die, or vice-versa. We train this algorithm with historical data, including medical history, demographic data, as well as COVID-19-related information. This is extracted from a database of confirmed and suspected COVID-19 infections in Mexico, constituting the official COVID-19 data compiled and made publicly available by the Mexican Federal Government. We demonstrate that the proposed method can detect high-risk patients with high accuracy, in each of four identified clinical stages, thus improving hospital capacity planning and timely treatment. Furthermore, we show that our method can be extended to provide optimal estimators for hypothesis-testing techniques commonly-used in biological and medical statistics. We believe that our work could be of use in the context of the current pandemic in assisting medical professionals with real-time assessments so as to determine health care priorities.
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Affiliation(s)
- Mario A. Quiroz-Juárez
- Departamento de Física, Universidad Autónoma Metropolitana Unidad Iztapalapa, Ciudad de México, México
- * E-mail:
| | | | | | | | - Alfred B. U’Ren
- Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Ciudad de México, México
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