Comparing different machine learning techniques for predicting COVID-19 severity

Prediction models based on machine learning algorithms for COVID-19 severity risk

BACKGROUND

The World Health Organization has highlighted the risk of Disease X, urging pandemic preparedness. Coronavirus disease 2019 (COVID-19) could be the first Disease X; therefore, understanding the epidemiological experiences of COVID-19 is crucial while preparing for future similar diseases.

METHODS

Prediction models for COVID-19 severity risk in hospitalized patients were constructed based on four machine learning algorithms, namely, logistic regression, Cox regression, support vector machine (SVM), and random forest. These models were evaluated for prediction accuracy, area under the curve (AUC), sensitivity, and specificity as well as were interpreted using SHapley Additive exPlanation.

RESULTS

Data were collected from 1,485 hospitalized patients across 6 centers, comprising 1,184 patients with severe or critical COVID-19 and 301 patients with nonsevere COVID-19. Among the four models, the SVM model achieved the highest prediction accuracy of 98.45%, with an AUC of 0.994, a sensitivity of 0.989, and a specificity of 0.969. Moreover, oxygenation index (OI), confusion, respiratory rate, and age were found to be predictors of COVID-19 severity risk.

CONCLUSIONS

SVM could accurately predict COVID-19 severity risk; thus, it can be prioritized as a prediction model. OI is the most critical predictor of COVID-19 severity risk and can serve as the primary and independent evaluation indicator.

An investigation into the impact of temporality on COVID-19 infection and mortality predictions: new perspective based on Shapley Values

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.

Prognostic Value of Biomarkers in COVID-19: Associations with Disease Severity, Viral Variants, and Comorbidities-A Retrospective Observational Single-Center Cohort Study

Coronavirus disease (COVID-19) exhibits a wide spectrum of clinical severity and has been associated with specific biomarkers linked to disease progression and outcomes. This retrospective study analyzed sera from 1222 adult COVID-19 patients hospitalized at the University Hospital for Infectious Diseases in Croatia. We examined the association between several laboratory biomarker levels measured at patient admission and disease severity, fatal outcomes, viral variants and clinical parameters. Deceased patients and surviving patients with severe COVID-19 exhibited significantly elevated levels of several biomarkers on admission, including hs-troponin T, N-terminal pro-brain natriuretic peptide, creatine kinase, C-reactive protein, procalcitonin, interleukin-6, lactate dehydrogenase, lactate, urea and creatinine. Random forest models identified lymphocyte percentage, D-dimers, and hs-troponin T as the most important biomarkers for fatal outcome prediction, achieving 84.1% accuracy. Patients infected with the Delta SARS-CoV-2 variant exhibited significantly higher levels of proinflammatory, cardiac and renal biomarkers. Vaccination correlated with reduced proinflammatory parameters and higher lymphocyte proportions. Hypertension, chronic renal disease and diabetes were associated with increased cardiac, renal and metabolic biomarker levels, respectively. These findings highlight the association of several laboratory biomarkers with COVID-19 severity, viral variants, vaccination status and comorbidities, potentially offering prognostic insights into COVID-19 outcomes.

Evaluation of inflammatory-thrombosis panel as a diagnostic tool for vascular Behçet's disease

OBJECTIVES

Vascular Behçet's disease (VBD) is prevalent in 40% of BD, but lacks laboratory biomarker for timely diagnosis. We aimed to establish a diagnostic panel for discerning VBD and non-VBD patients and identify hemostatic-thrombotic markers most related to VBD pathogenesis using machine learning algorithm.

OBJECTIVES

A total of 338 BD patients comprising 123 VBD and 215 non-VBD were enrolled. Twenty-six clinical and laboratory features selected from LassoCV were included in multiple classifier to choose the optimal model for VBD differentiation. The Shapley Additive exPlanations (SHAP) was employed to interpret the contribution of model features for VBD prediction. Logistic regression analysis and nomogram were conducted to screen risk factors of VBD.

RESULTS

Inflammatory (neutrophils%, NK cells, IL-6), hematological (hemoglobin, hemoglobin distribution width (HDW)) and thrombosis (activated partial thromboplastin clotting time (APTT), D-dimer) parameters were elevated in VBD. Then we chose top contributors from XGBoost model and performed ten-fold cross validation, the diagnostic accuracy of which exceeded 0.90. Utilizing SHAP method, we identified higher incidence of arterial thrombosis or aneurysm and deep vein thrombosis, upregulated NK cell count, HDW, APTT and D-dimer, downregulated reticulocyte%, B cell count, red blood cell distribution width, cellular hemoglobin (CH) and TNF-α would ultimately generate the phenotype of VBD. Severity, hemoglobin, mean corpuscular hemoglobin, CH, HDW, APTT and D-dimer were found as potential risk factors for vascular outcomes among BD.

RESULTS

Our study developed a well-performed model leveraging clinical and laboratory parameters for differentiating VBD. Inflammatory and thrombotic risk factors are potential contributors to VBD. Key Points • Inflammatory (neutrophils%, NK cells, IL-6), hematological (HGB, HDW) and thrombosis (APTT, D-dimer) parameters were elevated in VBD. • We firstly developed an inflammatory-thrombosis model as a diagnostic tool for VBD. • HGB, MCH, CH, HDW, APTT and D-dimer are potential risk factors for VBD.

