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1. Modeling and tracking Covid-19 cases using Big Data analytics on HPCC system platform

   https://doi.org/10.1186/s40537-021-00423-z  

   Villanustre, Flavio ; Chala, Arjuna ; Dev, Roger ; Xu, Lili ; LexisNexis, Jesse Shaw ; Furht, Borko ; Khoshgoftaar, Taghi ( December 2021 , Journal of Big Data)

   Abstract This project is funded by the US National Science Foundation (NSF) through their NSF RAPID program under the title “Modeling Corona Spread Using Big Data Analytics.” The project is a joint effort between the Department of Computer & Electrical Engineering and Computer Science at FAU and a research group from LexisNexis Risk Solutions. The novel coronavirus Covid-19 originated in China in early December 2019 and has rapidly spread to many countries around the globe, with the number of confirmed cases increasing every day. Covid-19 is officially a pandemic. It is a novel infection with serious clinical manifestations, including death, and it has reached at least 124 countries and territories. Although the ultimate course and impact of Covid-19 are uncertain, it is not merely possible but likely that the disease will produce enough severe illness to overwhelm the worldwide health care infrastructure. Emerging viral pandemics can place extraordinary and sustained demands on public health and health systems and on providers of essential community services. Modeling the Covid-19 pandemic spread is challenging. But there are data that can be used to project resource demands. Estimates of the reproductive number (R) of SARS-CoV-2 show that at the beginning of the epidemic, each infected person spreads the virus to at least two others, on average (Emanuel et al. in N Engl J Med. 2020, Livingston and Bucher in JAMA 323(14):1335, 2020). A conservatively low estimate is that 5 % of the population could become infected within 3 months. Preliminary data from China and Italy regarding the distribution of case severity and fatality vary widely (Wu and McGoogan in JAMA 323(13):1239–42, 2020). A recent large-scale analysis from China suggests that 80 % of those infected either are asymptomatic or have mild symptoms; a finding that implies that demand for advanced medical services might apply to only 20 % of the total infected. Of patients infected with Covid-19, about 15 % have severe illness and 5 % have critical illness (Emanuel et al. in N Engl J Med. 2020). Overall, mortality ranges from 0.25 % to as high as 3.0 % (Emanuel et al. in N Engl J Med. 2020, Wilson et al. in Emerg Infect Dis 26(6):1339, 2020). Case fatality rates are much higher for vulnerable populations, such as persons over the age of 80 years (> 14 %) and those with coexisting conditions (10 % for those with cardiovascular disease and 7 % for those with diabetes) (Emanuel et al. in N Engl J Med. 2020). Overall, Covid-19 is substantially deadlier than seasonal influenza, which has a mortality of roughly 0.1 %. Public health efforts depend heavily on predicting how diseases such as those caused by Covid-19 spread across the globe. During the early days of a new outbreak, when reliable data are still scarce, researchers turn to mathematical models that can predict where people who could be infected are going and how likely they are to bring the disease with them. These computational methods use known statistical equations that calculate the probability of individuals transmitting the illness. Modern computational power allows these models to quickly incorporate multiple inputs, such as a given disease’s ability to pass from person to person and the movement patterns of potentially infected people traveling by air and land. This process sometimes involves making assumptions about unknown factors, such as an individual’s exact travel pattern. By plugging in different possible versions of each input, however, researchers can update the models as new information becomes available and compare their results to observed patterns for the illness. In this paper we describe the development a model of Corona spread by using innovative big data analytics techniques and tools. We leveraged our experience from research in modeling Ebola spread (Shaw et al. Modeling Ebola Spread and Using HPCC/KEL System. In: Big Data Technologies and Applications 2016 (pp. 347-385). Springer, Cham) to successfully model Corona spread, we will obtain new results, and help in reducing the number of Corona patients. We closely collaborated with LexisNexis, which is a leading US data analytics company and a member of our NSF I/UCRC for Advanced Knowledge Enablement. The lack of a comprehensive view and informative analysis of the status of the pandemic can also cause panic and instability within society. Our work proposes the HPCC Systems Covid-19 tracker, which provides a multi-level view of the pandemic with the informative virus spreading indicators in a timely manner. The system embeds a classical epidemiological model known as SIR and spreading indicators based on causal model. The data solution of the tracker is built on top of the Big Data processing platform HPCC Systems, from ingesting and tracking of various data sources to fast delivery of the data to the public. The HPCC Systems Covid-19 tracker presents the Covid-19 data on a daily, weekly, and cumulative basis up to global-level and down to the county-level. It also provides statistical analysis for each level such as new cases per 100,000 population. The primary analysis such as Contagion Risk and Infection State is based on causal model with a seven-day sliding window. Our work has been released as a publicly available website to the world and attracted a great volume of traffic. The project is open-sourced and available on GitHub. The system was developed on the LexisNexis HPCC Systems, which is briefly described in the paper. 

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2. Human-network regions as effective geographic units for disease mitigation

   https://doi.org/10.1140/epjds/s13688-023-00426-1  

   Andris, Clio ; Koylu, Caglar ; Porter, Mason A. ( December 2023 , EPJ Data Science)

   Susceptibility to infectious diseases such as COVID-19 depends on how those diseases spread. Many studies have examined the decrease in COVID-19 spread due to reduction in travel. However, less is known about how much functional geographic regions, which capture natural movements and social interactions, limit the spread of COVID-19. To determine boundaries between functional regions, we apply community-detection algorithms to large networks of mobility and social-media connections to construct geographic regions that reflect natural human movement and relationships at the county level in the coterminous United States. We measure COVID-19 case counts, case rates, and case-rate variations across adjacent counties and examine how often COVID-19 crosses the boundaries of these functional regions. We find that regions that we construct using GPS-trace networks and especially commute networks have the lowest COVID-19 case rates along the boundaries, so these regions may reflect natural partitions in COVID-19 transmission. Conversely, regions that we construct from geolocated Facebook friendships and Twitter connections yield less effective partitions. Our analysis reveals that regions that are derived from movement flows are more appropriate geographic units than states for making policy decisions about opening areas for activity, assessing vulnerability of populations, and allocating resources. Our insights are also relevant for policy decisions and public messaging in future emergency situations.

