Detection of COVID-19 Infection from Routine Blood Exams with Machine Learning: A Feasibility Study

Predicting special care during the COVID-19 pandemic: a machine learning approach

More than ever, COVID-19 is putting pressure on health systems worldwide, especially in Brazil. In this study, we propose a method based on statistics and machine learning that uses blood lab exam data from patients to predict whether patients will require special care (hospitalization in regular or special-care units). We also predict the number of days the patients will stay under such care. The two-step procedure developed uses Bayesian Optimisation to select the best model among several candidates. This leads us to final models that achieve 0.94 area under ROC curve performance for the first target and 1.87 root mean squared error for the second target (which is a 77% improvement over the mean baseline)—making our model ready to be deployed as a decision system that could be available for everyone interested. The analytical approach can be used in other diseases and can help to plan hospital resources in other contexts.

Artificial Intelligence in Surveillance, Diagnosis, Drug Discovery and Vaccine Development against COVID-19

As of August 6th, 2021, the World Health Organization has notified 200.8 million laboratory-confirmed infections and 4.26 million deaths from COVID-19, making it the worst pandemic since the 1918 flu. The main challenges in mitigating COVID-19 are effective vaccination, treatment, and agile containment strategies. In this review, we focus on the potential of Artificial Intelligence (AI) in COVID-19 surveillance, diagnosis, outcome prediction, drug discovery and vaccine development. With the help of big data, AI tries to mimic the cognitive capabilities of a human brain, such as problem-solving and learning abilities. Machine Learning (ML), a subset of AI, holds special promise for solving problems based on experiences gained from the curated data. Advances in AI methods have created an unprecedented opportunity for building agile surveillance systems using the deluge of real-time data generated within a short span of time. During the COVID-19 pandemic, many reports have discussed the utility of AI approaches in prioritization, delivery, surveillance, and supply chain of drugs, vaccines, and non-pharmaceutical interventions. This review will discuss the clinical utility of AI-based models and will also discuss limitations and challenges faced by AI systems, such as model generalizability, explainability, and trust as pillars for real-life deployment in healthcare.

Artificial Intelligence in Surveillance, Diagnosis, Drug Discovery and Vaccine Development against COVID-19

As of August 6th, 2021, the World Health Organization has notified 200.8 million laboratory-confirmed infections and 4.26 million deaths from COVID-19, making it the worst pandemic since the 1918 flu. The main challenges in mitigating COVID-19 are effective vaccination, treatment, and agile containment strategies. In this review, we focus on the potential of Artificial Intelligence (AI) in COVID-19 surveillance, diagnosis, outcome prediction, drug discovery and vaccine development. With the help of big data, AI tries to mimic the cognitive capabilities of a human brain, such as problem-solving and learning abilities. Machine Learning (ML), a subset of AI, holds special promise for solving problems based on experiences gained from the curated data. Advances in AI methods have created an unprecedented opportunity for building agile surveillance systems using the deluge of real-time data generated within a short span of time. During the COVID-19 pandemic, many reports have discussed the utility of AI approaches in prioritization, delivery, surveillance, and supply chain of drugs, vaccines, and non-pharmaceutical interventions. This review will discuss the clinical utility of AI-based models and will also discuss limitations and challenges faced by AI systems, such as model generalizability, explainability, and trust as pillars for real-life deployment in healthcare.

Deep forest model for diagnosing COVID-19 from routine blood tests

The Coronavirus Disease 2019 (COVID-19) global pandemic has threatened the lives of people worldwide and posed considerable challenges. Early and accurate screening of infected people is vital for combating the disease. To help with the limited quantity of swab tests, we propose a machine learning prediction model to accurately diagnose COVID-19 from clinical and/or routine laboratory data. The model exploits a new ensemble-based method called the deep forest (DF), where multiple classifiers in multiple layers are used to encourage diversity and improve performance. The cascade level employs the layer-by-layer processing and is constructed from three different classifiers: extra trees, XGBoost, and LightGBM. The prediction model was trained and evaluated on two publicly available datasets. Experimental results show that the proposed DF model has an accuracy of 99.5%, sensitivity of 95.28%, and specificity of 99.96%. These performance metrics are comparable to other well-established machine learning techniques, and hence DF model can serve as a fast screening tool for COVID-19 patients at places where testing is scarce.

Comparison of machine learning techniques to handle imbalanced COVID-19 CBC datasets

The Coronavirus pandemic caused by the novel SARS-CoV-2 has significantly impacted human health and the economy, especially in countries struggling with financial resources for medical testing and treatment, such as Brazil's case, the third most affected country by the pandemic. In this scenario, machine learning techniques have been heavily employed to analyze different types of medical data, and aid decision making, offering a low-cost alternative. Due to the urgency to fight the pandemic, a massive amount of works are applying machine learning approaches to clinical data, including complete blood count (CBC) tests, which are among the most widely available medical tests. In this work, we review the most employed machine learning classifiers for CBC data, together with popular sampling methods to deal with the class imbalance. Additionally, we describe and critically analyze three publicly available Brazilian COVID-19 CBC datasets and evaluate the performance of eight classifiers and five sampling techniques on the selected datasets. Our work provides a panorama of which classifier and sampling methods provide the best results for different relevant metrics and discuss their impact on future analyses. The metrics and algorithms are introduced in a way to aid newcomers to the field. Finally, the panorama discussed here can significantly benefit the comparison of the results of new ML algorithms.

A machine learning PROGRAM to identify COVID-19 and other diseases from hematology data

AIM

We propose a method for screening full blood count metadata for evidence of communicable and noncommunicable diseases using machine learning (ML).

MATERIALS & METHODS

High dimensional hematology metadata was extracted over an 11-month period from Sysmex hematology analyzers from 43,761 patients. Predictive models for age, sex and individuality were developed to demonstrate the personalized nature of hematology data. Both numeric and raw flow cytometry data were used for both supervised and unsupervised ML to predict the presence of pneumonia, urinary tract infection and COVID-19. Heart failure was used as an objective to prove method generalizability.

RESULTS

Chronological age was predicted by a deep neural network with R2: 0.59; mean absolute error: 12; sex with AUROC: 0.83, phi: 0.47; individuality with 99.7% accuracy, phi: 0.97; pneumonia with AUROC: 0.74, sensitivity 58%, specificity 79%, 95% CI: 0.73-0.75, p < 0.0001; urinary tract infection AUROC: 0.68, sensitivity 52%, specificity 79%, 95% CI: 0.67-0.68, p < 0.0001; COVID-19 AUROC: 0.8, sensitivity 82%, specificity 75%, 95% CI: 0.79-0.8, p = 0.0006; and heart failure area under the receiver operator curve (AUROC): 0.78, sensitivity 72%, specificity 72%, 95% CI: 0.77-0.78; p < 0.0001.

CONCLUSION

ML applied to hematology data could predict communicable and noncommunicable diseases, both at local and global levels.

Machine learning application for the prediction of SARS-CoV-2 infection using blood tests and chest radiograph

Triaging and prioritising patients for RT-PCR test had been essential in the management of COVID-19 in resource-scarce countries. In this study, we applied machine learning (ML) to the task of detection of SARS-CoV-2 infection using basic laboratory markers. We performed the statistical analysis and trained an ML model on a retrospective cohort of 5148 patients from 24 hospitals in Hong Kong to classify COVID-19 and other aetiology of pneumonia. We validated the model on three temporal validation sets from different waves of infection in Hong Kong. For predicting SARS-CoV-2 infection, the ML model achieved high AUCs and specificity but low sensitivity in all three validation sets (AUC: 89.9-95.8%; Sensitivity: 55.5-77.8%; Specificity: 91.5-98.3%). When used in adjunction with radiologist interpretations of chest radiographs, the sensitivity was over 90% while keeping moderate specificity. Our study showed that machine learning model based on readily available laboratory markers could achieve high accuracy in predicting SARS-CoV-2 infection.

