The spreading pattern of COVID-19 differ a lot across the US states under different quarantine measures and reopening policies. We proposed to cluster the US states into distinct communities based on the daily new confirmed case counts via a nonnegative matrix factorization (NMF) followed by a k-means clustering procedure on the coefficients of the NMF basis. A cross-validation method was employed to select the rank of the NMF. Applying the method to the entire study period from March 22 to July 25, we clustered the 49 continental states (including District of Columbia) into 7 groups, two of which contained a single state. To investigate the dynamics of the clustering results over time, the same method was successively applied to the time periods with increment of one week, starting from the period of March 22 to March 28. The results suggested a change point in the clustering in the week starting on May 30, which might be explained by a combined impact of both quarantine measures and reopening policies.
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…
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 global spread of COVID-19, the disease caused by the novel coronavirus SARS-CoV-2, has cast a significant threat to mankind. As the COVID-19 situation continues to evolve, predicting localized disease severity is crucial for advanced resource allocation. This paper proposes a method named COURAGE (COUnty aggRegation mixup AuGmEntation) to generate a short-term prediction of 2-week-ahead COVID-19 related deaths for each county in the United States, leveraging modern deep learning techniques. Specifically, our method adopts a self-attention model from Natural Language Processing, known as th…
We present an interpretable high-resolution spatio-temporal model to estimate COVID-19 deaths together with confirmed cases one-week ahead of the current time, at the county-level and weekly aggregated, in the United States. A notable feature of our spatio-temporal model is that it considers the (a) temporal auto- and pairwise correlation of the two local time series (confirmed cases and death of the COVID-19), (b) dynamics between locations (propagation between counties), and (c) covariates such as local within-community mobility and social demographic factors. The within-community mobility a…
With COVID-19 affecting every country globally and changing everyday life, the ability to forecast the spread of the disease is more important than any previous epidemic. The conventional methods of disease-spread modeling, compartmental models, are based on the assumption of spatiotemporal homogeneity of the spread of the virus, which may cause forecasting to underperform, especially at high spatial resolutions. In this paper we approach the forecasting task with an alternative technique - spatiotemporal machine learning. We present COVID-LSTM, a data-driven model based on a Long Short-term M…
In mid of March 2020, Coronaviruses such as COVID-19 is declared as an international epidemic. More than 125000 confirmed cases and 4,607 death cases have been recorded around more than 118 countries. Unfortunately, a coronavirus vaccine is expected to take at least 18 months if it works at all. Moreover, COVID -19 epidemics can mutate into a more aggressive form. Day level information about the COVID -19 spread is crucial to measure the behavior of this new virus globally. Therefore, this study presents a comparison of day level forecasting models on COVID-19 affected cases using time series …
University of Virginia（弗吉尼亚大学）；Biocomplexity Institute and Initiative, University of Virginia（弗吉尼亚大学生物复杂性研究所与倡议中心）
The COVID-19 pandemic represents the most significant public health disaster since the 1918 influenza pandemic. During pandemics such as COVID-19, timely and reliable spatio-temporal forecasting of epidemic dynamics is crucial. Deep learning-based time series models for forecasting have recently gained popularity and have been successfully used for epidemic forecasting. Here we focus on the design and analysis of deep learning-based models for COVID-19 forecasting. We implement multiple recurrent neural network-based deep learning models and combine them using the stacking ensemble technique. …
This paper proposes a cluster-based method to analyze the evolution of multivariate time series and applies this to the COVID-19 pandemic. On each day, we partition countries into clusters according to both their case and death counts. The total number of clusters and individual countries' cluster memberships are algorithmically determined. We study the change in both quantities over time, demonstrating a close similarity in the evolution of cases and deaths. The changing number of clusters of the case counts precedes that of the death counts by 32 days. On the other hand, there is an optimal …
Motivated by the recent outbreak of coronavirus (COVID-19), we propose a stochastic model of epidemic temporal growth and mitigation based on a time-modulated Hawkes process. The model is sufficiently rich to incorporate specific characteristics of the novel coronavirus, to capture the impact of undetected, asymptomatic and super-diffusive individuals, and especially to take into account time-varying counter-measures and detection efforts. Yet, it is simple enough to allow scalable and efficient computation of the temporal evolution of the epidemic, and exploration of what-if scenarios. Compar…