AI-driven health analysis for emerging respiratory diseases: A case study of Yemen patients using COVID-19 data

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.

Utilizing machine learning-based QSAR model to overcome standalone consensus docking limitation in beta-lactamase inhibitors screening: a proof-of-concept study

In virtual drug screening, consensus docking is a standard in-silico approach consisting of a combined result from optimized docking experiments, a minimum of two results combination. Therefore, consensus docking is subjected to a lower success rate than the best docking method due to its mathematical nature, an unavoidable limitation. This study aims to overcome this drawback via random forest, an ensemble machine learning model. First, in vitro beta-lactamase inhibitory screening was performed using an in-house chemical library. The in vitro results were later used as a validation. Consequently, we optimized docking protocols for AutoDock Vina and DOCK6 programs. With an appropriate scoring function, we found that DOCK6 could identify up to 70% of all active molecules, double the inappropriate. Further consensus analysis reduced the success rate to 50%. Simultaneously, a false positive rate was down to 16%, which was experimentally favorable for a drug search. Finally, we trained two quantitative structure-activity relationship (QSAR) models using logistic regression as a reference model and a random forest as a test model. After combining consensus docking results, random forest-based QSAR outperformed a logistic regression by restoring the success rate to 70% and maintaining a low false positive rate of around 21%. In conclusion, this study demonstrated the benefit of using a random forest (machine learning)-based QSAR model to overcome a standard consensus docking limitation in beta-lactamase inhibitor search as a proof-of-concept.

Predicting Intensive Care Unit Admission in COVID-19-Infected Pregnant Women Using Machine Learning

Background: The rapid onset of COVID-19 placed immense strain on many already overstretched healthcare systems. The unique physiological changes in pregnancy, amplified by the complex effects of COVID-19 in pregnant women, rendered prioritization of infected expectant mothers more challenging. This work aims to use state-of-the-art machine learning techniques to predict whether a COVID-19-infected pregnant woman will be admitted to ICU (Intensive Care Unit). Methods: A retrospective study using data from COVID-19-infected women admitted to one hospital in Astana and one in Shymkent, Kazakhstan, from May to July 2021. The developed machine learning platform implements and compares the performance of eight binary classifiers, including Gaussian naïve Bayes, K-nearest neighbors, logistic regression with L2 regularization, random forest, AdaBoost, gradient boosting, eXtreme gradient boosting, and linear discriminant analysis. Results: Data from 1292 pregnant women with COVID-19 were analyzed. Of them, 10.4% were admitted to ICU. Logistic regression with L2 regularization achieved the highest F1-score during the model selection phase while achieving an AUC of 0.84 on the test set during the evaluation stage. Furthermore, the feature importance analysis conducted by calculating Shapley Additive Explanation values points to leucocyte counts, C-reactive protein, pregnancy week, and eGFR and hemoglobin as the most important features for predicting ICU admission. Conclusions: The predictive model obtained here may be an efficient support tool for prioritizing care of COVID-19-infected pregnant women in clinical practice.

A Genetic algorithm aided hyper parameter optimization based ensemble model for respiratory disease prediction with Explainable AI

In the current era, a lot of research is being done in the domain of disease diagnosis using machine learning. In recent times, one of the deadliest respiratory diseases, COVID-19, which causes serious damage to the lungs has claimed a lot of lives globally. Machine learning-based systems can assist clinicians in the early diagnosis of the disease, which can reduce the deadly effects of the disease. For the successful deployment of these machine learning-based systems, hyperparameter-based optimization and feature selection are important issues. Motivated by the above, in this proposal, we design an improved model to predict the existence of respiratory disease among patients by incorporating hyperparameter optimization and feature selection. To optimize the parameters of the machine learning algorithms, hyperparameter optimization with a genetic algorithm is proposed and to reduce the size of the feature set, feature selection is performed using binary grey wolf optimization algorithm. Moreover, to enhance the efficacy of the predictions made by hyperparameter-optimized machine learning models, an ensemble model is proposed using a stacking classifier. Also, explainable AI was incorporated to define the feature importance by making use of Shapely adaptive explanations (SHAP) values. For the experimentation, the publicly accessible Mexico clinical dataset of COVID-19 was used. The results obtained show that the proposed model has superior prediction accuracy in comparison to its counterparts. Moreover, among all the hyperparameter-optimized algorithms, adaboost algorithm outperformed all the other hyperparameter-optimized algorithms. The various performance assessment metrics, including accuracy, precision, recall, AUC, and F1-score, were used to assess the results.

