Title: Modeling and tracking Covid-19 cases using Big Data analytics on HPCC system platform
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. more »« less
Background Human movement is one of the forces that drive the spatial spread of infectious diseases. To date, reducing and tracking human movement during the COVID-19 pandemic has proven effective in limiting the spread of the virus. Existing methods for monitoring and modeling the spatial spread of infectious diseases rely on various data sources as proxies of human movement, such as airline travel data, mobile phone data, and banknote tracking. However, intrinsic limitations of these data sources prevent us from systematic monitoring and analyses of human movement on different spatial scales (from local to global). Objective Big data from social media such as geotagged tweets have been widely used in human mobility studies, yet more research is needed to validate the capabilities and limitations of using such data for studying human movement at different geographic scales (eg, from local to global) in the context of global infectious disease transmission. This study aims to develop a novel data-driven public health approach using big data from Twitter coupled with other human mobility data sources and artificial intelligence to monitor and analyze human movement at different spatial scales (from global to regional to local). Methods We will first develop a database with optimized spatiotemporal indexing to store and manage the multisource data sets collected in this project. This database will be connected to our in-house Hadoop computing cluster for efficient big data computing and analytics. We will then develop innovative data models, predictive models, and computing algorithms to effectively extract and analyze human movement patterns using geotagged big data from Twitter and other human mobility data sources, with the goal of enhancing situational awareness and risk prediction in public health emergency response and disease surveillance systems. Results This project was funded as of May 2020. We have started the data collection, processing, and analysis for the project. Conclusions Research findings can help government officials, public health managers, emergency responders, and researchers answer critical questions during the pandemic regarding the current and future infectious risk of a state, county, or community and the effectiveness of social/physical distancing practices in curtailing the spread of the virus. International Registered Report Identifier (IRRID) DERR1-10.2196/24432
Wevodau, Z.; Doshna, B.; Jhala, N.; Akhtar, I.; Obeid, I.; Picone, J.(
, Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB))
Obeid, I.
(Ed.)
The Neural Engineering Data Consortium (NEDC) is developing the Temple University Digital Pathology Corpus (TUDP), an open source database of high-resolution images from scanned pathology samples [1], as part of its National Science Foundation-funded Major Research Instrumentation grant titled “MRI: High Performance Digital Pathology Using Big Data and Machine Learning” [2]. The long-term goal of this project is to release one million images. We have currently scanned over 100,000 images and are in the process of annotating breast tissue data for our first official corpus release, v1.0.0. This release contains 3,505 annotated images of breast tissue including 74 patients with cancerous diagnoses (out of a total of 296 patients). In this poster, we will present an analysis of this corpus and discuss the challenges we have faced in efficiently producing high quality annotations of breast tissue.
It is well known that state of the art algorithms in machine learning require vast amounts of data. Fields such as speech recognition [3], image recognition [4] and text processing [5] are able to deliver impressive performance with complex deep learning models because they have developed large corpora to support training of extremely high-dimensional models (e.g., billions of parameters). Other fields that do not have access to such data resources must rely on techniques in which existing models can be adapted to new datasets [6]. A preliminary version of this breast corpus release was tested in a pilot study using a baseline machine learning system, ResNet18 [7], that leverages several open-source Python tools.
The pilot corpus was divided into three sets: train, development, and evaluation. Portions of these slides were manually annotated [1] using the nine labels in Table 1 [8] to identify five to ten examples of pathological features on each slide. Not every pathological feature is annotated, meaning excluded areas can include focuses particular to these labels that are not used for training. A summary of the number of patches within each label is given in Table 2. To maintain a balanced training set, 1,000 patches of each label were used to train the machine learning model. Throughout all sets, only annotated patches were involved in model development.
The performance of this model in identifying all the patches in the evaluation set can be seen in the confusion matrix of classification accuracy in Table 3. The highest performing labels were background, 97% correct identification, and artifact, 76% correct identification. A correlation exists between labels with more than 6,000 development patches and accurate performance on the evaluation set. Additionally, these results indicated a need to further refine the annotation of invasive ductal carcinoma (“indc”), inflammation (“infl”), nonneoplastic features (“nneo”), normal (“norm”) and suspicious (“susp”).