Leveraging artificial intelligence for pandemic preparedness and response: a scoping review to identify key use cases

Artificial intelligence (AI) represents a valuable tool that could be widely used to inform clinical and public health decision-making to effectively manage the impacts of a pandemic. The objective of this scoping review was to identify the key use cases for involving AI for pandemic preparedness and response from the peer-reviewed, preprint, and grey literature. The data synthesis had two parts: an in-depth review of studies that leveraged machine learning (ML) techniques and a limited review of studies that applied traditional modeling approaches. ML applications from the in-depth review were categorized into use cases related to public health and clinical practice, and narratively synthesized. One hundred eighty-three articles met the inclusion criteria for the in-depth review. Six key use cases were identified: forecasting infectious disease dynamics and effects of interventions; surveillance and outbreak detection; real-time monitoring of adherence to public health recommendations; real-time detection of influenza-like illness; triage and timely diagnosis of infections; and prognosis of illness and response to treatment. Data sources and types of ML that were useful varied by use case. The search identified 1167 articles that reported on traditional modeling approaches, which highlighted additional areas where ML could be leveraged for improving the accuracy of estimations or projections. Important ML-based solutions have been developed in response to pandemics, and particularly for COVID-19 but few were optimized for practical application early in the pandemic. These findings can support policymakers, clinicians, and other stakeholders in prioritizing research and development to support operationalization of AI for future pandemics.

COVID-19 in the Age of Artificial Intelligence: A Comprehensive Review

The recent COVID-19 pandemic, which broke at the end of the year 2019 in Wuhan, China, has infected more than 98.52 million people by today (January 23, 2021) with over 2.11 million deaths across the globe. To combat the growing pandemic on urgent basis, there is need to design effective solutions using new techniques that could exploit recent technology, such as machine learning, deep learning, big data, artificial intelligence, Internet of Things, for identification and tracking of COVID-19 cases in near real time. These technologies have offered inexpensive and rapid solution for proper screening, analyzing, prediction and tracking of COVID-19 positive cases. In this paper, a detailed review of the role of AI as a decisive tool for prognosis, analyze, and tracking the COVID-19 cases is performed. We searched various databases including Google Scholar, IEEE Library, Scopus and Web of Science using a combination of different keywords consisting of COVID-19 and AI. We have identified various applications, where AI can help healthcare practitioners in the process of identification and monitoring of COVID-19 cases. A compact summary of the corona virus cases are first highlighted, followed by the application of AI. Finally, we conclude the paper by highlighting new research directions and discuss the research challenges. Even though scientists and researchers have gathered and exchanged sufficient knowledge over last couple of months, but this structured review also examined technological perspectives while encompassing the medical aspect to help the healthcare practitioners, policymakers, decision makers, policymakers, AI scientists and virologists to quell this infectious COVID-19 pandemic outbreak.

NSGA-II as feature selection technique and AdaBoost classifier for COVID-19 prediction using patient's symptoms

Nowadays, humanity is facing one of the most dangerous pandemics known as COVID-19. Due to its high inter-person contagiousness, COVID-19 is rapidly spreading across the world. Positive patients are often suffering from different symptoms that can vary from mild to severe including cough, fever, sore throat, and body aches. In more dire cases, infected patients can experience severe symptoms that can cause breathing difficulties which lead to stern organ failure and die. The medical corps all over the world are overloaded because of the exponentially myriad number of contagions. Therefore, screening for the disease becomes overwrought with the limited tools of test. Additionally, test results may take a long time to acquire, leaving behind a higher potential for the prevalence of the virus among other individuals by the patients. To reduce the chances of infection, we suggest a prediction model that distinguishes the infected COVID-19 cases based on clinical symptoms and features. This model can be helpful for citizens to catch their infection without the need for visiting the hospital. Also, it helps the medical staff in triaging patients in case of a deficiency of medical amenities. In this paper, we use the non-dominated sorting genetic algorithm (NSGA-II) to select the interesting features by finding the best trade-offs between two conflicting objectives: minimizing the number of features and maximizing the weights of selected features. Then, a classification phase is conducted using an AdaBoost classifier. The proposed model is evaluated using two different datasets. To maximize results, we performed a natural selection of hyper-parameters of the classifier using the genetic algorithm. The obtained results prove the efficiency of NSGA-II as a feature selection algorithm combined with AdaBoost classifier. It exhibits higher classification results that outperformed the existing methods.

Future Forecasting of COVID-19: A Supervised Learning Approach

A little over a year after the official announcement from the WHO, the COVID-19 pandemic has led to dramatic consequences globally. Today, millions of doses of vaccines have already been administered in several countries. However, the positive effect of these vaccines will probably be seen later than expected. In these circumstances, the rapid diagnosis of COVID-19 still remains the only way to slow the spread of this virus. However, it is difficult to predict whether a person is infected or not by COVID-19 while relying only on apparent symptoms. In this context, we propose to use machine learning (ML) algorithms in order to diagnose COVID-19 infected patients more effectively. The proposed diagnosis method takes into consideration several symptoms, such as flu symptoms, throat pain, immunity status, diarrhea, voice type, body temperature, joint pain, dry cough, vomiting, breathing problems, headache, and chest pain. Based on these symptoms that are modelled as ML features, our proposed method is able to predict the probability of contamination with the COVID-19 virus. This method is evaluated using different experimental analysis metrics such as accuracy, precision, recall, and F1-score. The obtained experimental results have shown that the proposed method can predict the presence of COVID-19 with over 97% accuracy.

Extracting COVID-19 diagnoses and symptoms from clinical text: A new annotated corpus and neural event extraction framework

Coronavirus disease 2019 (COVID-19) is a global pandemic. Although much has been learned about the novel coronavirus since its emergence, there are many open questions related to tracking its spread, describing symptomology, predicting the severity of infection, and forecasting healthcare utilization. Free-text clinical notes contain critical information for resolving these questions. Data-driven, automatic information extraction models are needed to use this text-encoded information in large-scale studies. This work presents a new clinical corpus, referred to as the COVID-19 Annotated Clinical Text (CACT) Corpus, which comprises 1,472 notes with detailed annotations characterizing COVID-19 diagnoses, testing, and clinical presentation. We introduce a span-based event extraction model that jointly extracts all annotated phenomena, achieving high performance in identifying COVID-19 and symptom events with associated assertion values (0.83-0.97 F1 for events and 0.73-0.79 F1 for assertions). Our span-based event extraction model outperforms an extractor built on MetaMapLite for the identification of symptoms with assertion values. In a secondary use application, we predicted COVID-19 test results using structured patient data (e.g. vital signs and laboratory results) and automatically extracted symptom information, to explore the clinical presentation of COVID-19. Automatically extracted symptoms improve COVID-19 prediction performance, beyond structured data alone.

