The COVID-19 pandemic has placed forecasting models at the forefront of health policy making. Predictions of mortality and hospitalization help governments meet planning and resource allocation challenges. In this paper, we consider the weekly forecasting of the cumulative mortality due to COVID-19 at the national and state level in the U.S. Optimal decision-making requires a forecast of a probability distribution, rather than just a single point forecast. Interval forecasts are also important, as they can support decision making and provide situational awareness. We consider the case where probabilistic forecasts have been provided by multiple forecasting teams, and we aggregate the forecasts to extract the wisdom of the crowd. With only limited information available regarding the historical accuracy of the forecasting teams, we consider aggregation (i.e. combining) methods that do not rely on a record of past accuracy. In this empirical paper, we evaluate the accuracy of aggregation methods that have been previously proposed for interval forecasts and predictions of probability distributions. These include the use of the simple average, the median, and trimming methods, which enable robust estimation and allow the aggregate forecast to reduce the impact of a tendency for the forecasting teams to be under- or overconfident. We use data that has been made publicly available from the COVID-19 Forecast Hub. While the simple average performed well for the high mortality series, we obtained greater accuracy using the median and certain trimming methods for the low and medium mortality series. It will be interesting to see if this remains the case as the pandemic evolves.
I present three types of applications of generalized additive models (GAMs) to COVID-19 mortality rates in the US for the purpose of advancing methods to document inequities with respect to which communities suffered disproportionate COVID-19 mortality rates at specific times during the first three years of the pandemic. First, GAMs can be used to describe the changing relationship between COVID-19 mortality and county-level covariates (sociodemographic, economic, and political metrics) over time. Second, GAMs can be used to perform spatiotemporal smoothing that pools information over time and…
We present an extension of the Li and Lee model to quantify mortality in five European countries during the COVID-19 pandemic. The first two factors are used to model the pre-COVID mortality, with the first layer modelling the common trend and the second layer the country-specific deviation from the common trend. We add a third layer to capture the country-specific impact of COVID-19 in 2020 and 2021 in excess of the pre-COVID trend. We use weekly mortality data from the Short Term Mortality Fluctuations Database to calibrate this third factor, and we use a more granular dataset for deaths in …
The current outbreak of COVID-19 has called renewed attention to the need for sound statistical analysis for monitoring mortality patterns and trends over time. Excess mortality has been suggested as the most appropriate indicator to measure the overall burden of the pandemic on mortality. As such, excess mortality has received considerable interest during the first months of the COVID-19 pandemic. Previous approaches to estimate excess mortality are somewhat limited, as they do not include sufficiently long-term trends, correlations among different demographic and geographic groups, and the a…
In this article, we deal with COVID-19 data to study the trend of the epidemic at the global situation. Choosing the mortality rate as an appropriate metric which measures the relative relation between the cumulative confirmed cases and death cases, we utilize the modified kernel estimator for random density function (Petersen and Muller, 2016) to obtain the density of the mortality rate, and apply Frechet change point detection (Dubey and Muller, 2020) to check if there is any significant change on the dynamic pattern of COVID-19 deaths. The analysis shows that the pattern of global COVID-19 …
In this paper, we propose a Susceptible-Infected-Removal (SIR) model with time fused coefficients. In particular, our proposed model discovers the underlying time homogeneity pattern for the SIR model's transmission rate and removal rate via Bayesian shrinkage priors. MCMC sampling for the proposed method is facilitated by the nimble package in R. Extensive simulation studies are carried out to examine the empirical performance of the proposed methods. We further apply the proposed methodology to analyze different levels of COVID-19 data in the United States.
Coronavirus disease 2019 (COVID-19) is associated with a very high number of casualties in the general population. Assessing the exact magnitude of this number is a non-trivial problem, as relying only on officially reported COVID-19 associated fatalities runs the risk of incurring in several kinds of biases. One of the ways to approach the issue is to compare overall mortality during the pandemic with expected mortality computed using the observed mortality figures of previous years. In this paper, we build on existing methodology and propose two ways to compute expected as well as excess mor…
In this paper, we use SEIR equations to make predictions for the number of mortality due to COVID-19 in İstanbul. Using excess mortality method, we find the number of mortality for the previous three waves in 2020 and 2021. We show that the predictions of our model is consistent with number of moralities for each wave. Furthermore, we predict the number of mortality for the second wave of 2021. We also extend our analysis for Germany, Italy and Turkey to compare the basic reproduction number $R_0$ for Istanbul. Finally, we calculate the number of infected people in Istanbul for herd immunity.