We argue that information from countries who had earlier COVID-19 surges can be used to inform another country's current model, then generating what we call back-to-the-future (BTF) projections. We show that these projections can be used to accurately predict future COVID-19 surges prior to an inflection point of the daily infection curve. We show, across 12 different countries from all populated continents around the world, that our method can often predict future surges in scenarios where the traditional approaches would always predict no future surges. However, as expected, BTF projections …
Cumulative COVID-19 case counts by county in Ohio were gathered and combined with population data from the Census Bureau and student enrollment by county from the Integrated Postsecondary Education Data System (IPEDS) for colleges or universities that compete in NCAA sports. Monthly median percent increases, monthly average percent increases, and average cases per 100k of COVID cases between counties with colleges and counties without colleges were calculated. The Wilcoxon test was used to determine if the samples were similar, and the analysis found the differences were statistically signific…
Obtaining up to date information on the number of UK COVID-19 regional infections is hampered by the reporting lag in positive test results for people with COVID-19 symptoms. In the UK, for "Pillar 2" swab tests for those showing symptoms, it can take up to five days for results to be collated. We make use of the stability of the under reporting process over time to motivate a statistical temporal model that infers the final total count given the partial count information as it arrives. We adopt a Bayesian approach that provides for subjective priors on parameters and a hierarchical structure …
The coronavirus disease 2019 (COVID-19) has become a public health emergency of international concern affecting 201 countries and territories around the globe. As of April 4, 2020, it has caused a pandemic outbreak with more than 11,16,643 confirmed infections and more than 59,170 reported deaths worldwide. The main focus of this paper is two-fold: (a) generating short term (real-time) forecasts of the future COVID-19 cases for multiple countries; (b) risk assessment (in terms of case fatality rate) of the novel COVID-19 for some profoundly affected countries by finding various important demog…
Spatio-temporal models for count data are required in a wide range of scientific fields and they have become particularly crucial nowadays because of their ability to analyse COVID-19-related data. Models for count data are needed when the variable of interest take only non-negative integer values and these integers arise from counting occurrences. Several R-packages are currently available to deal with spatiotemporal areal count data. Each package focuses on different models and/or statistical methodologies. Unfortunately, the results generated by these models are rarely comparable due to dif…
We propose, implement, and evaluate a method to estimate the daily number of new symptomatic COVID-19 infections, at the level of individual U.S. counties, by deconvolving daily reported COVID-19 case counts using an estimated symptom-onset-to-case-report delay distribution. Importantly, we focus on estimating infections in real-time (rather than retrospectively), which poses numerous challenges. To address these, we develop new methodology for both the distribution estimation and deconvolution steps, and we employ a sensor fusion layer (which fuses together predictions from models that are tr…
This study explored the association between the five key air pollutants (Nitrogen Dioxide (NO2), Sulphur Dioxide (SO2), Particulate Matter (PM2.5, PM10), and Carbon Monoxide (CO)) and COVID-19 incidences in India. The COVID-19 confirmed cases, air pollution concentration and meteorological variables (temperature, wind speed, surface pressure) for district and city scale were obtained for 2019 and 2020. The location-based air pollution observations were converted to a raster surface using interpolation. The deaths and positive cases are reported so far were found highest in Mumbai (436 and 1139…
The academic, socioemotional, and health impacts of school policies throughout the COVID-19 pandemic have been a source of many important questions that require accurate information about the extent of onsite schooling that has been occurring throughout the pandemic. This paper investigates school operational status data sources during the COVID-19 pandemic, comparing self-report data collected nationally on the household level through a Facebook-based survey with data collected at district and county levels throughout the country. The percentage of households reporting in-person instruction w…
Facing the world wide coronavirus disease 2019 (COVID-19) pandemic, a new fitting method (QDF, quasi-distribution fitting) which could be used to analyze the data of COVID-19 is developed based on piecewise quasi-uniform B-spline curves. For any given country or district, it simulates the distribution histogram data which is made from the daily confirmed cases (or the other data including daily recovery cases and daily fatality cases) of the COVID-19 with piecewise quasi-uniform B-spline curves. Being dealt with area normalization method, the fitting curves could be regarded as a kind of proba…