Prediction models for COVID-19 disease outcomes

SARS-CoV-2 has caused over 6.9 million deaths and continues to produce lasting health consequences. COVID-19 manifests broadly from no symptoms to death. In a retrospective cross-sectional study, we developed personalized risk assessment models that predict clinical outcomes for individuals with COVID-19 and inform targeted interventions. We sequenced viruses from SARS-CoV-2-positive nasopharyngeal swab samples between July 2020 and July 2022 from 4450 individuals in Missouri and retrieved associated disease courses, clinical history, and urban-rural classification. We integrated this data to develop machine learning-based predictive models to predict hospitalization, ICU admission, and long COVID.The mean age was 38.3 years (standard deviation = 21.4) with 55.2% (N = 2453) females and 44.8% (N = 1994) males (not reported, N = 4). Our analyses revealed a comprehensive set of predictors for each outcome, encompassing human, environment, and virus genome-wide genetic markers. Immunosuppression, cardiovascular disease, older age, cardiac, gastrointestinal, and constitutional symptoms, rural residence, and specific amino acid substitutions were associated with hospitalization. ICU admission was associated with acute respiratory distress syndrome, ventilation, bacterial co-infection, rural residence, and non-wild type SARS-CoV-2 variants. Finally, long COVID was associated with hospital admission, ventilation, and female sex.Overall, we developed risk assessment models that offer the capability to identify patients with COVID-19 necessitating enhanced monitoring or early interventions. Of importance, we demonstrate the value of including key elements of virus, host, and environmental factors to predict patient outcomes, serving as a valuable platform in the field of personalized medicine with the potential for adaptation to other infectious diseases.

The use of machine and deep learning to model the relationship between discomfort temperature and labor productivity loss among petrochemical workers

BACKGROUND

Workplace may not only increase the risk of heat-related illnesses and injuries but also compromise work efficiency, particularly in a warming climate. This study aimed to utilize machine learning (ML) and deep learning (DL) algorithms to quantify the impact of temperature discomfort on productivity loss among petrochemical workers and to identify key influencing factors.

METHODS

A cross-sectional face-to-face questionnaire survey was conducted among petrochemical workers between May and September 2023 in Fujian Province, China. Initial feature selection was performed using Lasso regression. The dataset was divided into training (70%), validation (20%), and testing (10%) sets. Six predictive models were evaluated: support vector machine (SVM), random forest (RF), extreme gradient boosting (XGBoost), Gaussian Naive Bayes (GNB), multilayer perceptron (MLP), and logistic regression (LR). The most effective model was further analyzed with SHapley Additive exPlanations (SHAP).

RESULTS

Among the 2393 workers surveyed, 58.4% (1,747) reported productivity loss when working in high temperatures. Lasso regression identified twenty-seven predictive factors such as educational level and smoking. All six models displayed strong prediction accuracy (SVM = 0.775, RF = 0.760, XGBoost = 0.727, GNB = 0.863, MLP = 0.738, LR = 0.680). GNB model showed the best performance, with a cutoff of 0.869, accuracy of 0.863, precision of 0.897, sensitivity of 0.918, specificity of 0.715, and an F1-score of 0.642, indicating its efficacy as a predictive tool. SHAP analysis showed that occupational health training (SHAP value: -3.56), protective measures (-2.61), and less physically demanding jobs (-1.75) were negatively associated with heat-attributed productivity loss, whereas lack of air conditioning (1.92), noise (2.64), vibration (1.15), and dust (0.95) increased the risk of heat-induced productivity loss.

CONCLUSIONS

Temperature discomfort significantly undermined labor productivity in the petrochemical sector, and this impact may worsen in a warming climate if adaptation and prevention measures are insufficient. To effectively reduce heat-related productivity loss, there is a need to strengthen occupational health training and implement strict controls for occupational hazards, minimizing the potential combined effects of heat with other exposures.

Machine learning based predictive modeling and risk factors for prolonged SARS-CoV-2 shedding

BACKGROUND

The global outbreak of the coronavirus disease 2019 (COVID-19) has been enormously damaging, in which prolonged shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, previously 2019-nCoV) infection is a challenge in the prevention and treatment of COVID-19. However, there is still incomplete research on the risk factors that affect delayed shedding of SARS-CoV-2.

METHODS

In a retrospective analysis of 56,878 hospitalized patients in the Fangcang Shelter Hospital (National Convention and Exhibition Center) in Shanghai, China, we compared patients with the duration of SARS-CoV-2 viral shedding > 12 days with those days < 12 days. The results of real-time polymerase chain reaction (RT-PCR) tests determined the duration of viral shedding from the first day of SARS-CoV-2 positivity to the day of SARS-CoV-2 negativity. The extreme gradient boosting (XGBoost) machine learning method was employed to establish a prediction model for prolonged SARS-CoV-2 shedding and analyze significant risk factors. Filtering features retraining and Shapley Additive Explanations (SHAP) techniques were followed to demonstrate and further explain the risk factors for long-term SARS-CoV-2 infection.

RESULTS

We conducted an assessment of ten different features, including vaccination, hypertension, diabetes, admission cycle threshold (Ct) value, cardio-cerebrovascular disease, gender, age, occupation, symptom, and family accompaniment, to determine their impact on the prolonged SARS-CoV-2 shedding. This study involved a large cohort of 56,878 hospitalized patients, and we leveraged the XGBoost algorithm to establish a predictive model based on these features. Upon analysis, six of these ten features were significantly associated with the prolonged SARS-CoV-2 shedding, as determined by both the importance order of the model and our results obtained through model reconstruction. Specifically, vaccination, hypertension, admission Ct value, gender, age, and family accompaniment were identified as the key features associated with prolonged viral shedding.

CONCLUSIONS

We developed a predictive model and identified six risk factors associated with prolonged SARS-CoV-2 viral shedding. Our study contributes to identifying and screening individuals with potential long-term SARS-CoV-2 infections. Moreover, our research also provides a reference for future preventive control, optimizing medical resource allocation and guiding epidemiological prevention, and guidelines for personal protection against SARS-CoV-2.