Standard blood laboratory values as a clinical support tool to distinguish between SARS-CoV-2 positive and negative patients

Standard blood laboratory parameters may have diagnostic potential, if polymerase-chain-reaction (PCR) tests are not available on time. We evaluated standard blood laboratory parameters of 655 COVID-19 patients suspected to be infected with SARS-CoV-2, who underwent PCR testing in one of five hospitals in Vienna, Austria. We compared laboratory parameters, clinical characteristics, and outcomes between positive and negative PCR-tested patients and evaluated the ability of those parameters to distinguish between groups. Of the 590 patients (20-100 years, 276 females and 314 males), 208 were PCR-positive. Positive compared to negative PCR-tested patients had significantly lower levels of leukocytes, neutrophils, basophils, eosinophils, lymphocytes, neutrophil-to-lymphocyte ratio, monocytes, and thrombocytes; while significantly higher levels were detected with erythrocytes, hemoglobin, hematocrit, C-reactive-protein, ferritin, activated-partial-thromboplastin-time, alanine-aminotransferase, aspartate-aminotransferase, lipase, creatine-kinase, and lactate-dehydrogenase. From all blood parameters, eosinophils, ferritin, leukocytes, and erythrocytes showed the highest ability to distinguish between COVID-19 positive and negative patients (area-under-curve, AUC: 72.3-79.4%). The AUC of our model was 0.915 (95% confidence intervals, 0.876-0.955). Leukopenia, eosinopenia, elevated erythrocytes, and hemoglobin were among the strongest markers regarding accuracy, sensitivity, specificity, positive and negative predictive value, positive and negative likelihood ratio, and post-test probabilities. Our findings suggest that especially leukopenia, eosinopenia, and elevated hemoglobin are helpful to distinguish between COVID-19 positive and negative tested patients.

Artificial Intelligence Applications for COVID-19 in Intensive Care and Emergency Settings: A Systematic Review

Background: Little is known about the role of artificial intelligence (AI) as a decisive technology in the clinical management of COVID-19 patients. We aimed to systematically review and critically appraise the current evidence on AI applications for COVID-19 in intensive care and emergency settings. Methods: We systematically searched PubMed, Embase, Scopus, CINAHL, IEEE Xplore, and ACM Digital Library databases from inception to 1 October 2020, without language restrictions. We included peer-reviewed original studies that applied AI for COVID-19 patients, healthcare workers, or health systems in intensive care, emergency, or prehospital settings. We assessed predictive modelling studies and critically appraised the methodology and key findings of all other studies. Results: Of fourteen eligible studies, eleven developed prognostic or diagnostic AI predictive models, all of which were assessed to be at high risk of bias. Common pitfalls included inadequate sample sizes, poor handling of missing data, failure to account for censored participants, and weak validation of models. Conclusions: Current AI applications for COVID-19 are not ready for deployment in acute care settings, given their limited scope and poor quality. Our findings underscore the need for improvements to facilitate safe and effective clinical adoption of AI applications, for and beyond the COVID-19 pandemic.

Prediction and Feature Importance Analysis for Severity of COVID-19 in South Korea Using Artificial Intelligence: Model Development and Validation

Background

The number of deaths from COVID-19 continues to surge worldwide. In particular, if a patient’s condition is sufficiently severe to require invasive ventilation, it is more likely to lead to death than to recovery.

Objective

The goal of our study was to analyze the factors related to COVID-19 severity in patients and to develop an artificial intelligence (AI) model to predict the severity of COVID-19 at an early stage.

Methods

We developed an AI model that predicts severity based on data from 5601 COVID-19 patients from all national and regional hospitals across South Korea as of April 2020. The clinical severity of COVID-19 was divided into two categories: low and high severity. The condition of patients in the low-severity group corresponded to no limit of activity, oxygen support with nasal prong or facial mask, and noninvasive ventilation. The condition of patients in the high-severity group corresponded to invasive ventilation, multi-organ failure with extracorporeal membrane oxygenation required, and death. For the AI model input, we used 37 variables from the medical records, including basic patient information, a physical index, initial examination findings, clinical findings, comorbid diseases, and general blood test results at an early stage. Feature importance analysis was performed with AdaBoost, random forest, and eXtreme Gradient Boosting (XGBoost); the AI model for predicting COVID-19 severity among patients was developed with a 5-layer deep neural network (DNN) with the 20 most important features, which were selected based on ranked feature importance analysis of 37 features from the comprehensive data set. The selection procedure was performed using sensitivity, specificity, accuracy, balanced accuracy, and area under the curve (AUC).

Results

We found that age was the most important factor for predicting disease severity, followed by lymphocyte level, platelet count, and shortness of breath or dyspnea. Our proposed 5-layer DNN with the 20 most important features provided high sensitivity (90.2%), specificity (90.4%), accuracy (90.4%), balanced accuracy (90.3%), and AUC (0.96).

Conclusions

Our proposed AI model with the selected features was able to predict the severity of COVID-19 accurately. We also made a web application so that anyone can access the model. We believe that sharing the AI model with the public will be helpful in validating and improving its performance.

Artificial intelligence in the diagnosis of COVID-19: challenges and perspectives

Artificial intelligence (AI) is being used to aid in various aspects of the COVID-19 crisis, including epidemiology, molecular research and drug development, medical diagnosis and treatment, and socioeconomics. The association of AI and COVID-19 can accelerate to rapidly diagnose positive patients. To learn the dynamics of a pandemic with relevance to AI, we search the literature using the different academic databases (PubMed, PubMed Central, Scopus, Google Scholar) and preprint servers (bioRxiv, medRxiv, arXiv). In the present review, we address the clinical applications of machine learning and deep learning, including clinical characteristics, electronic medical records, medical images (CT, X-ray, ultrasound images, etc.) in the COVID-19 diagnosis. The current challenges and future perspectives provided in this review can be used to direct an ideal deployment of AI technology in a pandemic.

Classification Models for COVID-19 Test Prioritization in Brazil: Machine Learning Approach

BACKGROUND

Controlling the COVID-19 outbreak in Brazil is a challenge due to the population's size and urban density, inefficient maintenance of social distancing and testing strategies, and limited availability of testing resources.

OBJECTIVE

The purpose of this study is to effectively prioritize patients who are symptomatic for testing to assist early COVID-19 detection in Brazil, addressing problems related to inefficient testing and control strategies.

METHODS

Raw data from 55,676 Brazilians were preprocessed, and the chi-square test was used to confirm the relevance of the following features: gender, health professional, fever, sore throat, dyspnea, olfactory disorders, cough, coryza, taste disorders, and headache. Classification models were implemented relying on preprocessed data sets; supervised learning; and the algorithms multilayer perceptron (MLP), gradient boosting machine (GBM), decision tree (DT), random forest (RF), extreme gradient boosting (XGBoost), k-nearest neighbors (KNN), support vector machine (SVM), and logistic regression (LR). The models' performances were analyzed using 10-fold cross-validation, classification metrics, and the Friedman and Nemenyi statistical tests. The permutation feature importance method was applied for ranking the features used by the classification models with the highest performances.

RESULTS

Gender, fever, and dyspnea were among the highest-ranked features used by the classification models. The comparative analysis presents MLP, GBM, DT, RF, XGBoost, and SVM as the highest performance models with similar results. KNN and LR were outperformed by the other algorithms. Applying the easy interpretability as an additional comparison criterion, the DT was considered the most suitable model.

CONCLUSIONS

The DT classification model can effectively (with a mean accuracy≥89.12%) assist COVID-19 test prioritization in Brazil. The model can be applied to recommend the prioritizing of a patient who is symptomatic for COVID-19 testing.

Machine learning approaches in COVID-19 diagnosis, mortality, and severity risk prediction: A review

The existence of widespread COVID-19 infections has prompted worldwide efforts to control and manage the virus, and hopefully curb it completely. One important line of research is the use of machine learning (ML) to understand and fight COVID-19. This is currently an active research field. Although there are already many surveys in the literature, there is a need to keep up with the rapidly growing number of publications on COVID-19-related applications of ML. This paper presents a review of recent reports on ML algorithms used in relation to COVID-19. We focus on the potential of ML for two main applications: diagnosis of COVID-19 and prediction of mortality risk and severity, using readily available clinical and laboratory data. Aspects related to algorithm types, training data sets, and feature selection are discussed. As we cover work published between January 2020 and January 2021, a few key points have come to light. The bulk of the machine learning algorithms used in these two applications are supervised learning algorithms. The established models are yet to be used in real-world implementations, and much of the associated research is experimental. The diagnostic and prognostic features discovered by ML models are consistent with results presented in the medical literature. A limitation of the existing applications is the use of imbalanced data sets that are prone to selection bias.

