Comparative Analysis of Laboratory and Radiation Methods of Studies with the Degree of Severity of Patients with COVID-19

The study is devoted to a comparative analysis and retrospective evaluation of laboratory and instrumental data with the severity of lung tissue damage in COVID-19 of patients with COVID-19. An improvement was made in the methodology for interpreting and analyzing dynamic changes associated with COVID-19 on CT images of the lungs. The technique includes the following steps: pre-processing, segmentation with color coding, calculation and evaluation of signs to highlight areas with probable pathology (including combined evaluation of signs). Analysis and interpretation is carried out on the emerging database of patients. At the same time the following indicators are distinguished: the results of the analysis of CT images of the lungs in dynamics;the results of the analysis of clinical and laboratory data (severity course of the disease, temperature, saturation, etc.). The results of laboratory studies are analyzed with an emphasis on the values of the main indicator - interleukin-6. This indicator is a marker of significant and serious changes characterizing the severity of the patient's condition. © 2023 IEEE.

Benchmarking of analytical combinations for COVID-19 outcome prediction using single-cell RNA sequencing data.

The advances of single-cell transcriptomic technologies have led to increasing use of single-cell RNA sequencing (scRNA-seq) data in large-scale patient cohort studies. The resulting high-dimensional data can be summarized and incorporated into patient outcome prediction models in several ways; however, there is a pressing need to understand the impact of analytical decisions on such model quality. In this study, we evaluate the impact of analytical choices on model choices, ensemble learning strategies and integrate approaches on patient outcome prediction using five scRNA-seq COVID-19 datasets. First, we examine the difference in performance between using single-view feature space versus multi-view feature space. Next, we survey multiple learning platforms from classical machine learning to modern deep learning methods. Lastly, we compare different integration approaches when combining datasets is necessary. Through benchmarking such analytical combinations, our study highlights the power of ensemble learning, consistency among different learning methods and robustness to dataset normalization when using multiple datasets as the model input.

NLP Analysis of COVID-19 Radiology Reports in Indonesian using IndoBERT

The presence of COVID-19, a respiratory disease, can be detected through medical imaging, such as Chest X-Ray (CXR) and Computed Tomography (CT) scans. These radiology images can also show how the patient's condition progresses. Radiologists need to provide a written report for each image, so that other clinicians can use it in their decision making. In this study, we applied one of the Natural Language Processing (NLP) models called IndoBERT to analyze radiology reports of COVID-19 patients written in Indonesian. We performed two tasks, clustering to group reports by meaning and understand their content, and text classification to predict one of the five possible outcomes for each patient. We show the most frequent topics in radiology reports, and word scores in each topic. The IndoBERT model was fine tuned on a medical text, 'Kamus Kedokteran Dorland' in an attempt to further improve it. This proved unnecessary: on one hand, there were no additional benefits, on the other, the standard model alone achieved a very satisfactory classification accuracy of over 90 %. © 2022 IEEE.

High Anti-CoV2S Antibody Levels at Hospitalization Are Associated with Improved Survival in Patients with COVID-19 Vaccine Breakthrough Infection.

BACKGROUND: Although vaccination against COVID-19 is highly effective, breakthrough infections occur, often leading to severe courses and death. The extent of protection provided by individual antibody levels in breakthrough infections is still unknown and cut-off levels have yet to be determined. METHODS: In 80 consecutive fully vaccinated patients hospitalized between August and December 2021 with COVID-19 breakthrough infection (Delta variant), anti-CoV2S antibody levels were analyzed for the endpoint of death. RESULTS: Ten out of the 12 patients who died (83.3%) had antibody levels < 600 U/mL; 5 (41.7%) of these had antibody levels < 200 U/mL. Only 2 patients with a level of >600 U/mL died from vaccine breakthrough infection. Correction for the number of comorbidities and age revealed that anti-CoV2S antibody levels at the time of hospitalization were a significant predictor for reduced risk of death (OR = 0.402 for every 1000 U/mL, p = 0.018). CONCLUSIONS: In this retrospective data analysis, we show that almost all patients who died from COVID-19 vaccine breakthrough infection had antibody levels < 600 U/mL, most of them below 200 U/mL. In logistic regression corrected for the number of comorbidities and age, anti-CoV2S antibody levels at the time of hospitalization proved to be a significantly protective predictor against death.

Predicting the outcome for COVID-19 patients by applying time series classification to electronic health records.

