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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SymptomID: A Framework for Rapid Symptom Identification in Pandemics Using News Reports
The ability to quickly learn fundamentals about a new infectious disease, such as how it is transmitted, the incubation period, and related symptoms, is crucial in any novel pandemic. For instance, rapid identification of symptoms can enable interventions for dampening the spread of the disease. Traditionally, symptoms are learned from research publications associated with clinical studies. However, clinical studies are often slow and time intensive, and hence delays can have dire consequences in a rapidly spreading pandemic like we have seen with COVID-19. In this article, we introduce SymptomID, a modular artificial intelligence–based framework for rapid identification of symptoms associated with novel pandemics using publicly available news reports. SymptomID is built using the state-of-the-art natural language processing model (Bidirectional Encoder Representations for Transformers) to extract symptoms from publicly available news reports and cluster-related symptoms together to remove redundancy. Our proposed framework requires minimal training data, because it builds on a pre-trained language model. In this study, we present a case study of SymptomID using news articles about the current COVID-19 pandemic. Our COVID-19 symptom extraction module, trained on 225 articles, achieves an F1 score of over 0.8. SymptomID can correctly identify well-established symptoms (e.g., “fever” and “cough”) and less-prevalent symptoms (e.g., “rashes,” “hair loss,” “brain fog”) associated with the novel coronavirus. We believe this framework can be extended and easily adapted in future pandemics to quickly learn relevant insights that are fundamental for understanding and combating a new infectious disease.
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- Award ID(s):
- 2031546
- NSF-PAR ID:
- 10265913
- Date Published:
- Journal Name:
- ACM Transactions on Management Information Systems
- Volume:
- 12
- Issue:
- 4
- ISSN:
- 2158-656X
- Page Range / eLocation ID:
- 1 to 17
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Nicewonger, Todd E. ; McNair, Lisa D. ; Fritz, Stacey (Ed.)https://pressbooks.lib.vt.edu/alaskanative/ At the start of the pandemic, the editors of this annotated bibliography initiated a remote (i.e., largely virtual) ethnographic research project that investigated how COVID-19 was impacting off-site modular construction practices in Alaska Native communities. Many of these communities are located off the road system and thus face not only dramatically higher costs but multiple logistical challenges in securing licensed tradesmen and construction crews and in shipping building supplies and equipment to their communities. These barriers, as well as the region’s long winters and short building seasons, complicate the construction of homes and related infrastructure projects. Historically, these communities have also grappled with inadequate housing, including severe overcrowding and poor-quality building stock that is rarely designed for northern Alaska’s climate (Marino 2015). Moreover, state and federal bureaucracies and their associated funding opportunities often further complicate home building by failing to accommodate the digital divide in rural Alaska and the cultural values and practices of Native communities.[1] It is not surprising, then, that as we were conducting fieldwork for this project, we began hearing stories about these issues and about how the restrictions caused by the pandemic were further exacerbating them. Amidst these stories, we learned about how modular home construction was being imagined as a possible means for addressing both the complications caused by the pandemic and the need for housing in the region (McKinstry 2021). As a result, we began to investigate how modular construction practices were figuring into emergent responses to housing needs in Alaska communities. We soon realized that we needed to broaden our focus to capture a variety of prefabricated building methods that are often colloquially or idiomatically referred to as “modular.” This included a range of prefabricated building systems (e.g., manufactured, volumetric modular, system-built, and Quonset huts and other reused military buildings[2]). Our further questions about prefabricated housing in the region became the basis for this annotated bibliography. Thus, while this bibliography is one of multiple methods used to investigate these issues, it played a significant role in guiding our research and helped us bring together the diverse perspectives we were hearing from our interviews with building experts in the region and the wider debates that were circulating in the media and, to a lesser degree, in academia. The actual research for each of three sections was carried out by graduate students Lauren Criss-Carboy and Laura Supple.