This pilot experiment motivated changes to the corpus that will be discussed in detail in this poster presentation. To increase the accuracy of the machine learning model, we modified how we addressed underperforming labels. One common source of error arose with how non-background labels were converted into patches. Large areas of background within other labels were isolated within a patch resulting in connective tissue misrepresenting a non-background label. In response, the annotation overlay margins were revised to exclude benign connective tissue in non-background labels.
Corresponding patient reports and supporting immunohistochemical stains further guided annotation reviews. The microscopic diagnoses given by the primary pathologist in these reports detail the pathological findings within each tissue site, but not within each specific slide. The microscopic diagnoses informed revisions specifically targeting annotated regions classified as cancerous, ensuring that the labels “indc” and “dcis” were used only in situations where a micropathologist diagnosed it as such. Further differentiation of cancerous and precancerous labels, as well as the location of their focus on a slide, could be accomplished with supplemental immunohistochemically (IHC) stained slides. When distinguishing whether a focus is a nonneoplastic feature versus a cancerous growth, pathologists employ antigen targeting stains to the tissue in question to confirm the diagnosis. For example, a nonneoplastic feature of usual ductal hyperplasia will display diffuse staining for cytokeratin 5 (CK5) and no diffuse staining for estrogen receptor (ER), while a cancerous growth of ductal carcinoma in situ will have negative or focally positive staining for CK5 and diffuse staining for ER [9]. Many tissue samples contain cancerous and non-cancerous features with morphological overlaps that cause variability between annotators. The informative fields IHC slides provide could play an integral role in machine model pathology diagnostics.
Following the revisions made on all the annotations, a second experiment was run using ResNet18. Compared to the pilot study, an increase of model prediction accuracy was seen for the labels indc, infl, nneo, norm, and null. This increase is correlated with an increase in annotated area and annotation accuracy. Model performance in identifying the suspicious label decreased by 25% due to the decrease of 57% in the total annotated area described by this label. A summary of the model performance is given in Table 4, which shows the new prediction accuracy and the absolute change in error rate compared to Table 3.
The breast tissue subset we are developing includes 3,505 annotated breast pathology slides from 296 patients. The average size of a scanned SVS file is 363 MB. The annotations are stored in an XML format. A CSV version of the annotation file is also available which provides a flat, or simple, annotation that is easy for machine learning researchers to access and interface to their systems. Each patient is identified by an anonymized medical reference number. Within each patient’s directory, one or more sessions are identified, also anonymized to the first of the month in which the sample was taken. These sessions are broken into groupings of tissue taken on that date (in this case, breast tissue). A deidentified patient report stored as a flat text file is also available. Within these slides there are a total of 16,971 total annotated regions with an average of 4.84 annotations per slide. Among those annotations, 8,035 are non-cancerous (normal, background, null, and artifact,) 6,222 are carcinogenic signs (inflammation, nonneoplastic and suspicious,) and 2,714 are cancerous labels (ductal carcinoma in situ and invasive ductal carcinoma in situ.)
The individual patients are split up into three sets: train, development, and evaluation. Of the 74 cancerous patients, 20 were allotted for both the development and evaluation sets, while the remain 34 were allotted for train. The remaining 222 patients were split up to preserve the overall distribution of labels within the corpus. This was done in hope of creating control sets for comparable studies. Overall, the development and evaluation sets each have 80 patients, while the training set has 136 patients.
In a related component of this project, slides from the Fox Chase Cancer Center (FCCC) Biosample Repository (https://www.foxchase.org/research/facilities/genetic-research-facilities/biosample-repository -facility) are being digitized in addition to slides provided by Temple University Hospital. This data includes 18 different types of tissue including approximately 38.5% urinary tissue and 16.5% gynecological tissue. These slides and the metadata provided with them are already anonymized and include diagnoses in a spreadsheet with sample and patient ID. We plan to release over 13,000 unannotated slides from the FCCC Corpus simultaneously with v1.0.0 of TUDP. Details of this release will also be discussed in this poster.