BACKGROUND: COVID-19 caused more than 622 thousand deaths in Brazil. The infection can be asymptomatic and cause mild symptoms, but it also can evolve into a severe disease and lead to death. It is difficult to predict which patients will develop severe disease. There are, in the literature, machine learning models capable of assisting diagnose and predicting outcomes for several diseases, but usually these models require laboratory tests and/or imaging. METHODS: We conducted a observational cohort study that evaluated vital signs and measurements from patients who were admitted to Hospital das Clínicas (São Paulo, Brazil) between March 2020 and October 2021 due to COVID-19. The data was then represented as univariate and multivariate time series, that were used to train and test machine learning models capable of predicting a patient's outcome. RESULTS: Time series-based machine learning models are capable of predicting a COVID-19 patient's outcome with up to 96% general accuracy and 81% accuracy considering only the first hospitalization day. The models can reach up to 99% sensitivity (discharge prediction) and up to 91% specificity (death prediction). CONCLUSIONS: Results indicate that time series-based machine learning models combined with easily obtainable data can predict COVID-19 outcomes and support clinical decisions. With further research, these models can potentially help doctors diagnose other diseases.

Clinical outcome prediction in COVID-19 using self-supervised vision transformer representations

Automated analysis of chest imaging in coronavirus disease (COVID-19) has mostly been performed on smaller datasets leading to overfitting and poor generalizability. Training of deep neural networks on large datasets requires data labels. This is not always available and can be expensive to obtain. Self-supervision is being increasingly used in various medical imaging tasks to leverage large amount of unlabeled data during pretraining. Our proposed approach pretrains a vision transformer to perform two self-supervision tasks - image reconstruction and contrastive learning on a Chest Xray (CXR) dataset. In the process, we generate more robust image embeddings. The reconstruction module models visual semantics within the lung fields by reconstructing the input image through a mechanism which mimics denoising and autoencoding. On the other hand, the constrastive learning module learns the concept of similarity between two texture representations. After pretraining, the vision transformer is used as a feature extractor towards a clinical outcome prediction task on our target dataset. The pretraining multi-kaggle dataset comprises 27499 CXR scans while our target dataset contains 530 images. Specifically, our framework predicts ventilation and mortality outcomes for COVID-19 positive patients using baseline CXR. We compare our method against a baseline approach using pretrained ResNet50 features. Experimental results demonstrate that our proposed approach outperforms the supervised method. © 2022 SPIE.

Clinical Decision Making and Outcome Prediction for COVID-19 Patients Using Machine Learning

In this paper, we present the application of a Machine Learning (ML) approach that generates predictions to support healthcare professionals to identify the outcome of patients through optimization of treatment strategies. Based on Decision Tree algorithms, our approach has been trained and tested by analyzing the severity and the outcomes of 346 COVID-19 patients, treated through the first two pandemics “waves” in a tertiary center in Western Greece. Its’ performance was achieved, analyzing entry features, as demographic characteristics, comorbidity details, imaging analysis, blood values, and essential hospitalization details, like patient transfers to Intensive Care Unit (ICU), medications, and manifestation responses at each treatment stage. Furthermore, it has provided a total high prediction performance (97%) and translated the ML analysis to clinical managing decisions and suggestions for healthcare institution performance and other epidemiological or postmortem approaches. Consequently, healthcare decisions could be more accurately figured and predicted, towards better management of the fast-growing patient subpopulations, giving more time for the effective pharmaceutical or vaccine armamentarium that the medical, scientific community will produce. © 2022, ICST Institute for Computer Sciences, Social Informatics and Telecommunications Engineering.

Disease-Course Adapting Machine Learning Prognostication Models in Elderly Patients Critically Ill With COVID-19: Multicenter Cohort Study With External Validation.

