Curating a COVID-19 data repository and forecasting county-level death counts in the United States
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）
Nick Altieri, Rebecca L. Barter, James Duncan, Raaz Dwivedi, Karl Kumbier, Xiao Li, Robert Netzorg, Briton Park, Chandan Singh, Yan Shuo Tan, Tiffany Tang, Yu W… 展开作者
Nick Altieri, Rebecca L. Barter, James Duncan, Raaz Dwivedi, Karl Kumbier, Xiao Li, Robert Netzorg, Briton Park, Chandan Singh, Yan Shuo Tan, Tiffany Tang, Yu Wang, Chao Zhang, Bin Yu
备注：
Authors ordered alphabetically. All authors contributed significantly to this work. All collected data, modeling code, forecasts, and visualizations are updated daily and available at \url{https://github.com/Yu-Group/covid19-severity-prediction}
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 in an ensemble we refer to as Combined Linear and Exponential Predictors (CLEP). Our individual predictors include county-specific exponential and linear predictors, a shared exponential predictor that pools data together across counties, an expanded shared exponential predictor that uses data from neighboring counties, and a demographics-based shared exponential predictor. We use prediction errors from the past five days to assess the uncertainty of our death predictions, resulting in generally-applicable prediction intervals, Maximum (absolute) Error Prediction Intervals (MEPI). MEPI achieves a coverage rate of more than 94% when averaged across counties for predicting cumulative recorded death counts two weeks in the future. Our forecasts are currently being used by the non-profit organization, Response4Life, to determine the medical supply need for individual hospitals and have directly contributed to the distribution of medical supplies across the country. We hope that our forecasts and data repository at https://covidseverity.com can help guide necessary county-specific decision-making and help counties prepare for their continued fight against COVID-19.
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）
Virginia Tech（弗吉尼亚理工大学）；Mississippi State University（密西西比州立大学）
Modeling the spatiotemporal nature of the spread of infectious diseases can provide useful intuition in understanding the time-varying aspect of the disease spread and the underlying complex spatial dependency observed in people's mobility patterns. Besides, the county level multiple related time series information can be leveraged to make a forecast on an individual time series. Adding to this challenge is the fact that real-time data often deviates from the unimodal Gaussian distribution assumption and may show some complex mixed patterns. Motivated by this, we develop a deep learning-based …
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…
The Human Flourishing Geographic Index: A County-Level Dataset for the United States, 2013--2023
Institute for Quantitative Social Science, Harvard University（哈佛大学定量社会科学研究所）；Center for Geographic Analysis, Harvard University（哈佛大学地理分析中心）；Geographic Data Science Lab, University of Liverpool（利物浦大学地理数据科学实验室）；Department of Law, Economics and Culture, University of Insubria（Insubria大学法律、经济与文化系）；Department of Political and Social Sciences, University of Catania（卡塔尼亚大学政治与社会科学系）；Department of Economics, University of Insubria（Insubria大学经济学系）
The Burning Index (BI) produced daily by the United States government's National Fire Danger Rating System is commonly used in forecasting the hazard of wildfire activity in the United States. However, recent evaluations have shown the BI to be less effective at predicting wildfires in Los Angeles County, compared to simple point process models incorporating similar meteorological information. Here, we explore the forecasting power of a suite of more complex point process models that use seasonal wildfire trends, daily and lagged weather variables, and historical spatial burn patterns as covar…
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 United States has an opioid epidemic, and Pennsylvania's Allegheny County is among the worst. This motivates a deeper exploration of what characterizes the epidemic, such as what are risk factors for people who ultimately overdose and die due to opioids. We show that some interesting trends and factors can be identified from openly available autopsy data, and demonstrate the power of building an interactive data exploration tool for policy makers. However, there is still a pressing need to incorporate further demographic factors. We show this by using synthetic Electronic Medical Record (E…
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…
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）
While death rates due to diseases of the heart have experienced a sharp decline over the past 50 years, these diseases continue to be the leading cause of death in the United States, and the rate of decline varies by geographic location, race, and gender. We look to harness the power of hierarchical Bayesian methods to obtain a clearer picture of the declines from county-level, temporally varying heart disease death rates for men and women of different races in the US. Specifically, we propose a nonseparable multivariate spatio-temporal Bayesian model which allows for group-specific temporal c…
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…
In this article, we take a step back to distill seven principles out of our experience in the spring of 2020, when our 12-person rapid-response team used skills of data science and beyond to help distribute Covid PPE. This process included tapping into domain knowledge of epidemiology and medical logistics chains, curating a relevant data repository, developing models for short-term county-level death forecasting in the US, and building a website for sharing visualization (an automated AI machine). The principles are described in the context of working with Response4Life, a then-new nonprofit …
Geographic patterns in stroke mortality have been studied as far back as the 1960s, when a region of the southeastern United States became known as the "stroke belt" due to its unusually high rates of stroke mortality. While stroke mortality rates are known to increase exponentially with age, an investigation of spatiotemporal trends by age group at the county-level is daunting due to the preponderance of small population sizes and/or few stroke events by age group. Here, we harness the power of a complex, nonseparable multivariate space-time model which borrows strength across space, time, an…