The COVID-19 pandemic so far has caused huge negative impacts on different areas all over the world, and the United States (US) is one of the most affected countries. In this paper, we use methods from the functional data analysis to look into the COVID-19 data in the US. We explore the modes of variation of the data through a functional principal component analysis (FPCA), and study the canonical correlation between confirmed and death cases. In addition, we run a cluster analysis at the state level so as to investigate the relation between geographical locations and the clustering structure.…
Widespread vaccination campaigns have changed the landscape for COVID-19, vastly altering symptoms and reducing morbidity and mortality. We estimate trends in mortality by month of admission and vaccination status among those hospitalised with COVID-19 in England between March 2020 to September 2021, controlling for demographic factors and hospital load. Among 259,727 hospitalised COVID-19 cases, 51,948 (20.0%) experienced mortality in hospital. Hospitalised fatality risk ranged from 40.3% (95% confidence interval 39.4-41.3%) in March 2020 to 8.1% (7.2-9.0%) in June 2021. Older individuals and…
In the United States, from the start of the COVID-19 pandemic to December 31, 2020, 341,199 deaths and more than 19,663,976 infections were recorded. Recent literature establishes that communities with poverty-related health problems, such as obesity, cardiovascular disease, diabetes, and hypertension, are more susceptible to mortality from SARS-CoV-2 infection. Additionally, controversial public health policies implemented by the nation's political leaders have highlighted the socioeconomic inequalities of minorities. Therefore, through multivariate correlational analysis using machine learni…
The COVID-19 pandemic has impacted billions of people around the world. To capture some of these impacts in the United States, we are conducting a nationwide longitudinal survey collecting information about activity and travel-related behaviors and attitudes before, during, and after the COVID-19 pandemic. The survey questions cover a wide range of topics including commuting, daily travel, air travel, working from home, online learning, shopping, and risk perception, along with attitudinal, socioeconomic, and demographic information. The survey is deployed over multiple waves to the same respo…
Comparative Evaluation of Explainable Machine Learning Versus Linear Regression for Predicting County-Level Lung Cancer Mortality Rate in the United States
University of Tennessee Graduate School（田纳西大学研究生院）
As the COVID-19 ravaging through the globe, accurate forecasts of the disease spread is crucial for situational awareness, resource allocation, and public health decision-making. Alternative to the traditional disease surveillance data collected by the United States (US) Centers for Disease Control and Prevention (CDC), big data from Internet such as online search volumes has been previously shown to contain valuable information for tracking infectious disease dynamics. In this study, we evaluate the feasibility of using Internet search volume of relevant queries to track and predict COVID-19 …
Since December 2019, the world has been witnessing the gigantic effect of an unprecedented global pandemic called Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) - COVID-19. So far, 38,619,674 confirmed cases and 1,093,522 confirmed deaths due to COVID-19 have been reported. In the United States (US), the cases and deaths are recorded as 7,833,851 and 215,199. Several timely researches have discussed the local and global effects of the confounding factors on COVID-19 casualties in the US. However, most of these studies considered little about the time varying associations between an…
The ongoing COVID-19 pandemic has brought science to the fore of the public discourse and considering the complexity of the issues involved, with it also the challenge of effective and informative science communication. A particularly contentious topic, in that it is both highly emotional in and of itself, as well as in that it sits at the nexus of the decision-making process regarding the handling of the pandemic, which has effected lockdowns, social behaviour measures, business closures, and others, concerns the recording and the reporting of the disease mortality. To clarify a point which h…
COVID-19 related deaths underestimate the pandemic burden on mortality because they suffer from completeness and accuracy issues. Excess mortality is a popular alternative, as it compares observed with expected deaths based on the assumption that the pandemic did not occur. Expected deaths had the pandemic not occurred depend on population trends, temperature, and spatio-temporal patterns. In addition to this, high geographical resolution is required to examine within country trends and the effectiveness of the different public health policies. In this tutorial, we propose a framework using R …