BACKGROUND: The COVID-19 pandemic caused by SARS-CoV-2 is challenging health care systems globally. The disease disproportionately affects the elderly population, both in terms of disease severity and mortality risk. OBJECTIVE: The aim of this study was to evaluate machine learning-based prognostication models for critically ill elderly COVID-19 patients, which dynamically incorporated multifaceted clinical information on evolution of the disease. METHODS: This multicenter cohort study (COVIP study) obtained patient data from 151 intensive care units (ICUs) from 26 countries. Different models based on the Sequential Organ Failure Assessment (SOFA) score, logistic regression (LR), random forest (RF), and extreme gradient boosting (XGB) were derived as baseline models that included admission variables only. We subsequently included clinical events and time-to-event as additional variables to derive the final models using the same algorithms and compared their performance with that of the baseline group. Furthermore, we derived baseline and final models on a European patient cohort, which were externally validated on a non-European cohort that included Asian, African, and US patients. RESULTS: In total, 1432 elderly (≥70 years old) COVID-19-positive patients admitted to an ICU were included for analysis. Of these, 809 (56.49%) patients survived up to 30 days after admission. The average length of stay was 21.6 (SD 18.2) days. Final models that incorporated clinical events and time-to-event information provided superior performance (area under the receiver operating characteristic curve of 0.81; 95% CI 0.804-0.811), with respect to both the baseline models that used admission variables only and conventional ICU prediction models (SOFA score, P<.001). The average precision increased from 0.65 (95% CI 0.650-0.655) to 0.77 (95% CI 0.759-0.770). CONCLUSIONS: Integrating important clinical events and time-to-event information led to a superior accuracy of 30-day mortality prediction compared with models based on the admission information and conventional ICU prediction models. This study shows that machine-learning models provide additional information and may support complex decision-making in critically ill elderly COVID-19 patients. TRIAL REGISTRATION: ClinicalTrials.gov NCT04321265; https://clinicaltrials.gov/ct2/show/NCT04321265.

HIV Patients’ Tracer for Clinical Assistance and Research during the COVID-19 Epidemic (INTERFACE): A Paradigm for Chronic Conditions

The health emergency linked to the SARS-CoV-2 pandemic has highlighted problems in the health management of chronic patients due to their risk of infection, suggesting the need of new methods to monitor patients. People living with HIV/AIDS (PLWHA) represent a paradigm of chronic patients where an e-health-based remote monitoring could have a significant impact in maintaining an adequate standard of care. The key objective of the study is to provide both an efficient operating model to “follow” the patient, capture the evolution of their disease, and establish proximity and relief through a remote collaborative model. These dimensions are collected through a dedicated mobile application that triggers questionnaires on the basis of decision-making algorithms, tagging patients and sending alerts to staff in order to tailor interventions. All outcomes and alerts are monitored and processed through an innovative e-Clinical platform. The processing of the collected data aims into learning and evaluating predictive models for the possible upcoming alerts on the basis of past data, using machine learning algorithms. The models will be clinically validated as the study collects more data, and, if successful, the resulting multidimensional vector of past attributes will act as a digital composite biomarker capable of predicting HIV-related alerts. Design: All PLWH > 18 sears old and stable disease followed at the outpatient services of a university hospital (n = 1500) will be enrolled in the interventional study. The study is ongoing, and patients are currently being recruited. Preliminary results are yielding monthly data to facilitate learning of predictive models for the alerts of interest. Such models are learnt for one or two months of history of the questionnaire data. In this manuscript, the protocol—including the rationale, detailed technical aspects underlying the study, and some preliminary results—are described. Conclusions: The management of HIV-infected patients in the pandemic era represents a challenge for future patient management beyond the pandemic period. The application of artificial intelligence and machine learning systems as described in this study could enable remote patient management that takes into account the real needs of the patient and the monitoring of the most relevant aspects of PLWH management today. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.

Diagnosing hospital bacteraemia in the framework of predictive, preventive and personalised medicine using electronic health records and machine learning classifiers.

Background: The bacteraemia prediction is relevant because sepsis is one of the most important causes of morbidity and mortality. Bacteraemia prognosis primarily depends on a rapid diagnosis. The bacteraemia prediction would shorten up to 6 days the diagnosis, and, in conjunction with individual patient variables, should be considered to start the early administration of personalised antibiotic treatment and medical services, the election of specific diagnostic techniques and the determination of additional treatments, such as surgery, that would prevent subsequent complications. Machine learning techniques could help physicians make these informed decisions by predicting bacteraemia using the data already available in electronic hospital records. Objective: This study presents the application of machine learning techniques to these records to predict the blood culture's outcome, which would reduce the lag in starting a personalised antibiotic treatment and the medical costs associated with erroneous treatments due to conservative assumptions about blood culture outcomes. Methods: Six supervised classifiers were created using three machine learning techniques, Support Vector Machine, Random Forest and K-Nearest Neighbours, on the electronic health records of hospital patients. The best approach to handle missing data was chosen and, for each machine learning technique, two classification models were created: the first uses the features known at the time of blood extraction, whereas the second uses four extra features revealed during the blood culture. Results: The six classifiers were trained and tested using a dataset of 4357 patients with 117 features per patient. The models obtain predictions that, for the best case, are up to a state-of-the-art accuracy of 85.9%, a sensitivity of 87.4% and an AUC of 0.93. Conclusions: Our results provide cutting-edge metrics of interest in predictive medical models with values that exceed the medical practice threshold and previous results in the literature using classical modelling techniques in specific types of bacteraemia. Additionally, the consistency of results is reasserted because the three classifiers' importance ranking shows similar features that coincide with those that physicians use in their manual heuristics. Therefore, the efficacy of these machine learning techniques confirms their viability to assist in the aims of predictive and personalised medicine once the disease presents bacteraemia-compatible symptoms and to assist in improving the healthcare economy.