Few digitally annotated databases of pathology samples like TUDP exist due to the extensive data collection and processing required. The breast corpus subset should be released by November 2021. By December 2021 we should also release the unannotated FCCC data. We are currently annotating urinary tract data as well. We expect to release about 5,600 processed TUH slides in this subset. We have an additional 53,000 unprocessed TUH slides digitized. Corpora of this size will stimulate the development of a new generation of deep learning technology. In clinical settings where resources are limited, an assistive diagnoses model could support pathologists’ workload and even help prioritize suspected cancerous cases.
ACKNOWLEDGMENTS
This material is supported by the National Science Foundation under grants nos. CNS-1726188 and 1925494. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
REFERENCES
[1] N. Shawki et al., “The Temple University Digital Pathology Corpus,” in Signal Processing in Medicine and Biology: Emerging Trends in Research and Applications, 1st ed., I. Obeid, I. Selesnick, and J. Picone, Eds. New York City, New York, USA: Springer, 2020, pp. 67 104. https://www.springer.com/gp/book/9783030368432.
[2] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning.” Major Research Instrumentation (MRI), Division of Computer and Network Systems, Award No. 1726188, January 1, 2018 – December 31, 2021. https://www. isip.piconepress.com/projects/nsf_dpath/.
[3] A. Gulati et al., “Conformer: Convolution-augmented Transformer for Speech Recognition,” in Proceedings of the Annual Conference of the International Speech Communication Association (INTERSPEECH), 2020, pp. 5036-5040. https://doi.org/10.21437/interspeech.2020-3015.
[4] C.-J. Wu et al., “Machine Learning at Facebook: Understanding Inference at the Edge,” in Proceedings of the IEEE International Symposium on High Performance Computer Architecture (HPCA), 2019, pp. 331–344. https://ieeexplore.ieee.org/document/8675201.
[5] I. Caswell and B. Liang, “Recent Advances in Google Translate,” Google AI Blog: The latest from Google Research, 2020. [Online]. Available: https://ai.googleblog.com/2020/06/recent-advances-in-google-translate.html. [Accessed: 01-Aug-2021].
[6] V. Khalkhali, N. Shawki, V. Shah, M. Golmohammadi, I. Obeid, and J. Picone, “Low Latency Real-Time Seizure Detection Using Transfer Deep Learning,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2021, pp. 1 7. https://www.isip. piconepress.com/publications/conference_proceedings/2021/ieee_spmb/eeg_transfer_learning/.
[7] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning,” Philadelphia, Pennsylvania, USA, 2020. https://www.isip.piconepress.com/publications/reports/2020/nsf/mri_dpath/.
[8] I. Hunt, S. Husain, J. Simons, I. Obeid, and J. Picone, “Recent Advances in the Temple University Digital Pathology Corpus,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2019, pp. 1–4. https://ieeexplore.ieee.org/document/9037859.
[9] A. P. Martinez, C. Cohen, K. Z. Hanley, and X. (Bill) Li, “Estrogen Receptor and Cytokeratin 5 Are Reliable Markers to Separate Usual Ductal Hyperplasia From Atypical Ductal Hyperplasia and Low-Grade Ductal Carcinoma In Situ,” Arch. Pathol. Lab. Med., vol. 140, no. 7, pp. 686–689, Apr. 2016. https://doi.org/10.5858/arpa.2015-0238-OA.
Background People’s health-related knowledge influences health outcomes, as this knowledge may influence whether individuals follow advice from their doctors or public health agencies. Yet, little attention has been paid to where people obtain health information and how these information sources relate to the quality of knowledge. Objective We aim to discover what information sources people use to learn about health conditions, how these sources relate to the quality of their health knowledge, and how both the number of information sources and health knowledge change over time. Methods We surveyed 200 different individuals at 12 time points from March through September 2020. At each time point, we elicited participants’ knowledge about causes, risk factors, and preventative interventions for 8 viral (Ebola, common cold, COVID-19, Zika) and nonviral (food allergies, amyotrophic lateral sclerosis [ALS], strep throat, stroke) illnesses. Participants were further asked how they learned about each illness and to rate how much they trust various sources of health information. Results We found that participants used different information sources to obtain health information about common illnesses (food allergies, strep throat, stroke) compared to emerging illnesses (Ebola, common cold, COVID-19, Zika). Participants relied mainly on news media, government agencies, and social media for information about emerging illnesses, while learning about common illnesses from family, friends, and medical professionals. Participants relied on social media for information about COVID-19, with their knowledge accuracy of COVID-19 declining over the course of the pandemic. The number of information sources participants used was positively correlated with health knowledge quality, though there was no relationship with the specific source types consulted. Conclusions Building on prior work on health information seeking and factors affecting health knowledge, we now find that people systematically consult different types of information sources by illness type and that the number of information sources people use affects the quality of individuals’ health knowledge. Interventions to disseminate health information may need to be targeted to where individuals are likely to seek out information, and these information sources differ systematically by illness type.