Anticipating the quantity of new associated or affirmed cases with novel coronavirus ailment 2019 (COVID-19) is critical in the counteraction and control of the COVID-19 flare-up. The new associated cases with COVID-19 information were gathered from 20 January 2020 to 21 July 2020. We filtered out the countries which are converging and used those for training the network. We utilized the SARIMAX, Linear regression model to anticipate new suspected COVID-19 cases for the countries which did not converge yet. We predict the curve of non-converged countries with the help of proposed Statistical S…
Official counts of COVID-19 deaths have been criticized for potentially including people who did not die of COVID-19 but merely died with COVID-19. I address that critique by fitting a generalized additive model to weekly counts of all deaths registered in England and Wales during the 2010s. The model produces baseline rates of death registrations expected without the COVID-19 pandemic, and comparing those baselines to recent counts of registered deaths exposes the emergence of excess deaths late in March 2020. By April's end, England and Wales registered 45,300 $\pm$ 3200 excess deaths of adu…
University of California, Berkeley（加利福尼亚大学伯克利分校）；University of California, San Francisco（加利福尼亚大学旧金山分校）；Chan Zuckerberg Biohub（陈·扎克伯格生物中心）
As the COVID-19 outbreak evolves, accurate forecasting continues to play an extremely important role in informing policy decisions. In this paper, we present our continuous curation of a large data repository containing COVID-19 information from a range of sources. We use this data to develop predictions and corresponding prediction intervals for the short-term trajectory of COVID-19 cumulative death counts at the county-level in the United States up to two weeks ahead. Using data from January 22 to June 20, 2020, we develop and combine multiple forecasts using ensembling techniques, resulting…
The screening testing is an effective tool to control the early spread of an infectious disease such as COVID-19. When the total testing capacity is limited, we aim to optimally allocate testing resources among n counties. We build a (weighted) commute network on counties, with the weight between two counties a decreasing function of their traffic distance. We introduce a network-based disease model, in which the number of newly confirmed cases of each county depends on the numbers of hidden cases of all counties on the network. Our proposed testing allocation strategy first uses historical da…
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…
The ongoing COVID-19 pandemic has progressed with varying degrees of intensity in individual countries, suggesting it is important to analyse factors that vary between them. We study measures of `population-weighted density', which capture density as perceived by a randomly chosen individual. These measures of population density can significantly explain variation in the initial rate of spread of COVID-19 between countries within Europe. However, such measures do not explain differences on a global scale, particularly when considering countries in East Asia, or looking later into the epidemics…
In the last year many public health decisions were based on real-time monitoring the spread of the ongoing COVID-19 pandemic. For this one often considers the reproduction number which measures the amount of secondary cases produced by a single infectious individual. While estimates of this quantity are readily available on the national level, subnational estimates, e.g. on the county level, pose more difficulties since only few incidences occur there. However, as countermeasures to the pandemic are usually enforced on the subnational level, such estimates are of great interest to assess the e…
We introduce a minimalist outbreak forecasting model that combines data-driven parameter estimation with variational data assimilation. By focusing on the fundamental components of nonlinear disease transmission and representing data in a domain where model stochasticity simplifies into a process with independent increments, we design an approach that only requires four core parameters to be estimated. We illustrate this novel methodology on COVID-19 forecasts. Results include case count and deaths predictions for the US and all of its 50 states, the District of Columbia, and Puerto Rico. The …
A finite mixture model is used to learn trends from the currently available data on coronavirus (COVID-19). Data on the number of confirmed COVID-19 related cases and deaths for European countries and the United States (US) are explored. A semi-supervised clustering approach with positive equivalence constraints is used to incorporate country and state information into the model. The analysis of trends in the rates of cases and deaths is carried out jointly using a mixture of multivariate Gaussian non-linear regression models with a mean trend specified using a generalized logistic function. T…