Autoantibodies against ACE2 and angiotensin type-1 receptors increase severity of COVID-19.

The renin-angiotensin system (RAS) plays a major role in COVID-19. Severity of several inflammation-related diseases has been associated with autoantibodies against RAS, particularly agonistic autoantibodies for angiotensin type-1 receptors (AA-AT1) and autoantibodies against ACE2 (AA-ACE2). Disease severity of COVID-19 patients was defined as mild, moderate or severe following the WHO Clinical Progression Scale and determined at medical discharge. Serum AA-AT1 and AA-ACE2 were measured in COVID-19 patients (n = 119) and non-infected controls (n = 23) using specific solid-phase, sandwich enzyme-linked immunosorbent assays. Serum LIGHT (TNFSF14; tumor necrosis factor ligand superfamily member 14) levels were measured with the corresponding assay kit. At diagnosis, AA-AT1 and AA-ACE2 levels were significantly higher in the COVID-19 group relative to controls, and we observed significant association between disease outcome and serum AA-AT1 and AA-ACE2 levels. Mild disease patients had significantly lower levels of AA-AT1 (p < 0.01) and AA-ACE2 (p < 0.001) than moderate and severe patients. No significant differences were detected between males and females. The increase in autoantibodies was not related to comorbidities potentially affecting COVID-19 severity. There was significant positive correlation between serum levels of AA-AT1 and LIGHT (TNFSF14; rPearson = 0.70, p < 0.001). Both AA-AT1 (by agonistic stimulation of AT1 receptors) and AA-ACE2 (by reducing conversion of Angiotensin II into Angiotensin 1-7) may lead to increase in AT1 receptor activity, enhance proinflammatory responses and severity of COVID-19 outcome. Patients with high levels of autoantibodies require more cautious control after diagnosis. Additionally, the results encourage further studies on the possible protective treatment with AT1 receptor blockers in COVID-19.

Automated AI-Driven CT Quantification of Lung Disease Predicts Adverse Outcomes in Patients Hospitalized for COVID-19 Pneumonia.

The purpose of our work was to assess the independent and incremental value of AI-derived quantitative determination of lung lesions extent on initial CT scan for the prediction of clinical deterioration or death in patients hospitalized with COVID-19 pneumonia. 323 consecutive patients (mean age 65 ± 15 years, 192 men), with laboratory-confirmed COVID-19 and an abnormal chest CT scan, were admitted to the hospital between March and December 2020. The extent of consolidation and all lung opacities were quantified on an initial CT scan using a 3D automatic AI-based software. The outcome was known for all these patients. 85 (26.3%) patients died or experienced clinical deterioration, defined as intensive care unit admission. In multivariate regression based on clinical, biological and CT parameters, the extent of all opacities, and extent of consolidation were independent predictors of adverse outcomes, as were diabetes, heart disease, C-reactive protein, and neutrophils/lymphocytes ratio. The association of CT-derived measures with clinical and biological parameters significantly improved the risk prediction (p = 0.049). Automated quantification of lung disease at CT in COVID-19 pneumonia is useful to predict clinical deterioration or in-hospital death. Its combination with clinical and biological data improves risk prediction.

Predicting in-Hospital Mortality of Patients with COVID-19 Using Machine Learning Techniques.