COVID-19 is a continuing global pandemic causing significant changes and modifications in the ways we teach and learn here in the U.S as well as around the world. Most universities, faculty members, and students modified their learning system by incorporating significant online or mixed learning methods/modes to reduce in person contact time and to reduce the spread of the virus. Universities, faculty and students were challenged as they adapted to new learning modules, strategies and approaches. This adaption started in the Spring of 2020 and has continued to date through the Spring of 2022.
The main objective of this project was to investigate faculty perception of STEM student experiences and behavior during the Fall 2020 semester as compared to the Spring 2020 semester as COVID-19 impacts were prolonged. Through a qualitative methodology of zoom interviews administered to 32 STEM faculty members across six U.S. Universities nationwide and a theming scheme, the opinion and narratives of these faculty members were garnered in a round one and round two sets of interviews, in Summer 2020 and then in Spring 2021 (following the semesters of interest).
Some of the main new themes that were detected in faculty interviews during the Fall 2020 semester and which reflect faculty perceptions are represented as follow: COVID-19 impact on student and faculty motivation, COVID-19 impacts on labs and experiential learning, COVID-19 impact on mental health, COVID-19 impact on STEM students' involvement in STEM experiential learning opportunities and research. Other previous themes detected and which are revisited to analyze major differences with those themes obtained during the Spring 2020 are presented and not limited to: extra efforts from professors, student cheating behavior, cheating factors and prevention, student behavioral and performance changes, student struggles and challenges, University response and efforts to the COVID-19 pandemic. We explored the differences in these themes between the semesters to look at noticed adaptations and modifications.
Presented will also be recommendations to improve student and faculty motivation along with strategies to enhance the student learning experience during the COVID-19 pandemic. We report on common findings and suggest future strategies.
In June 2020, at the annual conference of the American Society for Engineering Education (ASEE), which was held entirely online due to the impacts of COVID-19 (SARS-CoV-2), engineering education researchers and social justice scholars diagnosed the spread of two diseases in the United States: COVID-19 and racism. During a virtual workshop (T614A) titled, “Using Power, Privilege, and Intersectionality as Lenses to Understand our Experiences and Begin to Disrupt and Dismantle Oppressive Structures Within Academia,” Drs. Nadia Kellam, Vanessa Svihla, Donna Riley, Alice Pawley, Kelly Cross, Susannah Davis, and Jay Pembridge presented what we might call a pathological analysis of institutionalized racism and various other “isms.” In order to address the intersecting impacts of this double pandemic, they prescribed counter practices and protocols of anti-racism, and strategies against other oppressive “isms” in academia. At the beginning of the virtual workshop, the presenters were pleasantly surprised to see that they had around a hundred attendees. Did the online format of the ASEE conference afford broader exposure of the workshop? Did recent uprising of Black Lives Matter (BLM) protests across the country, and internationally, generate broader interest in their topic?
Whatever the case, at a time when an in-person conference could not be convened without compromising public health safety, ASEE’s virtual conference platform, furnished by Pathable and supplemented by Zoom, made possible the broader social impacts of Dr. Svihla’s land acknowledgement of the unceded Indigenous lands from which she was presenting. Svihla attempted to go beyond a hollow gesture by including a hyperlink in her slides to a COVID-19 relief fund for the Navajo Nation, and encouraged attendees to make a donation as they copied and pasted the link in the Zoom Chat. Dr. Cross’s statement that you are either a racist or an anti-racist at this point also promised broader social impacts in the context of the virtual workshop. You could feel the intensity of the BLM social movements and the broader political climate in the tone of the presenters’ voices. The mobilizing masses on the streets resonated with a cutting-edge of social justice research and education at the ASEE virtual conference. COVID-19 has both exacerbated and made more obvious the unevenness and inequities in our educational practices, processes, and infrastructures.