Phenotype clustering of hospitalized high-risk patients with COVID-19 - a machine learning approach within the multicentre, multinational PCHF-COVICAV registry

IMTRODUCTION

The high-risk population of patients with cardiovascular (CV) disease or risk factors (RF) suffering from COVID-19 is heterogeneous. Several predictors for impaired prognosis have been identified. However, with machine learning (ML) approaches, certain phenotypes may be confined to classify the affected population and to predict outcome. This study aimed to phenotype patients using unsupervised ML technique within the International Postgraduate Course Heart Failure Registry for patients hospitalized with COVID-19 and Cardiovascular disease and/or RF (PCHF-COVICAV).

MATERIAL AND METHODS

Patients from the eight centres with follow-up data available from the PCHF-COVICAV registry were included in this ML analysis (K-medoids algorithm).

RESULTS

Out of 617 patients included into the prospective part of the registry, 458 [median age: 76 (IQR:65-84) years, 55% male] were analyzed and 46 baseline variables, including demographics, clinical status, comorbidities and biochemical characteristics were incorporated into the ML. Three clusters were extracted by this ML method. Cluster 1 (n = 181) represents mainly women with the least number of overall comorbidities and cardiovascular RF. Cluster 2 (n = 227) is characterized mainly by men with non-CV conditions and less severe symptoms of infection. Cluster 3 (n=50) mainly represents men with the highest prevalence of cardiac comorbidities and RF, more extensive inflammation and organ dysfunction with the highest 6-month all-cause mortality risk.

CONCLUSIONS

The ML process has identified three important clinical clusters from hospitalized COVID-19 CV and/or RF patients. The cluster of males with severe CV disease, particularly HF, and multiple RF presenting with increased inflammation had a particularly poor outcome.

Predictive health monitoring: Leveraging artificial intelligence for early detection of infectious diseases in nursing home residents through discontinuous vital signs analysis

This research addresses the problem of detecting acute respiratory, urinary tract, and other infectious diseases in elderly nursing home residents using machine learning algorithms. The study analyzes data extracted from multiple vital signs and other contextual information for diagnostic purposes. The daily data collection process encounters sampling constraints due to weekends, holidays, shift changes, staff turnover, and equipment breakdowns, resulting in numerous nulls, repeated readings, outliers, and meaningless values. The short time series generated also pose a challenge to analysis, preventing the extraction of seasonal information or consistent trends. Blind data collection results in most of the data coming from periods when residents are healthy, resulting in excessively imbalanced data. This study proposes a data cleaning process and then builds a mechanism that reproduces the basal activity of the residents to improve the classification of the disease. The results show that the proposed basal module-assisted machine learning techniques allow anticipating diagnostics 2, 3 or 4 days before doctors decide to start treatment with antibiotics, achieving a performance measured by the area-under-the-curve metric of 0.857. The contributions of this work are: (1) a new data cleaning process; (2) the analysis of contextual information to improve data quality; (3) the generation of a baseline measure for relative comparison; and (4) the use of either binary (disease/no disease) or multiclass classification, differentiating among types of infections and showing the advantages of multiclass versus binary classification. From a medical point of view, the anticipated detection of infectious diseases in institutionalized individuals is brand new.

Predictors of disease outbreaks at continental-scale in the African region: Insights and predictions with geospatial artificial intelligence using earth observations and routine disease surveillance data

Objectives

Our research adopts computational techniques to analyze disease outbreaks weekly over a large geographic area while maintaining local-level analysis by incorporating relevant high-spatial resolution cultural and environmental datasets. The abundance of data about disease outbreaks gives scientists an excellent opportunity to uncover patterns in disease spread and make future predictions. However, data over a sizeable geographic area quickly outpace human cognition. Our study area covers a significant portion of the African continent (about 17,885,000 km2). The data size makes computational analysis vital to assist human decision-makers.

Methods

We first applied global and local spatial autocorrelation for malaria, cholera, meningitis, and yellow fever case counts. We then used machine learning to predict the weekly presence of these diseases in the second-level administrative district. Lastly, we used machine learning feature importance methods on the variables that affect spread.

Results

Our spatial autocorrelation results show that geographic nearness is critical but varies in effect and space. Moreover, we identified many interesting hot and cold spots and spatial outliers. The machine learning model infers a binary class of cases or none with the best F1 score of 0.96 for malaria. Machine learning feature importance uncovered critical cultural and environmental factors affecting outbreaks and variations between diseases.

Conclusions

Our study shows that data analytics and machine learning are vital to understanding and monitoring disease outbreaks locally across vast areas. The speed at which these methods produce insights can be critical during epidemics and emergencies.

Development of a novel machine learning model based on laboratory and imaging indices to predict acute cardiac injury in cancer patients with COVID-19 infection: a retrospective observational study

PURPOSE

Due to the increased risk of acute cardiac injury (ACI) and poor prognosis in cancer patients with COVID-19 infection, our aim was to develop a novel and interpretable model for predicting ACI occurrence in cancer patients with COVID-19 infection.