[3] They worked with us to identify source materials and their hard work led to the team identifying three themes that cover intersecting topics related to housing security in Alaska during the pandemic. The source materials collected in these sections can be used in a variety of ways depending on what readers are interested in exploring, including insights into debates on housing security in the region as the pandemic was unfolding (2021-2022). The bibliography can also be used as a tool for thinking about the relational aspects of these themes or the diversity of ways in which information on housing was circulating during the pandemic (and the implications that may have had on community well-being and preparedness). That said, this bibliography is not a comprehensive analysis. Instead, by bringing these three sections together with one another to provide a snapshot of what was happening at that time, it provides a critical jumping off point for scholars working on these issues. The first section focuses on how modular housing figured into pandemic responses to housing needs. In exploring this issue, author Laura Supple attends to both state and national perspectives as part of a broader effort to situate Alaska issues with modular housing in relation to wider national trends. This led to the identification of multiple kinds of literature, ranging from published articles to publicly circulated memos, blog posts, and presentations. These materials are important source materials that will likely fade in the vastness of the Internet and thus may help provide researchers with specific insights into how off-site modular construction was used – and perhaps hyped – to address pandemic concerns over housing, which in turn may raise wider questions about how networks, institutions, and historical experiences with modular construction are organized and positioned to respond to major societal disruptions like the pandemic. As Supple pointed out, most of the material identified in this review speaks to national issues and only a scattering of examples was identified that reflect on the Alaskan context. The second section gathers a diverse set of communications exploring housing security and homelessness in the region. The lack of adequate, healthy housing in remote Alaska communities, often referred to as Alaska’s housing crisis, is well-documented and preceded the pandemic (Guy 2020). As the pandemic unfolded, journalists and other writers reported on the immense stress that was placed on already taxed housing resources in these communities (Smith 2020; Lerner 2021). The resulting picture led the editors to describe in their work how housing security in the region exists along a spectrum that includes poor quality housing as well as various forms of houselessness including, particularly relevant for the context, “hidden homelessness” (Hope 2020; Rogers 2020). The term houseless is a revised notion of homelessness because it captures a richer array of both permanent and temporary forms of housing precarity that people may experience in a region (Christensen et al. 2107). By identifying sources that reflect on the multiple forms of housing insecurity that people were facing, this section highlights the forms of disparity that complicated pandemic responses. Moreover, this section underscores ingenuity (Graham 2019; Smith 2020; Jason and Fashant 2021) that people on the ground used to address the needs of their communities. The third section provides a snapshot from the first year of the pandemic into how CARES Act funds were allocated to Native Alaska communities and used to address housing security. This subject was extremely complicated in Alaska due to the existence of for-profit Alaska Native Corporations and disputes over eligibility for the funds impacted disbursements nationwide. The resources in this section cover that dispute, impacts of the pandemic on housing security, and efforts to use the funds for housing as well as barriers Alaska communities faced trying to secure and use the funds. In summary, this annotated bibliography provides an overview of what was happening, in real time, during the pandemic around a specific topic: housing security in largely remote Alaska Native communities. The media used by housing specialists to communicate the issues discussed here are diverse, ranging from news reports to podcasts and from blogs to journal articles. This diversity speaks to the multiple ways in which information was circulating on housing at a time when the nightly news and radio broadcasts focused heavily on national and state health updates and policy developments. Finding these materials took time, and we share them here because they illustrate why attention to housing security issues is critical for addressing crises like the pandemic. For instance, one theme that emerged out of a recent National Science Foundation workshop on COVID research in the North NSF Conference[4] was that Indigenous communities are not only recovering from the pandemic but also evaluating lessons learned to better prepare for the next one, and resilience will depend significantly on more—and more adaptable—infrastructure and greater housing security.more » « less
