Prediction of the SARS-CoV-2 Derived T-Cell Epitopes' Response against COVID Variants

The COVID-19 outbreak began in December 2019 and was declared a global health emergency by the World Health Organization. The four most dominating variants are Beta, Gamma, Delta, and Omicron. After the administration of vaccine doses, an eminent decline in new cases has been observed. The COVID-19 vaccine induces neutralizing antibodies and T-cells in our bodies. However, strong variants like Delta and Omicron tend to escape these neutralizing antibodies elicited by COVID-19 vaccination. Therefore, it is indispensable to study, analyze and most importantly, predict the response of SARS-CoV-2-derived t-cell epitopes against Covid variants in vaccinated and unvaccinated persons. In this regard, machine learning can be effectively utilized for predicting the response of COVID-derived t-cell epitopes. In this study, prediction of T-cells Epitopes' response was conducted for vaccinated and unvaccinated people for Beta, Gamma, Delta, and Omicron variants. The dataset was divided into two classes, i.e., vaccinated and unvaccinated, and the predicted response of T-cell Epitopes was divided into three categories, i.e., Strong, Impaired, and Over-activated. For the aforementioned prediction purposes, a self-proposed Bayesian neural network has been designed by combining variational inference and flow normalization optimizers. Furthermore, the Hidden Markov Model has also been trained on the same dataset to compare the results of the self-proposed Bayesian neural network with this state-of-the-art statistical approach. Extensive experimentation and results demonstrate the efficacy of the proposed network in terms of accurate prediction and reduced error. © 2023 Tech Science Press. All rights reserved.

City-scale model for COVID-19 epidemiology with mobility and social activities represented by a set of hidden Markov models.

BACKGROUND AND OBJECTIVE: SARS-CoV-2 emerged by the end of 2019 and became a global pandemic due to its rapid spread. Various outbreaks of the disease in different parts of the world have been studied, and epidemiological analyses of these outbreaks have been useful for developing models with the aim of tracking and predicting the spread of epidemics. In this paper, an agent-based model that predicts the local daily evolution of the number of people hospitalized in intensive care due to COVID-19 is presented. METHODS: An agent-based model has been developed, taking into consideration the most relevant characteristics of the geography and climate of a mid-size city, its population and pathology statistics, and its social customs and mobility, including the state of public transportation. In addition to these inputs, the different phases of isolation and social distancing are also taken into account. By means of a set of hidden Markov models, the system captures and reproduces virus transmission associated with the stochastic nature of people's mobility and activities in the city. The spread of the virus in the host is also simulated by following the stages of the disease and by considering the existence of comorbidities and the proportion of asymptomatic carriers. RESULTS: As a case study, the model was applied to Paraná city (Entre Ríos, Argentina) in the second half of 2020. The model adequately predicts the daily evolution of people hospitalized in intensive care due to COVID-19. This adequacy is reflected by the fact that the prediction of the model (including its dispersion), as with the data reported in the field, never exceeded 90% of the capacity of beds installed in the city. In addition, other epidemiological variables of interest, with discrimination by age range, were also adequately reproduced, such as the number of deaths, reported cases, and asymptomatic individuals. CONCLUSIONS: The model can be used to predict the most likely evolution of the number of cases and hospital bed occupancy in the short term. By adjusting the model to match the data on hospitalizations in intensive care units and deaths due to COVID-19, it is possible to analyze the impact of isolation and social distancing measures on the disease spread dynamics. In addition, it allows for simulating combinations of characteristics that would lead to a potential collapse in the health system due to lack of infrastructure as well as predicting the impact of social events or increases in people's mobility.

The Predictive Power of Financial Stress on the Financial Markets Dynamics: Hidden Markov Model

This study investigates the predictive power of the financial stress on the dynamic of the Middle East and North Africa (MENA) financial market returns from 2007 to 2021. Based on a Quantile Regression, we show that financial stress has highest predictive abilities at the lower quantiles when the market is bearish. Then, we propose a Hidden Markov Model (HMM) based on the transition matrix to understand the relationship between financial stress index and the MENA stock market dynamics. We find that the effect of financial stress on stock market return reveals the persistence of regimes: Bullish state exists and persists, and has the longest conditional expected duration for the majority of MENA markets, except Bahrain, Qatar and Jordan. However, the transition probability from the bullish to the calm regime is too low for the financial market of Bahrain, United Arab Emirates and Egypt. Besides, the estimated mean returns for each regime divulge that the bearish and calm states are more attractive destination for both portfolio managers and investors. © 2022, Academy of Economics and Finance.