METHODS

This retrospective observational study screened 740 cancer patients with COVID-19 infection from December 2022 to April 2023. The least absolute shrinkage and selection operator (LASSO) regression was used for the preliminary screening of the indices. To enhance the model accuracy, we introduced an alpha index to further screen and rank the indices based on their significance. Random forest (RF) was used to construct the prediction model. The Shapley Additive Explanation (SHAP) and Local Interpretable Model-Agnostic Explanation (LIME) methods were utilized to explain the model.

RESULTS

According to the inclusion criteria, 201 cancer patients with COVID-19, including 36 variables indices, were included in the analysis. The top eight indices (albumin, lactate dehydrogenase, cystatin C, neutrophil count, creatine kinase isoenzyme, red blood cell distribution width, D-dimer and chest computed tomography) for predicting the occurrence of ACI in cancer patients with COVID-19 infection were included in the RF model. The model achieved an area under curve (AUC) of 0.940, an accuracy of 0.866, a sensitivity of 0.750 and a specificity of 0.900. The calibration curve and decision curve analysis showed good calibration and clinical practicability. SHAP results demonstrated that albumin was the most important index for predicting the occurrence of ACI. LIME results showed that the model could predict the probability of ACI in each cancer patient infected with COVID-19 individually.

CONCLUSION

We developed a novel machine-learning model that demonstrates high explainability and accuracy in predicting the occurrence of ACI in cancer patients with COVID-19 infection, using laboratory and imaging indices.

The role of pyroptosis-related genes in the diagnosis and subclassification of sepsis

Pyroptosis is a new form of programmed cell death recognized as crucial in developing sepsis. However, there is limited research on the mechanism of pyroptosis-related genes in sepsis-related from the Gene Expression Omnibus (GEO) database and standardized. The expression levels of pyroptosis-related genes were extracted, and differential expression analysis was conducted. A prediction model was constructed using random forest (RF), support vector machine (SVM), weighted gene co-expression new analysis (WGCNA), and nomogram techniques to assess the risk of sepsis. The relationship between pyroptosis-related subgroups and the immune microenvironment and inflammatory factors was studied using consistent clustering algorithms, principal component analysis (PCA), single-sample genomic enrichment analysis (ssGSEA), and immune infiltration. A risk prediction model based on 3 PRGs has been constructed and can effectively predict the risk of sepsis. Patients with sepsis can be divided into two completely different subtypes of pyroptosis-related clusters. Cluster B is highly correlated with the lower proportion of Th17 celld and has lower levels of expression of inflammatory factors. This study utilizes mechanical learning methods to further investigate the pathogenesis of sepsis, explore potential biomarkers, provide effective molecular targets for its diagnosis and treatment of sepsis.

Using artificial intelligence to improve public health: a narrative review

Artificial intelligence (AI) is a rapidly evolving tool revolutionizing many aspects of healthcare. AI has been predominantly employed in medicine and healthcare administration. However, in public health, the widespread employment of AI only began recently, with the advent of COVID-19. This review examines the advances of AI in public health and the potential challenges that lie ahead. Some of the ways AI has aided public health delivery are via spatial modeling, risk prediction, misinformation control, public health surveillance, disease forecasting, pandemic/epidemic modeling, and health diagnosis. However, the implementation of AI in public health is not universal due to factors including limited infrastructure, lack of technical understanding, data paucity, and ethical/privacy issues.

Augmentation strategies for an imbalanced learning problem on a novel COVID-19 severity dataset

Since the beginning of the COVID-19 pandemic, many different machine learning models have been developed to detect and verify COVID-19 pneumonia based on chest X-ray images. Although promising, binary models have only limited implications for medical treatment, whereas the prediction of disease severity suggests more suitable and specific treatment options. In this study, we publish severity scores for the 2358 COVID-19 positive images in the COVIDx8B dataset, creating one of the largest collections of publicly available COVID-19 severity data. Furthermore, we train and evaluate deep learning models on the newly created dataset to provide a first benchmark for the severity classification task. One of the main challenges of this dataset is the skewed class distribution, resulting in undesirable model performance for the most severe cases. We therefore propose and examine different augmentation strategies, specifically targeting majority and minority classes. Our augmentation strategies show significant improvements in precision and recall values for the rare and most severe cases. While the models might not yet fulfill medical requirements, they serve as an appropriate starting point for further research with the proposed dataset to optimize clinical resource allocation and treatment.

COVID-19 and cholesterol biosynthesis: Towards innovative decision support systems

With COVID-19 becoming endemic, there is a continuing need to find biomarkers characterizing the disease and aiding in patient stratification. We studied the relation between COVID-19 and cholesterol biosynthesis by comparing 10 intermediates of cholesterol biosynthesis during the hospitalization of 164 patients (admission, disease deterioration, discharge) admitted to the University Medical Center of Ljubljana. The concentrations of zymosterol, 24-dehydrolathosterol, desmosterol, and zymostenol were significantly altered in COVID-19 patients. We further developed a predictive model for disease severity based on clinical parameters alone and their combination with a subset of sterols. Our machine learning models applying 8 clinical parameters predicted disease severity with excellent accuracy (AUC = 0.96), showing substantial improvement over current clinical risk scores. After including sterols, model performance remained better than COVID-GRAM. This is the first study to examine cholesterol biosynthesis during COVID-19 and shows that a subset of cholesterol-related sterols is associated with the severity of COVID-19.