An observational study to develop a scoring system and model to detect risk of hospital admission due to COVID-19

BACKGROUND

COVID-19 has caused an unprecedented global health emergency. The strains of such a pandemic can overwhelm hospital capacity. Efficient clinical decision-making is crucial for proper healthcare resource utilization in this crisis. Using observational study data, we set out to create a predictive model that could anticipate which COVID-19 patients would likely be admitted and developed a scoring tool that could be used in the clinical setting and for population risk stratification.

METHODS

We retrospectively evaluated data from COVID-19 patients across a network of 6 hospitals in northeastern Pennsylvania. Analysis was limited to age, gender, and historical variables. After creating a variable importance plot, we chose a selection of the best predictors to train a logistic regression model. Variable selection was done using a lasso regularization technique. Using the coefficients in our logistic regression model, we then created a scoring tool and validated the score on a test set data.

RESULTS

A total of 6485 COVID-19 patients were included in our analysis, of which 707 were hospitalized. The biggest predictors of patient hospitalization included age, a history of hypertension, diabetes, chronic heart disease, gender, tobacco use, and chronic kidney disease. The logistic regression model demonstrated an AUC of 0.81. The coefficients for our logistic regression model were used to develop a scoring tool. Low-, intermediate-, and high-risk patients were deemed to have a 3.5%, 26%, and 38% chance of hospitalization, respectively. The best predictors of hospitalization included age (odds ratio [OR] = 1.03, confidence interval [CI] = 1.02-1.03), diabetes (OR = 2.08, CI = 1.69-2.57), hypertension (OR = 2.36, CI = 1.90-2.94), chronic heart disease (OR = 1.53, CI = 1.22-1.91), and male gender (OR = 1.32, CI = 1.11-1.58).

CONCLUSIONS

Using retrospective observational data from a 6-hospital network, we determined risk factors for admission and developed a predictive model and scoring tool for use in the clinical and population setting that could anticipate admission for COVID-19 patients.

COVIDetection-Net: A tailored COVID-19 detection from chest radiography images using deep learning

In this study, a medical system based on Deep Learning (DL) which we called "COVIDetection-Net" is proposed for automatic detection of new corona virus disease 2019 (COVID-19) infection from chest radiography images (CRIs). The proposed system is based on ShuffleNet and SqueezeNet architecture to extract deep learned features and Multiclass Support Vector Machines (MSVM) for detection and classification. Our dataset contains 1200 CRIs that collected from two different publicly available databases. Extensive experiments were carried out using the proposed model. The highest detection accuracy of 100 % for COVID/NonCOVID, 99.72 % for COVID/Normal/pneumonia and 94.44 % for COVID/Normal/Bacterial pneumonia/Viral pneumonia have been obtained. The proposed system superior all published methods in recall, specificity, precision, F1-Score and accuracy. Confusion Matrix (CM) and Receiver Operation Characteristics (ROC) analysis are also used to depict the performance of the proposed model. Hence the proposed COVIDetection-Net can serve as an efficient system in the current state of COVID-19 pandemic and can be used in everywhere that are facing shortage of test kits.

A novel classifier architecture based on deep neural network for COVID-19 detection using laboratory findings

Unfortunately, Coronavirus disease 2019 (COVID-19) is spreading rapidly all over the world. Along with causing many deaths, it has substantially affected the social life, economics, and infrastructure worldwide in a negative manner. Therefore, it is very important to be able to diagnose the COVID-19 quickly and correctly. In this study, a new feature group based on laboratory findings was obtained considering ethnical and genetic differences for interpretation of blood data. Then, using this feature group, a new hybrid classifier architecture based on deep learning was designed and COVID-19 detection was made. Classification performance indicators were obtained as accuracy of 94.95%, F1-score of 94.98%, precision of 94.98%, recall of 94.98% and AUC of 100%. Achieved results were compared with those of the deep learning classifiers suggested in literature. According to these results, proposed method shows superior performance and can provide more convenience and precision to experts for diagnosis of COVID-19 disease.

Machine learning and applications in microbiology

To understand the intricacies of microorganisms at the molecular level requires making sense of copious volumes of data such that it may now be humanly impossible to detect insightful data patterns without an artificial intelligence application called machine learning. Applying machine learning to address biological problems is expected to grow at an unprecedented rate, yet it is perceived by the uninitiated as a mysterious and daunting entity entrusted to the domain of mathematicians and computer scientists. The aim of this review is to identify key points required to start the journey of becoming an effective machine learning practitioner. These key points are further reinforced with an evaluation of how machine learning has been applied so far in a broad scope of real-life microbiology examples. This includes predicting drug targets or vaccine candidates, diagnosing microorganisms causing infectious diseases, classifying drug resistance against antimicrobial medicines, predicting disease outbreaks and exploring microbial interactions. Our hope is to inspire microbiologists and other related researchers to join the emerging machine learning revolution.

Explaining machine learning based diagnosis of COVID-19 from routine blood tests with decision trees and criteria graphs

The sudden outbreak of coronavirus disease 2019 (COVID-19) revealed the need for fast and reliable automatic tools to help health teams. This paper aims to present understandable solutions based on Machine Learning (ML) techniques to deal with COVID-19 screening in routine blood tests. We tested different ML classifiers in a public dataset from the Hospital Albert Einstein, São Paulo, Brazil. After cleaning and pre-processing the data has 608 patients, of which 84 are positive for COVID-19 confirmed by RT-PCR. To understand the model decisions, we introduce (i) a local Decision Tree Explainer (DTX) for local explanation and (ii) a Criteria Graph to aggregate these explanations and portrait a global picture of the results. Random Forest (RF) classifier achieved the best results (accuracy 0.88, F1-score 0.76, sensitivity 0.66, specificity 0.91, and AUROC 0.86). By using DTX and Criteria Graph for cases confirmed by the RF, it was possible to find some patterns among the individuals able to aid the clinicians to understand the interconnection among the blood parameters either globally or on a case-by-case basis. The results are in accordance with the literature and the proposed methodology may be embedded in an electronic health record system.

Detecting COVID-19 patients based on fuzzy inference engine and Deep Neural Network

COVID-19, as an infectious disease, has shocked the world and still threatens the lives of billions of people. Recently, the detection of coronavirus (COVID-19) is a critical task for the medical practitioner. Unfortunately, COVID-19 spreads so quickly between people and approaches millions of people worldwide in few months. It is very much essential to quickly and accurately identify the infected people so that prevention of spread can be taken. Although several medical tests have been used to detect certain injuries, the hopefully detection efficiency has not been accomplished yet. In this paper, a new Hybrid Diagnose Strategy (HDS) has been introduced. HDS relies on a novel technique for ranking selected features by projecting them into a proposed Patient Space (PS). A Feature Connectivity Graph (FCG) is constructed which indicates both the weight of each feature as well as the binding degree to other features. The rank of a feature is determined based on two factors; the first is the feature weight, while the second is its binding degree to its neighbors in PS. Then, the ranked features are used to derive the classification model that can classify new persons to decide whether they are infected or not. The classification model is a hybrid model that consists of two classifiers; fuzzy inference engine and Deep Neural Network (DNN). The proposed HDS has been compared against recent techniques. Experimental results have shown that the proposed HDS outperforms the other competitors in terms of the average value of accuracy, precision, recall, and F-measure in which it provides about of 97.658%, 96.756%, 96.55%, and 96.615% respectively. Additionally, HDS provides the lowest error value of 2.342%. Further, the results were validated statistically using Wilcoxon Signed Rank Test and Friedman Test.