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The COVID-19 pandemic highlighted two critical barriers hindering rapid response to novel pathogens. These include inefficient use of existing biological knowledge about treatments, compounds, gene interactions, proteins, etc. to fight new diseases, and the lack of assimilation and analysis of the fast-growing knowledge about new diseases to quickly develop new treatments, vaccines, and compounds. Overcoming these critical challenges has the potential to revolutionize global preparedness for future pandemics. Accordingly, this article introduces a novel knowledge graph application that functions as both a repository of life science knowledge and an analytics platform capable of extracting time-sensitive insights to uncover evolving disease dynamics and, importantly, researchers' evolving understanding. Specifically, we demonstrate how to extract time-bounded key concepts, also leveraging existing ontologies, from evolving scholarly articles to create a single temporal connected source of truth specifically related to COVID-19. By doing so, current knowledge can be promptly accessed by both humans and machines, from which further understanding of disease outbreaks can be derived. We present key findings from the temporal analysis, applied to a subset of the resulting knowledge graph known as the temporal keywords knowledge graph, and delve into the detailed capabilities provided by this innovative approach.more » « less
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Fernández-Alcántara, Manuel (Ed.)Background Nurse identification of patient deterioration is critical, particularly during the COVID-19 pandemic, as patients can deteriorate quickly. While the literature has shown that nurses rely on intuition to make decisions, there is limited information on what sources of data experienced nurses utilize to inform their intuition. The objectives of this study were to identify sources of data that inform nurse decision-making related to recognition of deteriorating patients, and explore how COVID-19 has impacted nurse decision-making. Methods In this qualitative study, experienced nurses voluntarily participated in focused interviews. During focused interviews, expert nurses were asked to share descriptions of memorable patient encounters, and questions were posed to facilitate reflections on thoughts and actions that hindered or helped their decision-making. They were also asked to consider the impact of COVID-19 on nursing and decision-making. Interviews were transcribed verbatim, study team members reviewed transcripts and coded responses, and organized key findings into themes. Results Several themes related to decision-making were identified by the research team, including: identifying patient care needs, workload management, and reflecting on missed care opportunities to inform learning. Participants (n = 10) also indicated that COVID-19 presented a number of unique barriers to nurse decision-making. Conclusions Findings from this study indicate that experienced nurses utilize several sources of information to inform their intuition. It is apparent that the demands on nurses in response to pandemics are heightened. Decision-making themes drawn from participants’ experiences can to assist nurse educators for training nursing students on decision-making for deteriorating patients and how to manage the potential barriers (e.g., resource constraints, lack of family) associated with caring for patients during these challenging times prior to encountering these issues in the clinical environment. Nurse practice can utilize these findings to increase awareness among experienced nurses on recognizing how pandemic situations can impact to their decision-making capability.more » « less
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The ongoing COVID-19 pandemic has justifiably captured the attention of people around the world since late 2019. It has produced in many people a new perspective on or, indeed, a new realization about our potential vulnerability to emerging infectious diseases. However, our species has experienced numerous catastrophic disease pandemics in the past, and in addition to concerns about the harm being produced during the pandemic and the potential long-term sequelae of the disease, what has been frustrating for many public health experts, anthropologists, and historians is awareness that many of the outcomes of COVID-19 are not inevitable and might have been preventable had we actually heeded lessons from the past. We are currently witnessing variation in exposure risk, symptoms, and mortality from COVID-19, but these patterns are not surprising given what we know about past pandemics. We review here the literature on the demographic and evolutionary consequences of the Second Pandemic of Plague (ca. fourteenth–nineteenth centuries C.E.) and the 1918 influenza pandemic, two of the most devastating pandemics in recorded human history. These both provide case studies of the ways in which sociocultural and environmental contexts shape the experiences and outcomes of pandemic disease. Many of the factors at work during these past pandemics continue to be reproduced in modern contexts, and ultimately our hope is that by highlighting the outcomes that are at least theoretically preventable, we can leverage our knowledge about past experiences to prepare for and respond to disease today.
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1145/3462441