We aim to assess the impact of a pandemic data point on the calibration of a stochastic multi-population mortality projection model and its resulting projections for future mortality rates. Throughout the paper we put focus on the Li & Lee mortality model, which has become a standard for projecting mortality in Belgium and the Netherlands. We calibrate this mortality model on annual deaths and exposures at the level of individual ages. This type of mortality data is typically collected, produced and reported with a significant delay of -- for some countries -- several years on a platform such …
Background: Most COVID-19 deaths occur among adults, not children, and attention has focused on mitigating COVID-19 burden among adults. However, a tragic consequence of adult deaths is that high numbers of children might lose their parents and caregivers to COVID-19-associated deaths. Methods: We quantified COVID-19-associated caregiver loss and orphanhood in the US and for each state using fertility and excess and COVID-19 mortality data. We assessed burden and rates of COVID-19-associated orphanhood and deaths of custodial and co-residing grandparents, overall and by race/ethnicity. We furt…
Epidemic modeling is an essential tool to understand the spread of the novel coronavirus and ultimately assist in disease prevention, policymaking, and resource allocation. In this article, we establish a state of the art interface between classic mathematical and statistical models and propose a novel space-time epidemic modeling framework to study the spatial-temporal pattern in the spread of infectious disease. We propose a quasi-likelihood approach via the penalized spline approximation and alternatively reweighted least-squares technique to estimate the model. Furthermore, we provide a sh…
The subset selection problem of linear algebra is applied to identify independent patterns of COVID-19 evolution within Brazil. The data consist of a set of mortality curves in states of Brazil. A subset of the most independent curves is selected by using a functional version of the QR matrix decomposition technique with column pivoting. The selected subset is used next as a basis to represent the remaining curves filtering out any data redundancy. For each independent curve, an associated epidemiological region of influence is defined. The results show two main independent curves with a simil…
F. Hoffmann-La Roche Ltd（罗氏制药公司）；Max Planck Institute for Intelligent Systems（马克斯·普朗克智能系统研究所）；ETH Zurich（苏黎世联邦理工学院）；John A. Paulson School of Engineering and Applied Sciences, Harvard University（哈佛大学约翰·A·保尔森工程与应用科学学院）；Beth Israel Deaconess Medical Center, Harvard Medical School（哈佛医学院贝斯以色列女执事医疗中心）；MIT Critical Data, Laboratory for Computational Physiology, Institute for Medical Engineering and Science, Harvard-MIT Health Sciences & Technology（哈佛-麻省理工健康科学与技术研究所医学工程与科学研究所计算生理学实验室MIT关键数据）；University Hospital of Tübingen（蒂宾根大学医院）；Kantonsspital Winterthur（温特图尔州立医院）
Coronavirus Disease 2019 (COVID-19) is an emerging respiratory disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with rapid human-to-human transmission and a high case fatality rate particularly in older patients. Due to the exponential growth of infections, many healthcare systems across the world are under pressure to care for increasing amounts of at-risk patients. Given the high number of infected patients, identifying patients with the highest mortality risk early is critical to enable effective intervention and optimal prioritisation of care. Here, we pre…
Socio-Spatial Patterns of Suicide Mortality in the United States
University of Pittsburgh（匹兹堡大学）；Old Dominion University（老道明大学）；Kaiser Permanente Northern California（凯撒永久北加州医疗中心）；University of California Berkeley（加州大学伯克利分校）；Boston Children’s Hospital（波士顿儿童医院）；Sorbonne Université（索邦大学）；INSERM（法国国家健康与医学研究院）
Updating observations of a signal due to the delays in the measurement process is a common problem in signal processing, with prominent examples in a wide range of fields. An important example of this problem is the nowcasting of COVID-19 mortality: given a stream of reported counts of daily deaths, can we correct for the delays in reporting to paint an accurate picture of the present, with uncertainty? Without this correction, raw data will often mislead by suggesting an improving situation. We present a flexible approach using a latent Gaussian process that is capable of describing the chang…