The continuously growing number of COVID-19 cases pressures healthcare services worldwide. Accurate short-term forecasting is thus vital to support country-level policy making. The strategies adopted by countries to combat the pandemic vary, generating different uncertainty levels about the actual number of cases. Accounting for the hierarchical structure of the data and accommodating extra-variability is therefore fundamental. We introduce a new modelling framework to describe the course of the pandemic with great accuracy, and provide short-term daily forecasts for every country in the world…
The success of public health policies aimed at curtailing the COVID-19 pandemic have relied on large-scale and protracted compliance by the public. A series of studies have recently argued that previous voting patterns are important predictors of such compliance. Our research further investigates such connection by tracking the relationships between parties' vote shares and mobility in six European countries over an extended period of time. We observe that while vote shares are occasionally related to variations in mobility within each country, there is no systematic pattern of decrease or inc…
Previous research has shown mixed evidence on the associations between mobility data and COVID-19 case rates, analysis of which is complicated by differences between places on factors influencing both behavior and health outcomes. We aimed to evaluate the county-level impact of shifting the distribution of mobility on the growth in COVID-19 case rates from June 1 - November 14, 2020. We utilized a modified treatment policy (MTP) approach, which considers the impact of shifting an exposure away from its observed value. The MTP approach facilitates studying the effects of continuous exposures wh…
During an ongoing epidemic, especially in the case of a new agent, data are partial and sparse, also affected by external factors as for example climatic effects or preparedness and response capability of healthcare structures. Despite that we showed how, under some universality assumptions, it is possible to extract strategic insights by modelling the pandemic trough a probabilistic Polya urn scheme. In the Polya framework, we provide both the distribution of infected cases and the asymptotic estimation of the incidence rate, showing that data are consistent with a general underlying process …
This paper introduces a dynamic panel SIR (DP-SIR) model to investigate the impact of non-pharmaceutical interventions (NPIs) on the COVID-19 transmission dynamics with panel data from 9 countries across the globe. By constructing scenarios with different combinations of NPIs, our empirical findings suggest that countries may avoid the lockdown policy with imposing school closure, mask wearing and centralized quarantine to reach similar outcomes on controlling the COVID-19 infection. Our results also suggest that, as of April 4th, 2020, certain countries such as the U.S. and Singapore may requ…
We point out an instantiation of Simpson's paradox in Covid-19 case fatality rates (CFRs): comparing a large-scale study from China (17 Feb) with early reports from Italy (9 Mar), we find that CFRs are lower in Italy for every age group, but higher overall. This phenomenon is explained by a stark difference in case demographic between the two countries. Using this as a motivating example, we introduce basic concepts from mediation analysis and show how these can be used to quantify different direct and indirect effects when assuming a coarse-grained causal graph involving country, age, and cas…
Are COVID-19 fatalities large when a federal government does not enforce containment policies and instead allow states to implement their own policies? We answer this question by developing a stochastic extension of a SIRD epidemiological model for a country composed of multiple states. Our model allows for interstate mobility. We consider three policies: mask mandates, stay-at-home orders, and interstate travel bans. We fit our model to daily U.S. state-level COVID-19 death counts and exploit our estimates to produce various policy counterfactuals. While the restrictions imposed by some state…
The number of Covid-19 cases is increasing dramatically worldwide. Therefore, the availability of reliable forecasts for the number of cases in the coming days is of fundamental importance. We propose a simple statistical method for short-term real-time forecasting of the number of Covid-19 cases and fatalities in countries that are latecomers -- i.e., countries where cases of the disease started to appear some time after others. In particular, we propose a penalized (LASSO) regression with an error correction mechanism to construct a model of a latecomer in terms of the other countries that w…
Princeton University（普林斯顿大学）；New York University（纽约大学）
With the severity of the COVID-19 outbreak, we characterize the nature of the growth trajectories of counties in the United States using a novel combination of spectral clustering and the correlation matrix. As the U.S. and the rest of the world are experiencing a severe second wave of infections, the importance of assigning growth membership to counties and understanding the determinants of the growth are increasingly evident. Subsequently, we select the demographic features that are most statistically significant in distinguishing the communities. Lastly, we effectively predict the future gr…