This paper is an extension of a broader collaborative research project that accounts for how an exceptional group of engineering educators have taken this opportunity to socially broaden their curricula to include not just public health matters, but also contemporary political and social movements. Engineering educators for change and advocates for social justice quickly recognized the affordances of diverse forms of digital technologies, and the possibilities of broadening their impact through educational practices and infrastructures of inclusion, openness, and accessibility. They are makers of what Gary Downy calls “scalable scholarship”—projects in support of marginalized epistemologies that can be scaled up from ideation to practice in ways that unsettle and displace the dominant epistemological paradigm of engineering education.[1] This paper is a work in progress. It marks the beginning of a much lengthier project that documents the key positionality of engineering educators for change, and how they are socially situated in places where they can connect social movements with industrial transitions, and participate in the production of “undone sciences” that address “a structured absence that emerges from relations of inequality.”[2]
In this paper, we offer a brief glimpse into ethnographic data we collected virtually through interviews, participant observation, and digital archiving from March 2019 to August 2019, during the initial impacts of COVID-19 in the United States. The collaborative research that undergirds this paper is ongoing, and what is presented here is a rough and early articulation of ideas and research findings that have begun to emerge through our engagement with engineering educators for change. This paper begins by introducing an image concept that will guide our analysis of how, in this historical moment, forms of social and racial justice are finding their way into the practices of engineering educators through slight changes in pedagogical techniques in response the debilitating impacts of the pandemic. Conceptually, we are interested in how small and subtle changes in learning conditions can socially broaden the impact of engineering educators for change. After introducing the image concept that guides this work, we will briefly discuss methodology and offer background information about the project. Next, we discuss literature that revolves around the question, what is engineering education for? Finally, we introduce the notion of situating engineering education and give readers a brief glimpse into our ethnographic data. The conclusion will indicate future directions for writing, research, and intervention.
Villanustre, Flavio, Chala, Arjuna, Dev, Roger, Xu, Lili, LexisNexis, Jesse Shaw, Furht, Borko, and Khoshgoftaar, Taghi. Modeling and tracking Covid-19 cases using Big Data analytics on HPCC system platform. Retrieved from https://par.nsf.gov/biblio/10353138. Journal of Big Data 8.1 Web. doi:10.1186/s40537-021-00423-z.
Villanustre, Flavio, Chala, Arjuna, Dev, Roger, Xu, Lili, LexisNexis, Jesse Shaw, Furht, Borko, & Khoshgoftaar, Taghi. Modeling and tracking Covid-19 cases using Big Data analytics on HPCC system platform. Journal of Big Data, 8 (1). Retrieved from https://par.nsf.gov/biblio/10353138. https://doi.org/10.1186/s40537-021-00423-z
Villanustre, Flavio, Chala, Arjuna, Dev, Roger, Xu, Lili, LexisNexis, Jesse Shaw, Furht, Borko, and Khoshgoftaar, Taghi.
"Modeling and tracking Covid-19 cases using Big Data analytics on HPCC system platform". Journal of Big Data 8 (1). Country unknown/Code not available. https://doi.org/10.1186/s40537-021-00423-z.https://par.nsf.gov/biblio/10353138.
@article{osti_10353138,
place = {Country unknown/Code not available},
title = {Modeling and tracking Covid-19 cases using Big Data analytics on HPCC system platform},
url = {https://par.nsf.gov/biblio/10353138},
DOI = {10.1186/s40537-021-00423-z},
abstractNote = {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.},
journal = {Journal of Big Data},
volume = {8},
number = {1},
author = {Villanustre, Flavio and Chala, Arjuna and Dev, Roger and Xu, Lili and LexisNexis, Jesse Shaw and Furht, Borko and Khoshgoftaar, Taghi},
}
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