Learning-based systems for assessing hazard places of contagious diseases and diagnosing patient possibility

To manage the propagation of infectious diseases, particularly fast-spreading pandemics, it is necessary to provide information about possible infected places and individuals, however, it needs diagnostic tests and is time-consuming and expensive. To smooth these issues, and motivated by the current Coronavirus disease (COVID-19) pandemic, in this paper, we propose a learning-based system and a hidden Markov model (i) to assess hazardous places of a contagious disease, and (ii) to predict the probability of individuals' infection. To this end, we track the trajectories of individuals in an environment. For evaluating the models and the approaches, we use the Covid-19 outbreak in an urban environment as a case study. Individuals in a closed population are explicitly represented by their movement trajectories over a period of time. The simulation results demonstrate that by adjusting the communicable disease parameters, the detector system and the predictor system are able to correctly assess the hazardous places and determine the infection possibility of individuals and cluster them accurately with high probability, i.e., on average more than 96%. In general, the proposed approaches to assessing hazardous places and predicting the infection possibility of individuals can be applied to contagious diseases by tailoring them to the influential features of the disease. • Utilizing the movement trajectories of individuals in a city to manage infection disease. • Proposing a learning-based system to assess hazardous places of a contagious disease. • Proposing a hidden Markov model to predict the probability of individuals infection. • Applying the Covid-19 outbreak in an urban environment as a case study. [Display omitted] [ FROM AUTHOR]

Summarizing Global SARS-CoV-2 Geographical Spread by Phylogenetic Multitype Branching Models

Using available phylogeographical data of 3585 SARS–CoV–2 genomes we attempt at providing a global picture of the virus's dynamics in terms of directly interpretable parameters. To this end we fit a hidden state multistate speciation and extinction model to a pre-estimated phylogenetic tree with information on the place of sampling of each strain. We find that even with such coarse–grained data the dominating transition rates exhibit weak similarities with the most popular, continent–level aggregated, airline passenger flight routes. © 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.

Intelligent and Interactive Healthcare System ((IHS)-H-2) Using Machine Learning

There has been a gigantic stir in the world's healthcare sector for the past couple of years with the advent of the Covid-19 pandemic. The healthcare system has suffered a major setback and, with the lack of doctors, nurses, and healthcare facilities the need for an intelligent healthcare system has come to the fore more than ever before. Smart healthcare technologies and AI/ML algorithms provide encouraging and favorable solutions to the healthcare sector's challenges. An Intelligent Human-Machine Interactive system is the need of the hour. This paper proposes a novel architecture for an Intelligent and Interactive Healthcare System that incorporates edge/fog/cloud computing techniques and focuses on Speech Recognition and its extensive application in an interactive system. The focal reason for using speech in the healthcare sector is that it is easily available and can easily predict any physical or psychological discomfort. Simply put, human speech is the most natural form of communication. The Hidden Markov Model is applied to process the proposed approach as using the probabilistic approach is more realistic for prediction purposes. Ongoing projects and directions for future work along with challenges/issues are also addressed.

Learning-based systems for assessing hazard places of contagious diseases and diagnosing patient possibility

To manage the propagation of infectious diseases, particularly fast-spreading pandemics, it is necessary to provide information about possible infected places and individuals, however, it needs diagnostic tests and is time-consuming and expensive. To smooth these issues, and motivated by the current Coronavirus disease (COVID-19) pandemic, in this paper, we propose a learning-based system and a hidden Markov model (i) to assess hazardous places of a contagious disease, and (ii) to predict the probability of individuals’ infection. To this end, we track the trajectories of individuals in an environment. For evaluating the models and the approaches, we use the Covid-19 outbreak in an urban environment as a case study. Individuals in a closed population are explicitly represented by their movement trajectories over a period of time. The simulation results demonstrate that by adjusting the communicable disease parameters, the detector system and the predictor system are able to correctly assess the hazardous places and determine the infection possibility of individuals and cluster them accurately with high probability, i.e., on average more than 96%. In general, the proposed approaches to assessing hazardous places and predicting the infection possibility of individuals can be applied to contagious diseases by tailoring them to the influential features of the disease.