Intelligent Framework for Early Detection of Severe Pediatric Diseases from Mild Symptoms

Children's health is one of the most significant fields in medicine. Most diseases that result in children's death or long-term morbidity are caused by preventable and treatable etiologies, and they appear in the child at the early stages as mild symptoms. This research aims to develop a machine learning (ML) framework to detect the severity of disease in children. The proposed framework helps in discriminating children's urgent/severe conditions and notifying parents whether a child needs to visit the emergency room immediately or not. The model considers several variables to detect the severity of cases, which are the symptoms, risk factors (e.g., age), and the child's medical history. The framework is implemented by using nine ML methods. The results achieved show the high performance of the proposed framework in identifying serious pediatric diseases, where decision tree and random forest outperformed the other methods with an accuracy rate of 94%. This shows the reliability of the proposed framework to be used as a pediatric decision-making system for detecting serious pediatric illnesses. The results are promising when compared to recent state-of-the-art studies. The main contribution of this research is to propose a framework that is viable for use by parents when their child suffers from any commonly developed symptoms.

Recent advances in wearable sensors and data analytics for continuous monitoring and analysis of biomarkers and symptoms related to COVID-19

The COVID-19 pandemic has changed the lives of many people around the world. Based on the available data and published reports, most people diagnosed with COVID-19 exhibit no or mild symptoms and could be discharged home for self-isolation. Considering that a substantial portion of them will progress to a severe disease requiring hospitalization and medical management, including respiratory and circulatory support in the form of supplemental oxygen therapy, mechanical ventilation, vasopressors, etc. The continuous monitoring of patient conditions at home for patients with COVID-19 will allow early determination of disease severity and medical intervention to reduce morbidity and mortality. In addition, this will allow early and safe hospital discharge and free hospital beds for patients who are in need of admission. In this review, we focus on the recent developments in next-generation wearable sensors capable of continuous monitoring of disease symptoms, particularly those associated with COVID-19. These include wearable non/minimally invasive biophysical (temperature, respiratory rate, oxygen saturation, heart rate, and heart rate variability) and biochemical (cytokines, cortisol, and electrolytes) sensors, sensor data analytics, and machine learning-enabled early detection and medical intervention techniques. Together, we aim to inspire the future development of wearable sensors integrated with data analytics, which serve as a foundation for disease diagnostics, health monitoring and predictions, and medical interventions.

A machine learning and explainable artificial intelligence triage-prediction system for COVID-19

COVID-19 is a respiratory disease caused by the SARS-CoV-2 contagion, severely disrupted the healthcare infrastructure. Various countries have developed COVID-19 vaccines that have effectively prevented the severe symptoms caused by the virus to a certain extent. However, a small section of people continues to perish. Artificial intelligence advances have revolutionized healthcare diagnosis and prognosis infrastructure. In this study, we predict the severity of COVID-19 using heterogenous Machine Learning and Deep Learning algorithms by considering clinical markers, vital signs, and other critical factors. This study extensively reviews various classifier architectures to predict the COVID-19 severity. We built and evaluated multiple pipelines entailing combinations of five state-of-the-art data-balancing techniques (Synthetic Minority Oversampling Technique (SMOTE), Adaptive Synthetic, Borderline SMOTE, SMOTE with Tomek links, and SMOTE with Edited Nearest Neighbor (ENN)) and twelve heterogeneous classifiers such as Logistic Regression, Decision Tree, Random Forest, Support Vector Machine, K-Nearest Neighbors, Naïve Bayes, Xgboost, Extratrees, Adaboost, Light GBM, Catboost, and 1-D Convolution Neural Network. The best-performing pipeline consists of Random Forest trained on Borderline SMOTE balanced data that produced the highest recall of 83%. We deployed Explainable Artificial Intelligence tools such as Shapley Additive Explanations and Local Interpretable Model-agnostic Explanations, ELI5, Qlattice, Anchor, and Feature Importance to demystify complex tree-based ensemble models. These tools provide valuable insights into the significance of critical features in the severity prediction of a COVID-19 patient. It was observed that changes in respiratory rate, blood pressure, lactate, and calcium values were the primary contributors to the increase in severity of a COVID-19 patient. This architecture aims to be an explainable decision-support triaging system for medical professionals in countries lacking advanced medical technology and infrastructure to reduce fatalities.

Prognostic models in COVID-19 infection that predict severity: a systematic review