    

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3. Assessing Reliability of Chinese Geotagged Social Media Data for Spatiotemporal Representation of Human Mobility

   https://doi.org/10.3390/ijgi11020145  

   Liu, Lingbo ; Wang, Ru ; Guan, Weihe Wendy ; Bao, Shuming ; Yu, Hanchen ; Fu, Xiaokang ; Liu, Hongqiang ( February 2022 , ISPRS International Journal of Geo-Information)

   Understanding the space-time dynamics of human activities is essential in studying human security issues such as climate change impacts, pandemic spreading, or urban sustainability. Geotagged social media posts provide an open and space-time continuous data source with user locations which is convenient for studying human movement. However, the reliability of Chinese geotagged social media data for representing human mobility remains unclear. This study compares human movement data derived from the posts of Sina Weibo, one of the largest social media software in China, and that of Baidu Qianxi, a high-resolution human movement dataset from ‘Baidu Map’, a popular location-based service in China with 1.3 billion users. Correlation analysis was conducted from multiple dimensions of time periods (weekly and monthly), geographic scales (cities and provinces), and flow directions (inflow and outflow), and a case study on COVID-19 transmission was further explored with such data. The result shows that Sina Weibo data can reveal similar patterns as that of Baidu Qianxi, and that the correlation is higher at the provincial level than at the city level and higher at the monthly scale than at the weekly scale. The study also revealed spatial variations in the degree of similarity between the two sources. Findings from this study reveal the values and properties and spatiotemporal heterogeneity of human mobility data extracted from Weibo tweets, providing a reference for the proper use of social media posts as the data sources for human mobility studies. 

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4. Intracounty modeling of COVID-19 infection with human mobility: Assessing spatial heterogeneity with business traffic, age, and race

   https://doi.org/10.1073/pnas.2020524118  

   Hou, Xiao ; Gao, Song ; Li, Qin ; Kang, Yuhao ; Chen, Nan ; Chen, Kaiping ; Rao, Jinmeng ; Ellenberg, Jordan S. ; Patz, Jonathan A. ( May 2021 , Proceedings of the National Academy of Sciences)

   The COVID-19 pandemic is a global threat presenting health, economic, and social challenges that continue to escalate. Metapopulation epidemic modeling studies in the susceptible–exposed–infectious–removed (SEIR) style have played important roles in informing public health policy making to mitigate the spread of COVID-19. These models typically rely on a key assumption on the homogeneity of the population. This assumption certainly cannot be expected to hold true in real situations; various geographic, socioeconomic, and cultural environments affect the behaviors that drive the spread of COVID-19 in different communities. What’s more, variation of intracounty environments creates spatial heterogeneity of transmission in different regions. To address this issue, we develop a human mobility flow-augmented stochastic SEIR-style epidemic modeling framework with the ability to distinguish different regions and their corresponding behaviors. This modeling framework is then combined with data assimilation and machine learning techniques to reconstruct the historical growth trajectories of COVID-19 confirmed cases in two counties in Wisconsin. The associations between the spread of COVID-19 and business foot traffic, race and ethnicity, and age structure are then investigated. The results reveal that, in a college town (Dane County), the most important heterogeneity is age structure, while, in a large city area (Milwaukee County), racial and ethnic heterogeneity becomes more apparent. Scenario studies further indicate a strong response of the spread rate to various reopening policies, which suggests that policy makers may need to take these heterogeneities into account very carefully when designing policies for mitigating the ongoing spread of COVID-19 and reopening.

    

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5. Twitter reveals human mobility dynamics during the COVID-19 pandemic

   https://doi.org/10.1371/journal.pone.0241957  

   Huang, Xiao ; Li, Zhenlong ; Jiang, Yuqin ; Li, Xiaoming ; Porter, Dwayne ( November 2020 , PLOS ONE)

   Gao, Song (Ed.)

   The current COVID-19 pandemic raises concerns worldwide, leading to serious health, economic, and social challenges. The rapid spread of the virus at a global scale highlights the need for a more harmonized, less privacy-concerning, easily accessible approach to monitoring the human mobility that has proven to be associated with viral transmission. In this study, we analyzed over 580 million tweets worldwide to see how global collaborative efforts in reducing human mobility are reflected from the user-generated information at the global, country, and U.S. state scale. Considering the multifaceted nature of mobility, we propose two types of distance: the single-day distance and the cross-day distance. To quantify the responsiveness in certain geographic regions, we further propose a mobility-based responsive index (MRI) that captures the overall degree of mobility changes within a time window. The results suggest that mobility patterns obtained from Twitter data are amenable to quantitatively reflect the mobility dynamics. Globally, the proposed two distances had greatly deviated from their baselines after March 11, 2020, when WHO declared COVID-19 as a pandemic. The considerably less periodicity after the declaration suggests that the protection measures have obviously affected people’s travel routines. The country scale comparisons reveal the discrepancies in responsiveness, evidenced by the contrasting mobility patterns in different epidemic phases. We find that the triggers of mobility changes correspond well with the national announcements of mitigation measures, proving that Twitter-based mobility implies the effectiveness of those measures. In the U.S., the influence of the COVID-19 pandemic on mobility is distinct. However, the impacts vary substantially among states. 

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