A Generalized Entropy Approach to Portfolio Selection under a Hidden Markov Model

This paper develops a dynamic portfolio selection model incorporating economic uncertainty for business cycles. It is assumed that the financial market at each point in time is defined by a hidden Markov model, which is characterized by the overall equity market returns and volatility. The risk associated with investment decisions is measured by the exponential Rényi entropy criterion, which summarizes the uncertainty in portfolio returns. Assuming asset returns are projected by a regime-switching regression model on the two market risk factors, we develop an entropy-based dynamic portfolio selection model constrained with the wealth surplus being greater than or equal to the shortfall over a target and the probability of shortfall being less than or equal to a specified level. In the empirical analysis, we use the select sector ETFs to test the asset pricing model and examine the portfolio performance. Weekly financial data from 31 December 1998 to 30 December 2018 is employed for the estimation of the hidden Markov model including the asset return parameters, while the out-of-sample period from 3 January 2019 to 30 April 2022 is used for portfolio performance testing. It is found that, under both the empirical Sharpe and return to entropy ratios, the dynamic portfolio under the proposed strategy is much improved in contrast with mean variance models.

The Predictive Power of Financial Stress on the Financial Markets Dynamics: Hidden Markov Model

This study investigates the predictive power of the financial stress on the dynamic of the Middle East and North Africa (MENA) financial market returns from 2007 to 2021. Based on a Quantile Regression, we show that financial stress has highest predictive abilities at the lower quantiles when the market is bearish. Then, we propose a Hidden Markov Model (HMM) based on the transition matrix to understand the relationship between financial stress index and the MENA stock market dynamics. We find that the effect of financial stress on stock market return reveals the persistence of regimes: Bullish state exists and persists, and has the longest conditional expected duration for the majority of MENA markets, except Bahrain, Qatar and Jordan. However, the transition probability from the bullish to the calm regime is too low for the financial market of Bahrain, United Arab Emirates and Egypt. Besides, the estimated mean returns for each regime divulge that the bearish and calm states are more attractive destination for both portfolio managers and investors. © 2022, Academy of Economics and Finance.

Finite mixture model of hidden Markov regression with covariate dependence

In recent days, a combination of finite mixture model (FMM) and hidden Markov model (HMM) is becoming popular for partitioning heterogeneous temporal data into homogeneous groups (clusters) with homogeneous time points (regimes). The regression mixtures commonly considered in this approach can also accommodate for covariates present in data. The classical fixed covariate approach, however, may not always serve as a reasonable assumption as it is incapable of accounting for the contribution of covariates in cluster formation. This paper introduces a novel approach for detecting clusters and regimes in time series data in the presence of random covariates. The computational challenges related to the proposed model has been discussed, and several simulation studies are performed. An application to United States COVID-19 data yields meaningful clusters and regimes.

Ambient Assisted Living for Elderly Care and Monitoring in CQVID-19 Pandemic

In late 2019, a novel Coronavirus broke out from China, which has dispersed all over the globe and has taken away countless lives. Despite the fact that every person is at risk of getting infected with the virus, older people are more likely to fall victim to the virus due to their declining immune systems. Although there has been significant development of vaccines, it is seen that the mutation of the COVID-19 has made it tough to control with the medication available. Due to an uncountable number of Coronavirus strains, many countries are now facing several waves of the pandemic. Assisted living technologies are evolving with time to give people a better life. This technology can be used for older people in Coronavirus pandemic situations as most of the older people have physical and cognitive impairments. In this paper, we have proposed an Internet of Things(loT)-architectured system incorporated with Artificial intelligence and deep learning that can help diagnose COVID-19 in older people. The proposed architecture will collect all the data from different medical loT sensors and relay them to the cloud, where the system will process and help us monitor the health of older people. This information could be seen from a dedicated dashboard where the user would be able to get diagnosis status of COVID-19 by our system. In order to be prepared for any future pandemic, this type of system will be beneficial. © 2021 IEEE

An HMM-ensemble approach to predict severity progression of ICU treatment for hospitalized COVID-19 patients

COVID-19-related pneumonia requires different modalities of Intensive Care Unit (ICU) interventions at different times to facilitate breathing, depending on severity progression. The ability for clinical staff to predict how patients admitted to hospital will require more or less ICU treatment on a daily basis is critical to ICU management. For real datasets that are sparse and incomplete and where the most important state transitions (dismissal, death) are rare, a standard Hidden Markov Model (HMM) approach is insufficient, as it is prone to overfitting. In this paper we propose a more sophisticated ensemble-based approach that involves training multiple HMMs, each specialized in a subset of the state transitions, and then selecting the more plausible predictions either by selecting or combining the models. We have validated the approach on a live dataset of about 1, 000 patients from a partner hospital. Our results show that rare events, as well as the transitions to the most severe treatments outperform state of the art approaches. © 2021 IEEE.

