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Title: COVID-FACT: A Fully-Automated Capsule Network-Based Framework for Identification of COVID-19 Cases from Chest CT Scans
The newly discovered Coronavirus Disease 2019 (COVID-19) has been globally spreading and causing hundreds of thousands of deaths around the world as of its first emergence in late 2019. The rapid outbreak of this disease has overwhelmed health care infrastructures and arises the need to allocate medical equipment and resources more efficiently. The early diagnosis of this disease will lead to the rapid separation of COVID-19 and non-COVID cases, which will be helpful for health care authorities to optimize resource allocation plans and early prevention of the disease. In this regard, a growing number of studies are investigating the capability of deep learning for early diagnosis of COVID-19. Computed tomography (CT) scans have shown distinctive features and higher sensitivity compared to other diagnostic tests, in particular the current gold standard, i.e., the Reverse Transcription Polymerase Chain Reaction (RT-PCR) test. Current deep learning-based algorithms are mainly developed based on Convolutional Neural Networks (CNNs) to identify COVID-19 pneumonia cases. CNNs, however, require extensive data augmentation and large datasets to identify detailed spatial relations between image instances. Furthermore, existing algorithms utilizing CT scans, either extend slice-level predictions to patient-level ones using a simple thresholding mechanism or rely on a sophisticated infection segmentation to more » identify the disease. In this paper, we propose a two-stage fully automated CT-based framework for identification of COVID-19 positive cases referred to as the “COVID-FACT”. COVID-FACT utilizes Capsule Networks, as its main building blocks and is, therefore, capable of capturing spatial information. In particular, to make the proposed COVID-FACT independent from sophisticated segmentations of the area of infection, slices demonstrating infection are detected at the first stage and the second stage is responsible for classifying patients into COVID and non-COVID cases. COVID-FACT detects slices with infection, and identifies positive COVID-19 cases using an in-house CT scan dataset, containing COVID-19, community acquired pneumonia, and normal cases. Based on our experiments, COVID-FACT achieves an accuracy of 90.82 % , a sensitivity of 94.55 % , a specificity of 86.04 % , and an Area Under the Curve (AUC) of 0.98, while depending on far less supervision and annotation, in comparison to its counterparts. « less
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Frontiers in Artificial Intelligence
Sponsoring Org:
National Science Foundation
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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 infectedmore »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). 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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. 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  5. Abstract Objective

    Online patient portals become important during disruptions to in-person health care, like when cases of coronavirus disease 2019 (COVID-19) and other respiratory viruses rise, yet underlying structural inequalities associated with race, socio-economic status, and other socio-demographic characteristics may affect their use. We analyzed a population-based survey to identify disparities within the United States in access to online portals during the early period of COVID-19 in 2020.

    Materials and Methods

    The National Cancer Institute fielded the 2020 Health and Information National Trends Survey from February to June 2020. We conducted multivariable analysis to identify socio-demographic characteristics of US patients who were offered and accessed online portals, and reasons for nonuse.


    Less than half of insured adult patients reported accessing an online portal in the prior 12 months, and this was less common among patients who are male, are Hispanic, have less than a college degree, have Medicaid insurance, have no regular provider, or have no internet. Reasons for nonuse include: wanting to speak directly to a provider, not having an online record, concerns about privacy, and discomfort with technology.


    Despite the rapid expansion of digital health technologies due to COVID-19, we found persistent socio-demographic disparities in access to patient portals. Ensuringmore »that digital health tools are secure, private, and trustworthy would address some patient concerns that are barriers to portal access.


    Expanding the use of online portals requires explicitly addressing fundamental inequities to prevent exacerbating existing disparities, particularly during surges in cases of COVID-19 and other respiratory viruses that tax health care resources.

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