Deep learning and medical image processing for coronavirus (COVID-19) pandemic: A survey

Since December 2019, the coronavirus disease (COVID-19) outbreak has caused many death cases and affected all sectors of human life. With gradual progression of time, COVID-19 was declared by the world health organization (WHO) as an outbreak, which has imposed a heavy burden on almost all countries, especially ones with weaker health systems and ones with slow responses. In the field of healthcare, deep learning has been implemented in many applications, e.g., diabetic retinopathy detection, lung nodule classification, fetal localization, and thyroid diagnosis. Numerous sources of medical images (e.g., X-ray, CT, and MRI) make deep learning a great technique to combat the COVID-19 outbreak. Motivated by this fact, a large number of research works have been proposed and developed for the initial months of 2020. In this paper, we first focus on summarizing the state-of-the-art research works related to deep learning applications for COVID-19 medical image processing. Then, we provide an overview of deep learning and its applications to healthcare found in the last decade. Next, three use cases in China, Korea, and Canada are also presented to show deep learning applications for COVID-19 medical image processing. Finally, we discuss several challenges and issues related to deep learning implementations for COVID-19 medical image processing, which are expected to drive further studies in controlling the outbreak and controlling the crisis, which results in smart healthy cities.

Rapid triage for COVID-19 using routine clinical data for patients attending hospital: development and prospective validation of an artificial intelligence screening test

BACKGROUND

The early clinical course of COVID-19 can be difficult to distinguish from other illnesses driving presentation to hospital. However, viral-specific PCR testing has limited sensitivity and results can take up to 72 h for operational reasons. We aimed to develop and validate two early-detection models for COVID-19, screening for the disease among patients attending the emergency department and the subset being admitted to hospital, using routinely collected health-care data (laboratory tests, blood gas measurements, and vital signs). These data are typically available within the first hour of presentation to hospitals in high-income and middle-income countries, within the existing laboratory infrastructure.

METHODS

We trained linear and non-linear machine learning classifiers to distinguish patients with COVID-19 from pre-pandemic controls, using electronic health record data for patients presenting to the emergency department and admitted across a group of four teaching hospitals in Oxfordshire, UK (Oxford University Hospitals). Data extracted included presentation blood tests, blood gas testing, vital signs, and results of PCR testing for respiratory viruses. Adult patients (>18 years) presenting to hospital before Dec 1, 2019 (before the first COVID-19 outbreak), were included in the COVID-19-negative cohort; those presenting to hospital between Dec 1, 2019, and April 19, 2020, with PCR-confirmed severe acute respiratory syndrome coronavirus 2 infection were included in the COVID-19-positive cohort. Patients who were subsequently admitted to hospital were included in their respective COVID-19-negative or COVID-19-positive admissions cohorts. Models were calibrated to sensitivities of 70%, 80%, and 90% during training, and performance was initially assessed on a held-out test set generated by an 80:20 split stratified by patients with COVID-19 and balanced equally with pre-pandemic controls. To simulate real-world performance at different stages of an epidemic, we generated test sets with varying prevalences of COVID-19 and assessed predictive values for our models. We prospectively validated our 80% sensitivity models for all patients presenting or admitted to the Oxford University Hospitals between April 20 and May 6, 2020, comparing model predictions with PCR test results.

FINDINGS

We assessed 155 689 adult patients presenting to hospital between Dec 1, 2017, and April 19, 2020. 114 957 patients were included in the COVID-negative cohort and 437 in the COVID-positive cohort, for a full study population of 115 394 patients, with 72 310 admitted to hospital. With a sensitive configuration of 80%, our emergency department (ED) model achieved 77·4% sensitivity and 95·7% specificity (area under the receiver operating characteristic curve [AUROC] 0·939) for COVID-19 among all patients attending hospital, and the admissions model achieved 77·4% sensitivity and 94·8% specificity (AUROC 0·940) for the subset of patients admitted to hospital. Both models achieved high negative predictive values (NPV; >98·5%) across a range of prevalences (≤5%). We prospectively validated our models for all patients presenting and admitted to Oxford University Hospitals in a 2-week test period. The ED model (3326 patients) achieved 92·3% accuracy (NPV 97·6%, AUROC 0·881), and the admissions model (1715 patients) achieved 92·5% accuracy (97·7%, 0·871) in comparison with PCR results. Sensitivity analyses to account for uncertainty in negative PCR results improved apparent accuracy (ED model 95·1%, admissions model 94·1%) and NPV (ED model 99·0%, admissions model 98·5%).

INTERPRETATION

Our models performed effectively as a screening test for COVID-19, excluding the illness with high-confidence by use of clinical data routinely available within 1 h of presentation to hospital. Our approach is rapidly scalable, fitting within the existing laboratory testing infrastructure and standard of care of hospitals in high-income and middle-income countries.

FUNDING

Wellcome Trust, University of Oxford, Engineering and Physical Sciences Research Council, National Institute for Health Research Oxford Biomedical Research Centre.

A Novel Bayesian Optimization-Based Machine Learning Framework for COVID-19 Detection From Inpatient Facility Data

The whole world faces a pandemic situation due to the deadly virus, namely COVID-19. It takes considerable time to get the virus well-matured to be traced, and during this time, it may be transmitted among other people. To get rid of this unexpected situation, quick identification of COVID-19 patients is required. We have designed and optimized a machine learning-based framework using inpatient's facility data that will give a user-friendly, cost-effective, and time-efficient solution to this pandemic. The proposed framework uses Bayesian optimization to optimize the hyperparameters of the classifier and ADAptive SYNthetic (ADASYN) algorithm to balance the COVID and non-COVID classes of the dataset. Although the proposed technique has been applied to nine state-of-the-art classifiers to show the efficacy, it can be used to many classifiers and classification problems. It is evident from this study that eXtreme Gradient Boosting (XGB) provides the highest Kappa index of 97.00%. Compared to without ADASYN, our proposed approach yields an improvement in the kappa index of 96.94%. Besides, Bayesian optimization has been compared to grid search, random search to show efficiency. Furthermore, the most dominating features have been identified using SHapely Adaptive exPlanations (SHAP) analysis. A comparison has also been made among other related works. The proposed method is capable enough of tracing COVID patients spending less time than that of the conventional techniques. Finally, two potential applications, namely, clinically operable decision tree and decision support system, have been demonstrated to support clinical staff and build a recommender system.

Accurately Differentiating Between Patients With COVID-19, Patients With Other Viral Infections, and Healthy Individuals: Multimodal Late Fusion Learning Approach

BACKGROUND

Effectively identifying patients with COVID-19 using nonpolymerase chain reaction biomedical data is critical for achieving optimal clinical outcomes. Currently, there is a lack of comprehensive understanding in various biomedical features and appropriate analytical approaches for enabling the early detection and effective diagnosis of patients with COVID-19.

OBJECTIVE

We aimed to combine low-dimensional clinical and lab testing data, as well as high-dimensional computed tomography (CT) imaging data, to accurately differentiate between healthy individuals, patients with COVID-19, and patients with non-COVID viral pneumonia, especially at the early stage of infection.

METHODS

In this study, we recruited 214 patients with nonsevere COVID-19, 148 patients with severe COVID-19, 198 noninfected healthy participants, and 129 patients with non-COVID viral pneumonia. The participants' clinical information (ie, 23 features), lab testing results (ie, 10 features), and CT scans upon admission were acquired and used as 3 input feature modalities. To enable the late fusion of multimodal features, we constructed a deep learning model to extract a 10-feature high-level representation of CT scans. We then developed 3 machine learning models (ie, k-nearest neighbor, random forest, and support vector machine models) based on the combined 43 features from all 3 modalities to differentiate between the following 4 classes: nonsevere, severe, healthy, and viral pneumonia.