Current evidence on COVID-19 prognostic models is inconsistent and clinical applicability remains controversial. We performed a systematic review to summarize and critically appraise the available studies that have developed, assessed and/or validated prognostic models of COVID-19 predicting health outcomes. We searched six bibliographic databases to identify published articles that investigated univariable and multivariable prognostic models predicting adverse outcomes in adult COVID-19 patients, including intensive care unit (ICU) admission, intubation, high-flow nasal therapy (HFNT), extracorporeal membrane oxygenation (ECMO) and mortality. We identified and assessed 314 eligible articles from more than 40 countries, with 152 of these studies presenting mortality, 66 progression to severe or critical illness, 35 mortality and ICU admission combined, 17 ICU admission only, while the remaining 44 studies reported prediction models for mechanical ventilation (MV) or a combination of multiple outcomes. The sample size of included studies varied from 11 to 7,704,171 participants, with a mean age ranging from 18 to 93 years. There were 353 prognostic models investigated, with area under the curve (AUC) ranging from 0.44 to 0.99. A great proportion of studies (61.5%, 193 out of 314) performed internal or external validation or replication. In 312 (99.4%) studies, prognostic models were reported to be at high risk of bias due to uncertainties and challenges surrounding methodological rigor, sampling, handling of missing data, failure to deal with overfitting and heterogeneous definitions of COVID-19 and severity outcomes. While several clinical prognostic models for COVID-19 have been described in the literature, they are limited in generalizability and/or applicability due to deficiencies in addressing fundamental statistical and methodological concerns. Future large, multi-centric and well-designed prognostic prospective studies are needed to clarify remaining uncertainties.

Multi-omics and immune cells' profiling of COVID-19 patients for ICU admission prediction: in silico analysis and an integrated machine learning-based approach in the framework of Predictive, Preventive, and Personalized Medicine

Background

Intensive care unit admission (ICUA) triage has been urgent need for solving the shortage of ICU beds, during the coronavirus disease 2019 (COVID-19) surge. In silico analysis and integrated machine learning (ML) approach, based on multi-omics and immune cells (ICs) profiling, might provide solutions for this issue in the framework of predictive, preventive, and personalized medicine (PPPM).

Methods

Multi-omics was used to screen the synchronous differentially expressed protein-coding genes (SDEpcGs), and an integrated ML approach to develop and validate a nomogram for prediction of ICUA. Finally, the independent risk factor (IRF) with ICs profiling of the ICUA was identified.

Results

Colony-stimulating factor 1 receptor (CSF1R) and peptidase inhibitor 16 (PI16) were identified as SDEpcGs, and each fold change (FC_ij) of CSF1R and PI16 was selected to develop and validate a nomogram to predict ICUA. The area under curve (AUC) of the nomogram was 0.872 (95% confidence interval (CI): 0.707 to 0.950) on the training set, and 0.822 (95% CI: 0.659 to 0.917) on the testing set. CSF1R was identified as an IRF of ICUA, expressed in and positively correlated with monocytes which had a lower fraction in COVID-19 ICU patients.

Conclusion

The nomogram and monocytes could provide added value to ICUA prediction and targeted prevention, which are cost-effective platform for personalized medicine of COVID-19 patients. The log₂fold change (log₂FC) of the fraction of monocytes could be monitored simply and economically in primary care, and the nomogram offered an accurate prediction for secondary care in the framework of PPPM.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13167-023-00317-5.

Multi-region machine learning-based novel ensemble approaches for predicting COVID-19 pandemic in Africa

Coronavirus disease 2019 (COVID-19) has produced a global pandemic, which has devastating effects on health, economy and social interactions. Despite the less contraction and spread of COVID-19 in Africa compared to some other continents in the world, Africa remains amongst the most vulnerable regions due to less technology and unequipped or poor health system. Recent happenings showed that COVID-19 may stay for years owing to the discoveries of new variants (such as Omicron) and new wave of infections in several countries. Therefore, accurate prediction of new cases is vital to make informed decisions and in evaluating the measures that should be implemented. Studies on COVID-19 prediction are limited in Africa despite the risks and dangers that the virus possessed. Hence, this study was performed to predict daily COVID-19 cases in 10 African countries spread across the north, south, east, west and central Africa considering countries with few and large number of daily COVID-19 cases. Machine learning (ML) models due to their nonlinearity and accurate prediction capabilities were employed for this purpose, including artificial neural network (ANN), adaptive neuro-fuzzy inference system (ANFIS), support vector machine (SVM) and conventional multiple linear regression (MLR) models. As any other natural process, the COVID-19 pandemic may contain both linear and nonlinear aspects. In such circumstances, neither nonlinear (ML) nor linear (MLR) models could be sufficient; hence, combining both ML and MLR models may produce better accuracy. Consequently, to improve the prediction efficiency of the ML models, novel ensemble approaches including ANN-E and SVM-E were employed. The advantage of using ensemble approaches is that they provide collective benefits of all the standalone models, thereby reducing their weaknesses and enhancing their prediction capabilities. The obtained results showed that ANFIS led to better prediction performance with MAD = 0.0106, MSE = 0.0003, RMSE = 0.0185 and R2 = 0.9059 in the validation step. The results of the proposed ensemble approaches demonstrated very high improvements in predicting the COVID-19 pandemic in Africa with MAD = 0.0073, MSE = 0.0002, RMSE = 0.0155 and R2 = 0.9616. The ANN-E improved the standalone models performance in the validation step up to 10%, 14%, 42%, 6%, 83%, 11%, 7%, 5%, 7% and 31% for Morocco, Sudan, Namibia, South Africa, Uganda, Rwanda, Nigeria, Senegal, Gabon and Cameroon, respectively. This study results offer a solid foundation in the application of ensemble approaches for predicting COVID-19 pandemic across all regions and countries in the world.