Dynamic modeling of hospitalized COVID-19 patients reveals disease state-dependent risk factors.

OBJECTIVE: The study sought to investigate the disease state-dependent risk profiles of patient demographics and medical comorbidities associated with adverse outcomes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. MATERIALS AND METHODS: A covariate-dependent, continuous-time hidden Markov model with 4 states (moderate, severe, discharged, and deceased) was used to model the dynamic progression of COVID-19 during the course of hospitalization. All model parameters were estimated using the electronic health records of 1362 patients from ProMedica Health System admitted between March 20, 2020 and December 29, 2020 with a positive nasopharyngeal PCR test for SARS-CoV-2. Demographic characteristics, comorbidities, vital signs, and laboratory test results were retrospectively evaluated to infer a patient's clinical progression. RESULTS: The association between patient-level covariates and risk of progression was found to be disease state dependent. Specifically, while being male, being Black or having a medical comorbidity were all associated with an increased risk of progressing from the moderate disease state to the severe disease state, these same factors were associated with a decreased risk of progressing from the severe disease state to the deceased state. DISCUSSION: Recent studies have not included analyses of the temporal progression of COVID-19, making the current study a unique modeling-based approach to understand the dynamics of COVID-19 in hospitalized patients. CONCLUSION: Dynamic risk stratification models have the potential to improve clinical outcomes not only in COVID-19, but also in a myriad of other acute and chronic diseases that, to date, have largely been assessed only by static modeling techniques.

The detection of the epidemic phase of COVID-19 and the timing of social distancing policies in Korea.

OBJECTIVES: Observing cumulative and new daily confirmed cases of COVID-19, disease control authorities respond to a surge in cases with social distancing measures or economic lockdown. The question in this article is whether we can gather more useful information from a readily available time series data set of day-to-day changes in confirmed cases of COVID-19. STUDY DESIGN: Time-series data analysis was done using a hidden Markov model. METHODS: Day-to-day differences in confirmed cases of COVID-19 in Korea from February 19, 2020, to July 13, 2021, were modeled via a hidden Markov model. The results from the model were compared with the effective reproduction number and the Korean government's response. RESULTS: The model reports that Korea was in an epidemic phase from August 2020 and from mid-November 2020, the second and third epidemic waves. The government's response, represented by the Government Response Stringency Index, was not timely during the epidemic phases. The results from the model may also be more helpful to detect the onset of the epidemic phase of an infectious disease than the effective reproduction number. CONCLUSIONS: The model can reveal a hidden epidemic phase and help disease control authorities to respond more promptly and effectively.

Shift in Social Media App Usage During COVID-19 Lockdown and Clinical Anxiety Symptoms: Machine Learning-Based Ecological Momentary Assessment Study.

BACKGROUND: Anxiety symptoms during public health crises are associated with adverse psychiatric outcomes and impaired health decision-making. The interaction between real-time social media use patterns and clinical anxiety during infectious disease outbreaks is underexplored. OBJECTIVE: We aimed to evaluate the usage pattern of 2 types of social media apps (communication and social networking) among patients in outpatient psychiatric treatment during the COVID-19 surge and lockdown in Madrid, Spain and their short-term anxiety symptoms (7-item General Anxiety Disorder scale) at clinical follow-up. METHODS: The individual-level shifts in median social media usage behavior from February 1 through May 3, 2020 were summarized using repeated measures analysis of variance that accounted for the fixed effects of the lockdown (prelockdown versus postlockdown), group (clinical anxiety group versus nonclinical anxiety group), the interaction of lockdown and group, and random effects of users. A machine learning-based approach that combined a hidden Markov model and logistic regression was applied to predict clinical anxiety (n=44) and nonclinical anxiety (n=51), based on longitudinal time-series data that comprised communication and social networking app usage (in seconds) as well as anxiety-associated clinical survey variables, including the presence of an essential worker in the household, worries about life instability, changes in social interaction frequency during the lockdown, cohabitation status, and health status. RESULTS: Individual-level analysis of daily social media usage showed that the increase in communication app usage from prelockdown to lockdown period was significantly smaller in the clinical anxiety group than that in the nonclinical anxiety group (F1,72=3.84, P=.05). The machine learning model achieved a mean accuracy of 62.30% (SD 16%) and area under the receiver operating curve 0.70 (SD 0.19) in 10-fold cross-validation in identifying the clinical anxiety group. CONCLUSIONS: Patients who reported severe anxiety symptoms were less active in communication apps after the mandated lockdown and more engaged in social networking apps in the overall period, which suggested that there was a different pattern of digital social behavior for adapting to the crisis. Predictive modeling using digital biomarkers-passive-sensing of shifts in category-based social media app usage during the lockdown-can identify individuals at risk for psychiatric sequelae.