RESULTS

Multimodal features provided substantial performance gain from the use of any single feature modality. All 3 machine learning models had high overall prediction accuracy (95.4%-97.7%) and high class-specific prediction accuracy (90.6%-99.9%).

CONCLUSIONS

Compared to the existing binary classification benchmarks that are often focused on single-feature modality, this study's hybrid deep learning-machine learning framework provided a novel and effective breakthrough for clinical applications. Our findings, which come from a relatively large sample size, and analytical workflow will supplement and assist with clinical decision support for current COVID-19 diagnostic methods and other clinical applications with high-dimensional multimodal biomedical features.

Intelligent system for COVID-19 prognosis: a state-of-the-art survey

This 21st century is notable for experiencing so many disturbances at economic, social, cultural, and political levels in the entire world. The outbreak of novel corona virus 2019 (COVID-19) has been treated as a Public Health crisis of global Concern by the World Health Organization (WHO). Various outbreak models for COVID-19 are being utilized by researchers throughout the world to get well-versed decisions and impose significant control measures. Amid the standard methods for COVID-19 worldwide epidemic prediction, easy statistical, as well as epidemiological methods have got more consideration by researchers and authorities. One main difficulty in controlling the spreading of COVID-19 is the inadequacy and lack of medical tests for detecting as well as identifying a solution. To solve this problem, a few statistical-based advances are being enhanced and turn into a partial resolution up-to some level. To deal with the challenges of the medical field, a broad range of intelligent based methods, frameworks, and equipment have been recommended by Machine Learning (ML) and Deep Learning. As ML and DL have the ability of identifying and predicting patterns in complex large datasets, they are recognized as a suitable procedure for producing effective solutions for the diagnosis of COVID-19. In this paper, a perspective research has been conducted in the applicability of intelligent systems such as ML, DL and others in solving COVID-19 related outbreak issues. The main intention behind this study is (i) to understand the importance of intelligent approaches such as ML and DL for COVID-19 pandemic, (ii) discussing the efficiency and impact of these methods in the prognosis of COVID-19, (iii) the growth in the development of type of ML and advanced ML methods for COVID-19 prognosis,(iv) analyzing the impact of data types and the nature of data along with challenges in processing the data for COVID-19,(v) to focus on some future challenges in COVID-19 prognosis to inspire the researchers for innovating and enhancing their knowledge and research on other impacted sectors due to COVID-19.

Applications of artificial intelligence in battling against covid-19: A literature review

Colloquially known as coronavirus, the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2), that causes CoronaVirus Disease 2019 (COVID-19), has become a matter of grave concern for every country around the world. The rapid growth of the pandemic has wreaked havoc and prompted the need for immediate reactions to curb the effects. To manage the problems, many research in a variety of area of science have started studying the issue. Artificial Intelligence is among the area of science that has found great applications in tackling the problem in many aspects. Here, we perform an overview on the applications of AI in a variety of fields including diagnosis of the disease via different types of tests and symptoms, monitoring patients, identifying severity of a patient, processing covid-19 related imaging tests, epidemiology, pharmaceutical studies, etc. The aim of this paper is to perform a comprehensive survey on the applications of AI in battling against the difficulties the outbreak has caused. Thus we cover every way that AI approaches have been employed and to cover all the research until the writing of this paper. We try organize the works in a way that overall picture is comprehensible. Such a picture, although full of details, is very helpful in understand where AI sits in current pandemonium. We also tried to conclude the paper with ideas on how the problems can be tackled in a better way and provide some suggestions for future works.

Longitudinal changes of laboratory measurements after discharged from hospital in 268 COVID-19 pneumonia patients

BACKGROUND AND OBJECTIVE

Monitoring recovery process of coronavirus disease 2019 (COVID-19) patients released from hospital is crucial for exploring residual effects of COVID-19 and beneficial for clinical care. In this study, a comprehensive analysis was carried out to clarify residual effects of COVID-19 on hospital discharged patients.

METHODS

Two hundred sixty-eight cases with laboratory measured data at hospital discharge record and five follow-up visits were retrospectively collected to carry out statistical data analysis comprehensively, which includes multiple statistical methods (e.g., chi-square, T-test and regression) used in this study.

RESULTS

Study found that 13 of 21 hematologic parameters in laboratory measured dataset and volume ratio of right lung lesions on CT images highly associated with COVID-19. Moderate patients had statistically significant lower neutrophils than mild and severe patients after hospital discharge, which is probably caused by more efforts on severe patients and slightly neglection of moderate patients. COVID-19 has residual effects on neutrophil-to-lymphocyte ratio (NLR) of patients who have hypertension or chronic obstructive pulmonary disease (COPD). After released from hospital, female showed better performance in T lymphocytes subset cells, especially T helper lymphocyte% (16% higher than male). According to this sex-based differentiation of COVID-19, male should be recommended to take clinical test more frequently to monitor recovery of immune system. Patients over 60 years old showed unstable recovery process of immune cells (e.g., CD45 + lymphocyte) within 75 days after discharge requiring longer clinical care. Additionally, right lung was vulnerable to COVID-19 and required more time to recover than left lung.

CONCLUSIONS

Criterion of hospital discharge and strategy of clinical care should be flexible in different cases due to residual effects of COVID-19, which depend on several impact factors. Revealing remaining effects of COVID-19 is an effective way to eliminate disorder of mental health caused by COVID-19 infection.

Predicting the COVID-19 infection with fourteen clinical features using machine learning classification algorithms

While the RT-PCR is the silver bullet test for confirming the COVID-19 infection, it is limited by the lack of reagents, time-consuming, and the need for specialized labs. As an alternative, most of the prior studies have focused on Chest CT images and Chest X-Ray images using deep learning algorithms. However, these two approaches cannot always be used for patients' screening due to the radiation doses, high costs, and the low number of available devices. Hence, there is a need for a less expensive and faster diagnostic model to identify the positive and negative cases of COVID-19. Therefore, this study develops six predictive models for COVID-19 diagnosis using six different classifiers (i.e., BayesNet, Logistic, IBk, CR, PART, and J48) based on 14 clinical features. This study retrospected 114 cases from the Taizhou hospital of Zhejiang Province in China. The results showed that the CR meta-classifier is the most accurate classifier for predicting the positive and negative COVID-19 cases with an accuracy of 84.21%. The results could help in the early diagnosis of COVID-19, specifically when the RT-PCR kits are not sufficient for testing the infection and assist countries, specifically the developing ones that suffer from the shortage of RT-PCR tests and specialized laboratories.

Development and External Validation of a Machine Learning Tool to Rule Out COVID-19 Among Adults in the Emergency Department Using Routine Blood Tests: A Large, Multicenter, Real-World Study

Background

Conventional diagnosis of COVID-19 with reverse transcription polymerase chain reaction (RT-PCR) testing (hereafter, PCR) is associated with prolonged time to diagnosis and significant costs to run the test. The SARS-CoV-2 virus might lead to characteristic patterns in the results of widely available, routine blood tests that could be identified with machine learning methodologies. Machine learning modalities integrating findings from these common laboratory test results might accelerate ruling out COVID-19 in emergency department patients.

Objective

We sought to develop (ie, train and internally validate with cross-validation techniques) and externally validate a machine learning model to rule out COVID 19 using only routine blood tests among adults in emergency departments.

Methods

Using clinical data from emergency departments (EDs) from 66 US hospitals before the pandemic (before the end of December 2019) or during the pandemic (March-July 2020), we included patients aged ≥20 years in the study time frame. We excluded those with missing laboratory results. Model training used 2183 PCR-confirmed cases from 43 hospitals during the pandemic; negative controls were 10,000 prepandemic patients from the same hospitals. External validation used 23 hospitals with 1020 PCR-confirmed cases and 171,734 prepandemic negative controls. The main outcome was COVID 19 status predicted using same-day routine laboratory results. Model performance was assessed with area under the receiver operating characteristic (AUROC) curve as well as sensitivity, specificity, and negative predictive value (NPV).