Assessing the Nationwide COVID-19 Risk in Mexico through the Lens of Comorbidity by an XGBoost-Based Logistic Regression Model

The outbreak of the new COVID-19 disease is a serious health problem that has affected a large part of the world population, especially older adults and people who suffer from a previous comorbidity. In this work, we proposed a classifier model that allows for deciding whether or not a patient might suffer from the COVID-19 disease, considering spatio-temporal variables, physical characteristics of the patients and the presence of previous diseases. We used XGBoost to maximize the likelihood function of the multivariate logistic regression model. The estimated and observed values of percentage occurrence of cases were very similar, and indicated that the proposed model was suitable to predict new cases (AUC = 0.75). The main results revealed that patients without comorbidities are less likely to be COVID-19 positive, unlike people with diabetes, obesity and pneumonia. The distribution function by age group showed that, during the first and second wave of COVID-19, young people aged ≤20 were the least affected by the pandemic, while the most affected were people between 20 and 40 years, followed by adults older than 40 years. In the case of the third and fourth wave, there was an increased risk for young individuals (under 20 years), while older adults over 40 years decreased their chances of infection. Estimates of positive COVID cases with both the XGBoost-LR model and the multivariate logistic regression model were used to create maps to visualize the spatial distribution of positive cases across the country. Spatial analysis was carried out to determine, through the data, the main geographical areas where a greater number of positive cases occurred. The results showed that the areas most affected by COVID-19 were in the central and northern regions of Mexico.

A Comprehensive Review of Machine Learning Used to Combat COVID-19

Coronavirus disease (COVID-19) has had a significant impact on global health since the start of the pandemic in 2019. As of June 2022, over 539 million cases have been confirmed worldwide with over 6.3 million deaths as a result. Artificial Intelligence (AI) solutions such as machine learning and deep learning have played a major part in this pandemic for the diagnosis and treatment of COVID-19. In this research, we review these modern tools deployed to solve a variety of complex problems. We explore research that focused on analyzing medical images using AI models for identification, classification, and tissue segmentation of the disease. We also explore prognostic models that were developed to predict health outcomes and optimize the allocation of scarce medical resources. Longitudinal studies were conducted to better understand COVID-19 and its effects on patients over a period of time. This comprehensive review of the different AI methods and modeling efforts will shed light on the role that AI has played and what path it intends to take in the fight against COVID-19.

Effectiveness of Tocilizumab in Patients with Severe or Critical Lung Involvement in COVID-19: A Retrospective Study

Introduction: Acute lung injury is associated with dysfunctional immune response to SARS-CoV-2. This leads to CRS, which require immunomodulatory treatments aiming to limit the excessive production of cytokines. The literature so far indicates the effectiveness of tocilizumab in patients with COVID-19-associated pneumonia, but there is no clear evidence of its effectiveness in patients with at least 50% lung involvement; therefore, we aimed to bridge this gap in knowledge. Materials and methods: Longitudinal data for 4287 patients with confirmed COVID-19 infection were collected between 1st March 2020 and 16th of January 2022. In total, 182 cases with lung involvement >50% and biochemical indicators of cytokine release storm (Il-6 >100 pg/mL) were selected and analyzed using non-parametric statistics and multivariate Cox models. Results: Among the 182 included patients, 100 (55%) were treated with TCZ, while 82 (45%) did not receive TCZ. The groups were balanced regarding demographics, lung involvement and biochemical markers. Overall mortality in the group was 63.1%. Mortality in the TCZ group was 58.0% compared to 69.5% (n = 57) in the non-TCZ group (p = 0.023). In multivariate Cox proportional hazards models, intravenous administration of tocilizumab was associated with lower probability of ICU admission (HR: 0333 (CI: 0.159−0.700, p = 0.004)) and lower mortality (HR: 0.57306 (CI: 0.354−0.927, p = 0.023)). Conclusions: Tocilizumab is effective as a treatment in the most severely ill patients, in whom the level of lung involvement by the inflammatory process can exceed 50% with coexisting biochemical indices of cytokine storm (Il-6 > 100 pg/mL).

Severe COVID-19 is characterised by inflammation and immature myeloid cells early in disease progression

SARS-CoV-2 infection causes a wide spectrum of disease severity. Identifying the immunological characteristics of severe disease and the risk factors for their development are important in the management of COVID-19. This study aimed to identify and rank clinical and immunological features associated with progression to severe COVID-19 in order to investigate an immunological signature of severe disease. One hundred and eight patients with positive SARS-CoV-2 PCR were recruited. Routine clinical and laboratory markers were measured, as well as myeloid and lymphoid whole-blood immunophenotyping and measurement of the pro-inflammatory cytokines IL-6 and soluble CD25. All analysis was carried out in a routine hospital diagnostic laboratory. Univariate analysis demonstrated that severe disease was most strongly associated with elevated CRP and IL-6, loss of DLA-DR expression on monocytes and CD10 expression on neutrophils. Unbiased machine learning demonstrated that these four features were strongly associated with severe disease, with an average prediction score for severe disease of 0.925. These results demonstrate that these four markers could be used to identify patients developing severe COVID-19 and allow timely delivery of therapeutics.

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Severe COVID-19 is characterised by a combination of emergency myelopoiesis and inflammation.

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These changes can be rapidly identified in a diagnostic laboratory, facilitating intervention.

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This disease signature was derived from a cohort of patients with a wide range of ages, frailty and COVID-19 severity.