The Impact of Control Measures and Holiday Seasons on Incidence and Mortality Rate of COVID-19 in Iran.

BACKGROUND: Preventive measures on the COVID-19 pandemic is an effective way to control its spread. We aimed to investigate the effect of control measures and holiday seasons on the incidence and mortality rate of COVID-19 in Iran. STUDY DESIGN: An observational study. METHODS: The daily data of confirmed new cases and deaths in Iran were taken from the Johns Hopkins University COVID-19 database. We calculated weekly data from 19 Feb to 6 Oct 2020. To estimate the impact of control measures and holiday seasons on the incidence rate of new cases and deaths, an autoregressive hidden Markov model (ARHMM) with two hidden states fitted the data. The hidden states of the fitted model can distinguish the peak period from the non-peak period. RESULTS: The control measures with a delay of one-week and two-week had a decreasing effect on the new cases in the peak and non-peak periods, respectively (P=0.005). The holiday season with a two-week delay increased the total number of new cases in the peak periods (P=0.031). The peak period for the occurrence of COVID-19 was estimated at 3 weeks. In the peak period of mortality, the control measures with a three-week delay decreased the COVID-19 mortality (P=0.010). The expected duration of staying in the peak period of mortality was around 6 weeks. CONCLUSION: When an increasing trend was seen in the country, the control measures could decline the incidence and mortality related to COVID-19. Implementation of official restrictions on holiday seasons could prevent an upward trend of incidence for COVID-19 during the peak period.

Growth Rate and Acceleration Analysis of the COVID-19 Pandemic Reveals the Effect of Public Health Measures in Real Time.

Background: Ending the COVID-19 pandemic is arguably one of the most prominent challenges in recent human history. Following closely the growth dynamics of the disease is one of the pillars toward achieving that goal. Objective: We aimed at developing a simple framework to facilitate the analysis of the growth rate (cases/day) and growth acceleration (cases/day2) of COVID-19 cases in real-time. Methods: The framework was built using the Moving Regression (MR) technique and a Hidden Markov Model (HMM). The dynamics of the pandemic was initially modeled via combinations of four different growth stages: lagging (beginning of the outbreak), exponential (rapid growth), deceleration (growth decay), and stationary (near zero growth). A fifth growth behavior, namely linear growth (constant growth above zero), was further introduced to add more flexibility to the framework. An R Shiny application was developed, which can be accessed at https://theguarani.com.br/ or downloaded from https://github.com/adamtaiti/SARS-CoV-2. The framework was applied to data from the European Center for Disease Prevention and Control (ECDC), which comprised 3,722,128 cases reported worldwide as of May 8th 2020. Results: We found that the impact of public health measures on the prevalence of COVID-19 could be perceived in seemingly real-time by monitoring growth acceleration curves. Restriction to human mobility produced detectable decline in growth acceleration within 1 week, deceleration within ~2 weeks and near-stationary growth within ~6 weeks. Countries exhibiting different permutations of the five growth stages indicated that the evolution of COVID-19 prevalence is more complex and dynamic than previously appreciated. Conclusions: These results corroborate that mass social isolation is a highly effective measure against the dissemination of SARS-CoV-2, as previously suggested. Apart from the analysis of prevalence partitioned by country, the proposed framework is easily applicable to city, state, region and arbitrary territory data, serving as an asset to monitor the local behavior of COVID-19 cases.