Results

Of 192,779 patients included in the training, external validation, and sensitivity data sets (median age decile 50 [IQR 30-60] years, 40.5% male [78,249/192,779]), AUROC for training and external validation was 0.91 (95% CI 0.90-0.92). Using a risk score cutoff of 1.0 (out of 100) in the external validation data set, the model achieved sensitivity of 95.9% and specificity of 41.7%; with a cutoff of 2.0, sensitivity was 92.6% and specificity was 59.9%. At the cutoff of 2.0, the NPVs at a prevalence of 1%, 10%, and 20% were 99.9%, 98.6%, and 97%, respectively.

Conclusions

A machine learning model developed with multicenter clinical data integrating commonly collected ED laboratory data demonstrated high rule-out accuracy for COVID-19 status, and might inform selective use of PCR-based testing.

A survey on artificial intelligence approaches in supporting frontline workers and decision makers for the COVID-19 pandemic

While the world has experience with many different types of infectious diseases, the current crisis related to the spread of COVID-19 has challenged epidemiologists and public health experts alike, leading to a rapid search for, and development of, new and innovative solutions to combat its spread. The transmission of this virus has infected more than 18.92 million people as of August 6, 2020, with over half a million deaths across the globe; the World Health Organization (WHO) has declared this a global pandemic. A multidisciplinary approach needs to be followed for diagnosis, treatment and tracking, especially between medical and computer sciences, so, a common ground is available to facilitate the research work at a faster pace. With this in mind, this survey paper aimed to explore and understand how and which different technological tools and techniques have been used within the context of COVID-19. The primary contribution of this paper is in its collation of the current state-of-the-art technological approaches applied to the context of COVID-19, and doing this in a holistic way, covering multiple disciplines and different perspectives. The analysis is widened by investigating Artificial Intelligence (AI) approaches for the diagnosis, anticipate infection and mortality rate by tracing contacts and targeted drug designing. Moreover, the impact of different kinds of medical data used in diagnosis, prognosis and pandemic analysis is also provided. This review paper covers both medical and technological perspectives to facilitate the virologists, AI researchers and policymakers while in combating the COVID-19 outbreak.

Evidence of significant difference in key COVID-19 biomarkers during the Italian lockdown strategy. A retrospective study on patients admitted to a hospital emergency department in Northern Italy

BACKGROUND

The Lombardy region, Italy, has been severely affected by COVID-19. During the epidemic peak, in March 2020, patients needing intensive care unit treatments were approximately 10% of those infected. This fraction decreased to approximately 2% in the second part of April, and to 0.4% at the beginning of July. COVID-19 is characterized by several biochemical abnormalities whose discrepancy from normal values was associated to the severity of the disease. The aim of this retrospective study was to compare the biochemical patterns of patients during and after the pandemic peak in order to verify whether later patients were experiencing a milder COVID-19 course, as anecdotally observed by several clinicians of the same Hospital.

MATERIAL AND METHODS

The laboratory findings of two equivalent groups of 84 patients each, admitted at the emergency department of the San Raffaele Hospital (Milan, Italy), during March and April respectively, were analyzed and compared.  Results. White blood cell, platelets, lymphocytes and lactate dehydrogenase showed a statistically significant improvement (i.e. closer or within the normal clinical range) in the April group compared to March. Creatinine, C-reactive protein, Calcium and liver enzymes, were also pointing in that direction, although the differences were not significant.

DISCUSSION

The laboratory findings analyzed in this study were consistent with a milder COVID-19 course in the April group. After excluding several hypotheses, we concluded that our observation was likely the consequence of the lockdown strategy enforcement, which, by imposing social distancing and the use of respiratory protective devices, reduced viral loads upon infection.

Development, evaluation, and validation of machine learning models for COVID-19 detection based on routine blood tests

Objectives

The rRT-PCR test, the current gold standard for the detection of coronavirus disease (COVID-19), presents with known shortcomings, such as long turnaround time, potential shortage of reagents, false-negative rates around 15-20%, and expensive equipment. The hematochemical values of routine blood exams could represent a faster and less expensive alternative.

Methods

Three different training data set of hematochemical values from 1,624 patients (52% COVID-19 positive), admitted at San Raphael Hospital (OSR) from February to May 2020, were used for developing machine learning (ML) models: the complete OSR dataset (72 features: complete blood count (CBC), biochemical, coagulation, hemogasanalysis and CO-Oxymetry values, age, sex and specific symptoms at triage) and two sub-datasets (COVID-specific and CBC dataset, 32 and 21 features respectively). 58 cases (50% COVID-19 positive) from another hospital, and 54 negative patients collected in 2018 at OSR, were used for internal-external and external validation.

Results

We developed five ML models: for the complete OSR dataset, the area under the receiver operating characteristic curve (AUC) for the algorithms ranged from 0.83 to 0.90; for the COVID-specific dataset from 0.83 to 0.87; and for the CBC dataset from 0.74 to 0.86. The validations also achieved good results: respectively, AUC from 0.75 to 0.78; and specificity from 0.92 to 0.96.

Conclusions

ML can be applied to blood tests as both an adjunct and alternative method to rRT-PCR for the fast and cost-effective identification of COVID-19-positive patients. This is especially useful in developing countries, or in countries facing an increase in contagions.

Ensemble learning model for diagnosing COVID-19 from routine blood tests

BACKGROUND AND OBJECTIVES

The pandemic of novel coronavirus disease 2019 (COVID-19) has severely impacted human society with a massive death toll worldwide. There is an urgent need for early and reliable screening of COVID-19 patients to provide better and timely patient care and to combat the spread of the disease. In this context, recent studies have reported some key advantages of using routine blood tests for initial screening of COVID-19 patients. In this article, first we present a review of the emerging techniques for COVID-19 diagnosis using routine laboratory and/or clinical data. Then, we propose ERLX which is an ensemble learning model for COVID-19 diagnosis from routine blood tests.

METHOD

The proposed model uses three well-known diverse classifiers, extra trees, random forest and logistic regression, which have different architectures and learning characteristics at the first level, and then combines their predictions by using a second level extreme gradient boosting (XGBoost) classifier to achieve a better performance. For data preparation, the proposed methodology employs a KNNImputer algorithm to handle null values in the dataset, isolation forest (iForest) to remove outlier data, and a synthetic minority oversampling technique (SMOTE) to balance data distribution. For model interpretability, features importance are reported by using the SHapley Additive exPlanations (SHAP) technique.

RESULTS

The proposed model was trained and evaluated by using a publicly available data set from Albert Einstein Hospital in Brazil, which consisted of 5644 data samples with 559 confirmed COVID-19 cases. The ensemble model achieved outstanding performance with an overall accuracy of 99.88% [95% CI: 99.6-100], AUC of 99.38% [95% CI: 97.5-100], a sensitivity of 98.72% [95% CI: 94.6-100] and a specificity of 99.99% [95% CI: 99.99-100].