Currently, Brazil has one of the fastest increasing COVID-19 epidemics in the world, that has caused at least 94 thousand confirmed deaths until now. The city of Sao Paulo is particularly vulnerable because it is the most populous in the country. Analyzing the spatiotemporal dynamics of COVID-19 is important to help the urgent need to integrate better actions to face the pandemic. Thus, this study aimed to analyze the COVID-19 mortality, from March to July 2020, considering the spatio-time architectures, the socio-economic context of the population, and using a fine granular level, in the most…
Estimating the true mortality burden of COVID-19 for every country in the world is a difficult, but crucial, public health endeavor. Attributing deaths, direct or indirect, to COVID-19 is problematic. A more attainable target is the "excess deaths", the number of deaths in a particular period, relative to that expected during "normal times", and we estimate this for all countries on a monthly time scale for 2020 and 2021. The excess mortality requires two numbers, the total deaths and the expected deaths, but the former is unavailable for many countries, and so modeling is required for these c…
In the initial wave of the COVID-19 pandemic we observed great discrepancies in both infection and mortality rates between countries. Besides the biological and epidemiological factors, a multitude of social and economic criteria also influence the extent to which these discrepancies appear. Consequently, there is an active debate regarding the critical socio-economic and health factors that correlate with the infection and mortality rates outcome of the pandemic. Here, we leverage Bayesian model averaging techniques and country level data to investigate the potential of 28 variables, describi…
Covid-19 is responsible for high mortality in all countries, with the maternal population it is no different. Countries with a high rate of maternal mortality have deficiencies in the health care of pregnant women and women who have recently given birth, which will certainly be enhanced in a situation of overload in the health system, as occurred in this pandemic. Understanding the impact of the pandemic on maternal health is essential to discuss public policies and assist in solutions to future crises. With that in mind, we present the Brazilian Obstetric Observatory COVID-19 (OOBr COVID-19).…
A multiple objective space-time forecasting approach is presented involving cyclical curve log-regression, and multivariate time series spatial residual correlation analysis. Specifically, the mean quadratic loss function is minimized in the framework of trigonometric regression. While, in our subsequent spatial residual correlation analysis, maximization of the likelihood allows us to compute the posterior mode in a Bayesian multivariate time series soft-data framework. The presented approach is applied to the analysis of COVID-19 mortality in the first wave affecting the Spanish Communities,…
The coronavirus disease (COVID-19) has spread worldwide with an unprecedented impact on society. In the Philippines, several interventions such as mobility restrictions for different age groups and vaccination prioritization programs have been implemented to reduce the risks of infections and mortality. This study aimed to identify age-sex composition with greater susceptibility, longer hospitalization and higher fatality. The COVID-19 cases from March 2020 to April 2021 provided by the Department of Health Davao Region in the Philippines were analyzed. A Chi-square test was used to determine …
Respiratory complications due to coronavirus disease COVID-19 have claimed tens of thousands of lives in 2020. Many cases of COVID-19 escalate from Severe Acute Respiratory Syndrome (SARS-CoV-2) to viral pneumonia to acute respiratory distress syndrome (ARDS) to death. Extracorporeal membranous oxygenation (ECMO) is a life-sustaining oxygenation and ventilation therapy that may be used for patients with severe ARDS when mechanical ventilation is insufficient to sustain life. While early planning and surgical cannulation for ECMO can increase survival, clinicians report the lack of a risk score…
Mixed Time Series Quasi-Likelihood Models for Uncovering Covid-19 Viral Load and Mortality Dynamics
Loyola University Chicago（芝加哥洛约拉大学）；Southern Methodist University（南方卫理公会大学）；Queen Mary University of London（伦敦大学玛丽女王学院）；University College Dublin（都柏林大学学院）