We study the spatial heterogeneity effect on regional COVID-19 pandemic timing and severity by analyzing the COVID-19 growth rate curves in the United States. We propose a geographically detailed functional data grouping method equipped with a functional conditional autoregressive (CAR) prior to fully capture the spatial correlation in the pandemic curves. The spatial homogeneity pattern can then be detected by a geographically weighted Chinese restaurant process prior which allows both locally spatially contiguous groups and globally discontiguous groups. We design an efficient Markov chain M…
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…
Governments issue "stay at home" orders to reduce the spread of contagious diseases, but the magnitude of such orders' effectiveness is uncertain. In the United States these orders were not coordinated at the national level during the coronavirus disease 2019 (COVID-19) pandemic, which creates an opportunity to use spatial and temporal variation to measure the policies' effect with greater accuracy. Here, we combine data on the timing of stay-at-home orders with daily confirmed COVID-19 cases and fatalities at the county level in the United States. We estimate the effect of stay-at-home orders…
Since two people came down a county of north Seattle with positive COVID-19 (coronavirus-19) in 2019, the current total cases in the United States (U.S.) are over 12 million. Predicting the pandemic trend under effective variables is crucial to help find a way to control the epidemic. Based on available literature, we propose a validated Vector Autoregression (VAR) time series model to predict the positive COVID-19 cases. A real data prediction for U.S. is provided based on the U.S. coronavirus data. The key message from our study is that the situation of the pandemic will getting worse if the…
We have obtained a "hierarchical regionalization" of 3,107 county-level units of the United States based upon census-recorded 1995-2000 intercounty migration flows. The methodology employed was the two-stage (double-standardization and strong component [directed graph] hierarchical clustering) algorithm described in the 2009 PNAS (106 [26], E66) letter (arXiv:0904.4863). Various features (e. g., cosmopolitan vs. provincial aspects, and indices of isolation) of the regionalization have been previously discussed in arXiv:0907.2393, arXiv:0903.3623 and arXiv:0809.2768. However, due to the lengthy…
NASA Jet Propulsion Lab（NASA喷气推进实验室）；UT Dallas（德克萨斯大学达拉斯分校）；Princeton University（普林斯顿大学）
As multiple adverse events in 2021 illustrated, virtually all aspects of our societal functioning -- from water and food security to energy supply to healthcare -- more than ever depend on the dynamics of environmental factors. Nevertheless, the social dimensions of weather and climate are noticeably less explored by the machine learning community, largely, due to the lack of reliable and easy access to use data. Here we present a unique not yet broadly available NASA's satellite dataset on aerosol optical depth (AOD), temperature and relative humidity and discuss the utility of these new data…
Background: Opioid misuse is a major public health issue in the United States and in particular Ohio. However, the burden of the epidemic is challenging to quantify as public health surveillance measures capture different aspects of the problem. Here we synthesize county-level death and treatment counts to compare the relative burden across counties and assess associations with social environmental covariates. Methods: We construct a generalized spatial factor model to jointly model death and treatment rates for each county. For each outcome, we specify a spatial rates parameterization for a P…
Dynamic Spatial Bayesian Machine Learning Model: Applications to Intergenerational Economic Mobility and Geographic Income Inequality in the United States
For epidemics control and prevention, timely insights of potential hot spots are invaluable. Alternative to traditional epidemic surveillance, which often lags behind real time by weeks, big data from the Internet provide important information of the current epidemic trends. Here we present a methodology, ARGOX (Augmented Regression with GOogle data CROSS space), for accurate real-time tracking of state-level influenza epidemics in the United States. ARGOX combines Internet search data at the national, regional and state levels with traditional influenza surveillance data from the Centers for …
Accurate estimates of subnational populations are important for policy formulation and monitoring population health indicators. For example, estimates of the number of women of reproductive age are important to understand the population at risk to maternal mortality and unmet need for contraception. However, in many low-income countries, data on population counts and components of population change are limited, and so levels and trends subnationally are unclear. We present a Bayesian constrained cohort component model for the estimation and projection of subnational populations. The model buil…
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…
Recently, the Centers for Disease Control and Prevention (CDC) has worked with other federal agencies to identify counties with increasing coronavirus disease 2019 (COVID-19) incidence (hotspots) and offers support to local health departments to limit the spread of the disease. Understanding the spatio-temporal dynamics of hotspot events is of great importance to support policy decisions and prevent large-scale outbreaks. This paper presents a spatio-temporal Bayesian framework for early detection of COVID-19 hotspots (at the county level) in the United States. We assume both the observed numb…
Over the past few months, the outbreak of Coronavirus disease (COVID-19) has been expanding over the world. A reliable and accurate dataset of the cases is vital for scientists to conduct related research and for policy-makers to make better decisions. We collect the United States COVID-19 daily reported data from four open sources: the New York Times, the COVID-19 Data Repository by Johns Hopkins University, the COVID Tracking Project at the Atlantic, and the USAFacts, then compare the similarities and differences among them. To obtain reliable data for further analysis, we first examine the …