DISCUSSION

The proposed model revealed better performance when compared against existing state-of-the-art studies (Banerjee et al., 2020; de Freitas Barbosa et al., 2020; de Moraes Batista et al., 2020; Soares et al., 2020) [3,22,56,71] for the same set of features employed by them. As compared to the best performing Bayes Net model (de Freitas Barbosa et al., 2020) [22] average accuracy of 95.159%, ERLX achieved an average accuracy of 99.94%. In comparison with AUC of 85% reported by the SVM model (de Moraes Batista et al., 2020) [56], ERLX obtained AUC of 99.77% in addition to improvements in sensitivity, and specificity. As compared with ER-COV model (Soares et al., 2020) [71] average sensitivity of 70.25% and specificity of 85.98%, ERLX model achieved sensitivity of 99.47% and specificity of 99.99%. The ERLX model obtained a considerably higher score as compared with ANN model (Banerjee et al., 2020) [3] in all performance metrics. Therefore, the model presented is robust and can be deployed for reliable early and rapid screening of COVID-19 patients.

Predicting CoVID-19 community mortality risk using machine learning and development of an online prognostic tool

BACKGROUND

The recent pandemic of CoVID-19 has emerged as a threat to global health security. There are very few prognostic models on CoVID-19 using machine learning.

OBJECTIVES

To predict mortality among confirmed CoVID-19 patients in South Korea using machine learning and deploy the best performing algorithm as an open-source online prediction tool for decision-making.

MATERIALS AND METHODS

Mortality for confirmed CoVID-19 patients (n = 3,524) between January 20, 2020 and May 30, 2020 was predicted using five machine learning algorithms (logistic regression, support vector machine, K nearest neighbor, random forest and gradient boosting). The performance of the algorithms was compared, and the best performing algorithm was deployed as an online prediction tool.

RESULTS

The logistic regression algorithm was the best performer in terms of discrimination (area under ROC curve = 0.830), calibration (Matthews Correlation Coefficient = 0.433; Brier Score = 0.036) and. The best performing algorithm (logistic regression) was deployed as the online CoVID-19 Community Mortality Risk Prediction tool named CoCoMoRP (https://ashis-das.shinyapps.io/CoCoMoRP/).

CONCLUSIONS

We describe the development and deployment of an open-source machine learning tool to predict mortality risk among CoVID-19 confirmed patients using publicly available surveillance data. This tool can be utilized by potential stakeholders such as health providers and policymakers to triage patients at the community level in addition to other approaches.

Routine blood analysis greatly reduces the false-negative rate of RT-PCR testing for Covid-19

BACKGROUND

The COVID-19 outbreak is now a pandemic disease reaching as much as 210 countries worldwide with more than 2.5 million infected people and nearly 200.000 deaths. Amplification of viral RNA by RT-PCR represents the gold standard for confirmation of infection, yet it showed false-negative rates as large as 15-20% which may jeopardize the effect of the restrictive measures taken by governments. We previously showed that several hematological parameters were significantly different between COVID-19 positive and negative patients. Among them aspartate aminotransferase and lactate dehydrogenase had predictive values as large as 90%. Thus a combination of RT-PCR and blood tests could reduce the false-negative rate of the genetic test.

METHODS

We retrospectively analyzed 24 patients showing multiple and inconsistent RT-PCR, test during their first hospitalization period, and compared the genetic tests results with their AST and LDH levels.

RESULTS

We showed that when considering the hematological parameters, the RT-PCR false-negative rates were reduced by almost 4-fold.

CONCLUSIONS

The study represents a preliminary work aiming at the development of strategies that, by combining RT-PCR tests with routine blood tests, will lower or even abolish the rate of RT-PCR false-negative results and thus will identify, with high accuracy, patients infected by COVID-19.

Routine blood tests as an active surveillance to monitor COVID-19 prevalence. A retrospective study

BACKGROUND

In Italy, one of the country most affected by the COVID-19 pandemic, the first autochthonous case appeared in Lombardy on February 20th, 2020. One month later, the number of -COVID-19 patients in Lombardy exceeded 17000 and about 3500 had died. Because of this rapid increase in infected people scientists wonder whether SARS-CoV-2 was already highly circulating in Lombardy before such date. Plasma levels of aspartate aminotransferase (AST) and lactate dehydrogenase (LDH) were shown to be -highly increased in COVID-19 patients. Monitoring their levels in Emergency Room patients during the months preceding February 20th, 2020, might shade light on the prevalence of the disease in the pre-COVID-19 period.

METHODS

We retrospectively analyzed the AST and LDH levels from more than 30.000 patients admitted to the San Raffaele Hospital Emergency Room (ER) between September 2019 and May 2020 as well as between September 2018 and May 2019. The number of patients diagnosed with respiratory tract diseases were also analyzed.

RESULTS

Data showed that the ER averaged AST and LDH levels are highly sensitive to the presence of COVID-19 patients. During, the months preceding February 20th, 2020, AST and LDH levels, as well as the number of patients diagnosed with respiratory tract diseases were similar to their 2019 counterparts.

CONCLUSIONS

No significant evidence showing that a large number of COVID-19 patients were admitted to the San Raffaele Hospital ER before February 20th, 2020, was found. Thus, the virus was likely circulating, within the Hospital catchment area, either in low amounts or through asymptomatic individuals. Because of the high LDH and AST levels' variations induced by COVID-19, routine blood tests might be exploited as a surveillance indicator for a possible second wave.

Diagnostic significance of C-reactive protein and hematological parameters in acute toxoplasmosis

Abstract

Toxoplasmosis is a zoonosis caused by Toxoplasma gondii, which can be acquired by oral contact and may cause severe health problems especially for pregnant (congenital toxoplasmosis) and immunocompromised patients. This study aimed to verify the diagnostic significance of hematological parameters and C-reactive protein (CRP) for toxoplasmosis acute detection. A case-control study was carried out between December 2017 and May 2018, in samples of convenience independent of age and sex. The case group was formed by 25 patients with positive anti-Toxoplasma gondii IgG/IgM antibody and the control group was formed by 21 patients with non-positive anti-Toxoplasma gondii IgG/IgM antibody. The results of the hematological parameters and CRP were analyzed in these patients. The patients with Toxoplasma gondii IgM antibody reagent showed higher lymphocytes counting and lower neutrophils counting than the control group. C-reactive protein levels were not different between the groups case and control. ROC curve analysis highlighted that the cut-off value of > 32.00% for lymphocytes and < 57.50% for neutrophils were able to produce specificity higher than 90% for IgM antibody detection. The Naïve Bayes classifier was considered suitable (AUC ≈ 0.700) to separate both groups according to their white cell counting. Changes in lymphocytes and neutrophils may be useful parameters for toxoplasmosis identification and may be used as a tool in the complementary diagnosis of toxoplasmosis.

Graphic abstract

Predicting CoVID-19 community mortality risk using machine learning and development of an online prognostic tool

BACKGROUND

The recent pandemic of CoVID-19 has emerged as a threat to global health security. There are very few prognostic models on CoVID-19 using machine learning.

OBJECTIVES

To predict mortality among confirmed CoVID-19 patients in South Korea using machine learning and deploy the best performing algorithm as an open-source online prediction tool for decision-making.

MATERIALS AND METHODS

Mortality for confirmed CoVID-19 patients (n = 3,524) between January 20, 2020 and May 30, 2020 was predicted using five machine learning algorithms (logistic regression, support vector machine, K nearest neighbor, random forest and gradient boosting). The performance of the algorithms was compared, and the best performing algorithm was deployed as an online prediction tool.

RESULTS

The logistic regression algorithm was the best performer in terms of discrimination (area under ROC curve = 0.830), calibration (Matthews Correlation Coefficient = 0.433; Brier Score = 0.036) and. The best performing algorithm (logistic regression) was deployed as the online CoVID-19 Community Mortality Risk Prediction tool named CoCoMoRP (https://ashis-das.shinyapps.io/CoCoMoRP/).

CONCLUSIONS

We describe the development and deployment of an open-source machine learning tool to predict mortality risk among CoVID-19 confirmed patients using publicly available surveillance data. This tool can be utilized by potential stakeholders such as health providers and policymakers to triage patients at the community level in addition to other approaches.