Forest fires impact on soil, water and biota resources has been widely researched. Although forest fires profoundly impact the atmosphere and air quality across the ecosystems, much less research has been developed to examine its impact on the current pandemic. In-situ air pollution data were utilized to examine the effects of the 2020 forest fire on atmosphere and coronavirus (COVID 19) casualties. The spatiotemporal concentrations of particulate matter (PM2.5 and PM10) and Nitrogen Dioxide (NO2) were collected from August 1 to October 30 for 2020 (fire year) and 2019 (reference year). Both s…
As COVID-19 pandemic progresses, severe flu seasons may happen alongside an increase in cases in cases and death of COVID-19, causing severe burdens on health care resources and public safety. A consequence of a twindemic may be a mixture of two different infections in the same person at the same time, "flurona". Admist the raising trend of "flurona", forecasting both influenza outbreaks and COVID-19 waves in a timely manner is more urgent than ever, as accurate joint real-time tracking of the twindemic aids health organizations and policymakers in adequate preparation and decision making. Und…
We investigate patterns of COVID-19 mortality across 20 Italian regions and their association with mobility, positivity, and socio-demographic, infrastructural and environmental covariates. Notwithstanding limitations in accuracy and resolution of the data available from public sources, we pinpoint significant trends exploiting information in curves and shapes with Functional Data Analysis techniques. These depict two starkly different epidemics; an "exponential" one unfolding in Lombardia and the worst hit areas of the north, and a milder, "flat(tened)" one in the rest of the country -- inclu…
The statistical dynamics of a pathogen within a population depend on a range of factors: population density, the effectiveness and investment into social distancing, public policy measures and non-pharmaceutical interventions (NPIs) are only some examples of factors that influence the number of cases over time by state. This paper outlines an analysis of time series vector quantisation and paritioning of COVID-19 cases in the United States, using a soft-DTW (Dynamic Time Warping) k-means clustering and a k-shape based clustering algorithm to identify internally consistent clusters of case coun…
Indian Institute of Technology, Roorkee（鲁尔基印度理工学院）；UIC（伊利诺伊大学芝加哥分校）；College of Medicine, UIC（伊利诺伊大学芝加哥分校医学院）
COVID19 is now one of the most leading causes of death in the United States. Systemic health, social and economic disparities have put the minorities and economically poor communities at a higher risk than others. There is an immediate requirement to develop a reliable measure of county-level vulnerabilities that can capture the heterogeneity of both vulnerable communities and the COVID19 pandemic. This study reports a COVID19 Vulnerability Index (C19VI) for identification and mapping of vulnerable counties in the United States. We proposed a Random Forest machine learning based COVID19 vulner…
The first cases of COVID-19 in France were detected on January 24, 2020. The number of screening tests carried out and the methodology used to target the patients tested do not allow for a direct computation of the real number of cases and the mortality rate.In this report, we develop a 'mechanistic-statistical' approach coupling a SIR ODE model describing the unobserved epidemiological dynamics, a probabilistic model describing the data acquisition process and a statistical inference method. The objective of this model is not to make forecasts but to estimate the real number of people infecte…
Imperial College London（伦敦帝国理工学院）；National University of Singapore（新加坡国立大学）；University of Copenhagen（哥本哈根大学）
The COVID-19 pandemic has caused over 6.4 million registered deaths to date and has had a profound impact on economic activity. Here, we study the interaction of transmission, mortality, and the economy during the SARS-CoV-2 pandemic from January 2020 to December 2022 across 25 European countries. We adopt a Bayesian Mixed Effects model with auto-regressive terms. We find that increases in disease transmission intensity decreases Gross domestic product (GDP) and increases daily excess deaths, with a longer lasting impact on excess deaths in comparison to GDP, which recovers more rapidly. Broad…
Currently, there are 14 ongoing clinical studies on low dose radiotherapy (LDRT) for COVID-19 pneumonia. An underlying assumption is that irradiation of about 1 Gy is effective at ameliorating viral pneumonia. Its rationale, however, relies on early human case series or animal studies mostly obtained in the pre-antibiotic era, where rigorous statistical analyses were not performed. It therefore remains unclear whether those early data support such assumptions. With standard statistical survival models, and based on a systematic literature review, we re-analyzed 14 radiobiological animal datase…