The present work aims to identify the predictors of COVID-19 in-hospital mortality testing a set of Machine Learning Techniques (MLTs), comparing their ability to predict the outcome of interest. The model with the best performance will be used to identify in-hospital mortality predictors and to build an in-hospital mortality prediction tool. The study involved patients with COVID-19, proved by PCR test, admitted to the "Ospedali Riuniti Padova Sud" COVID-19 referral center in the Veneto region, Italy. The algorithms considered were the Recursive Partition Tree (RPART), the Support Vector Machine (SVM), the Gradient Boosting Machine (GBM), and Random Forest. The resampled performances were reported for each MLT, considering the sensitivity, specificity, and the Receiving Operative Characteristic (ROC) curve measures. The study enrolled 341 patients. The median age was 74 years, and the male gender was the most prevalent. The Random Forest algorithm outperformed the other MLTs in predicting in-hospital mortality, with a ROC of 0.84 (95% C.I. 0.78-0.9). Age, together with vital signs (oxygen saturation and the quick SOFA) and lab parameters (creatinine, AST, lymphocytes, platelets, and hemoglobin), were found to be the strongest predictors of in-hospital mortality. The present work provides insights for the prediction of in-hospital mortality of COVID-19 patients using a machine-learning algorithm.

An Algorithm for Classifying Patients Most Likely to Develop Severe Coronavirus Disease 2019 Illness.

OBJECTIVES: To develop an algorithm that predicts an individualized risk of severe coronavirus disease 2019 illness (i.e., ICU admission or death) upon testing positive for coronavirus disease 2019. DESIGN: A retrospective cohort study. SETTING: Cleveland Clinic Health System. PATIENTS: Those hospitalized with coronavirus disease 2019 between March 8, 2020, and July 13, 2020. INTERVENTIONS: A temporal coronavirus disease 2019 test positive cut point of June 1 was used to separate the development from validation cohorts. Fine and Gray competing risk regression modeling was performed. MEASUREMENTS AND MAIN RESULTS: The development set contained 4,520 patients who tested positive for coronavirus disease 2019 between March 8, 2020, and May 31, 2020. The validation set contained 3,150 patients who tested positive between June 1 and July 13. Approximately 9% of patients were admitted to the ICU or died of coronavirus disease 2019 within 2 weeks of testing positive. A prediction cut point of 15% was proposed. Those who exceed the cutoff have a 21% chance of future severe coronavirus disease 2019, whereas those who do not have a 96% chance of avoiding the severe coronavirus disease 2019. In addition, application of this decision rule identifies 89% of the population at the very low risk of severe coronavirus disease 2019 (< 4%). CONCLUSIONS: We have developed and internally validated an algorithm to assess whether someone is at high risk of admission to the ICU or dying from coronavirus disease 2019, should he or she test positive for coronavirus disease 2019. This risk should be a factor in determining resource allocation, protection from less safe working conditions, and prioritization for vaccination.

Integrative analysis for COVID-19 patient outcome prediction.

While image analysis of chest computed tomography (CT) for COVID-19 diagnosis has been intensively studied, little work has been performed for image-based patient outcome prediction. Management of high-risk patients with early intervention is a key to lower the fatality rate of COVID-19 pneumonia, as a majority of patients recover naturally. Therefore, an accurate prediction of disease progression with baseline imaging at the time of the initial presentation can help in patient management. In lieu of only size and volume information of pulmonary abnormalities and features through deep learning based image segmentation, here we combine radiomics of lung opacities and non-imaging features from demographic data, vital signs, and laboratory findings to predict need for intensive care unit (ICU) admission. To our knowledge, this is the first study that uses holistic information of a patient including both imaging and non-imaging data for outcome prediction. The proposed methods were thoroughly evaluated on datasets separately collected from three hospitals, one in the United States, one in Iran, and another in Italy, with a total 295 patients with reverse transcription polymerase chain reaction (RT-PCR) assay positive COVID-19 pneumonia. Our experimental results demonstrate that adding non-imaging features can significantly improve the performance of prediction to achieve AUC up to 0.884 and sensitivity as high as 96.1%, which can be valuable to provide clinical decision support in managing COVID-19 patients. Our methods may also be applied to other lung diseases including but not limited to community acquired pneumonia. The source code of our work is available at https://github.com/DIAL-RPI/COVID19-ICUPrediction.

Utility of Artificial Intelligence Amidst the COVID 19 Pandemic: A Review.

The term machine learning refers to a collection of tools used for identifying patterns in data. As opposed to traditional methods of pattern identification, machine learning tools relies on artificial intelligence to map out patters from large amounts of data, can self-improve as and when new data becomes available and is quicker in accomplishing these tasks. This review describes various techniques of machine learning that have been used in the past in the prediction, detection and management of infectious diseases, and how these tools are being brought into the battle against COVID-19. In addition, we also discuss their applications in various stages of the pandemic, the advantages, disadvantages and possible pit falls.