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We propose a two-stage Convolutional Neural Network (CNN) based classification framework for detecting COVID-19 and Community-Acquired Pneumonia (CAP) using the chest Computed Tomography (CT) scan images. In the first stage, an infection - COVID-19 or CAP, is detected using a pre-trained DenseNet architecture. Then, in the second stage, a fine-grained three-way classification is done using EfficientNet architecture. The proposed COVID+CAP-CNN framework achieved a slice-level classification accuracy of over 94% at identifying COVID-19 and CAP. Further, the proposed framework has the potential to be an initial screening tool for differential diagnosis of COVID-19 and CAP, achieving a validation accuracy of over 89.3% at the finer three-way COVID-19, CAP, and healthy classification. Within the IEEE ICASSP 2021 Signal Processing Grand Challenge (SPGC) on COVID-19 Diagnosis, our proposed two-stage classification framework achieved an overall accuracy of 90% and sensitivity of .857, .9, and .942 at distinguishing COVID-19, CAP, and normal individuals respectively, to rank first in the evaluation. Code and model weights are available at https://github.com/shubhamchaudhary2015/ct_covid19_c

There is an urgent need for automated methods to assist accurate and effective assessment of COVID-19. Radiology and nucleic acid test (NAT) are complementary COVID-19 diagnosis methods. In this paper, we present an end-to-end multitask learning (MTL) framework (COVID-MTL) that is capable of automated and simultaneous detection (against both radiology and NAT) and severity assessment of COVID-19. COVID-MTL learns different COVID-19 tasks in parallel through our novel random-weighted loss function, which assigns learning weights under Dirichlet distribution to prevent task dominance; our new 3D real-time augmentation algorithm (Shift3D) introduces space variances for 3D CNN components by shifting low-level feature representations of volumetric inputs in three dimensions; thereby, the MTL framework is able to accelerate convergence and improve joint learning performance compared to single-task models. By only using chest CT scans, COVID-MTL was trained on 930 CT scans and tested on separate 399 cases. COVID-MTL achieved AUCs of 0.939 and 0.846, and accuracies of 90.23% and 79.20% for detection of COVID-19 against radiology and NAT, respectively, which outperformed the state-of-the-ar

As COVID-19 ravages the world, social media analytics could augment traditional surveys in assessing how the pandemic evolves and capturing consumer chatter that could help healthcare agencies in addressing it. This typically involves mining disclosure events that mention testing positive for the disease or discussions surrounding perceptions and beliefs in preventative or treatment options. The 2020 shared task on COVID-19 event extraction (conducted as part of the W-NUT workshop during the EMNLP conference) introduced a new Twitter dataset for benchmarking event extraction from COVID-19 tweets. In this paper, we cast the problem of event extraction as extractive question answering using recent advances in continuous prompting in language models. On the shared task test dataset, our approach leads to over 5% absolute micro-averaged F1-score improvement over prior best results, across all COVID-19 event slots. Our ablation study shows that continuous prompts have a major impact on the eventual performance.

The explosion of disinformation accompanying the COVID-19 pandemic has overloaded fact-checkers and media worldwide, and brought a new major challenge to government responses worldwide. Not only is disinformation creating confusion about medical science amongst citizens, but it is also amplifying distrust in policy makers and governments. To help tackle this, we developed computational methods to categorise COVID-19 disinformation. The COVID-19 disinformation categories could be used for a) focusing fact-checking efforts on the most damaging kinds of COVID-19 disinformation; b) guiding policy makers who are trying to deliver effective public health messages and counter effectively COVID-19 disinformation. This paper presents: 1) a corpus containing what is currently the largest available set of manually annotated COVID-19 disinformation categories; 2) a classification-aware neural topic model (CANTM) designed for COVID-19 disinformation category classification and topic discovery; 3) an extensive analysis of COVID-19 disinformation categories with respect to time, volume, false type, media type and origin source.

COVID-19 had a strong and disruptive impact on our society, and yet further analyses on most relevant factors explaining the spread of the pandemic are needed. Interdisciplinary studies linking epidemiological, mobility, environmental, and socio-demographic data analysis can help understanding how historical conditions, concurrent social policies and environmental factors impacted on the evolution of the pandemic crisis. This work deals with a regression analysis linking COVID-19 mortality to socio-demographic, mobility, and environmental data in the US during the first half of 2020, i.e., during the COVID-19 pandemic first wave. This study can provide very useful insights about risk factors enhancing mortality rates before non-pharmaceutical interventions or vaccination campaigns took place. Our cross-sectional ecological regression analysis demonstrates that, when considering the entire US area, the socio-demographic variables globally play the most important role with respect to environmental and mobility variables in describing COVID-19 mortality. Compared to the complete generalized linear model considering all socio-demographic, mobility, and environmental data, the regressio

This paper investigates the application of deep learning models for lung Computed Tomography (CT) image analysis. Traditional deep learning frameworks encounter compatibility issues due to variations in slice numbers and resolutions in CT images, which stem from the use of different machines. Commonly, individual slices are predicted and subsequently merged to obtain the final result; however, this approach lacks slice-wise feature learning and consequently results in decreased performance. We propose a novel slice selection method for each CT dataset to address this limitation, effectively filtering out uncertain slices and enhancing the model's performance. Furthermore, we introduce a spatial-slice feature learning (SSFL) technique\cite{hsu2022} that employs a conventional and efficient backbone model for slice feature training, followed by extracting one-dimensional data from the trained model for COVID and non-COVID classification using a dedicated classification model. Leveraging these experimental steps, we integrate one-dimensional features with multiple slices for channel merging and employ a 2D convolutional neural network (CNN) model for classification. In addition to the

This study compared the effectiveness of COVID-19 control policies, including wearing masks, and the vaccine rates through proportional infection rate in 28 states of the United States using the eSIR model. The effective rate of policies was measured by the difference between the predicted daily infection proportion rate using the data before the policy and the actual daily infection proportion rate. The study suggests that both mask and vaccine policy had a significant impact on mitigating the pandemic. We further explored how different social factors influenced the effectiveness of a specific policy through the linear regression model. Out of 9 factors, the population density, number of hospital beds per 1000 people, and percent of the population over 65 are the most substantial factors on mask policy effectiveness, while public health funding per person, percent of immigration have the most significant influence on vaccine policy effectiveness. This study summarized the effectiveness of different policies and factors they associated with. It can be served as a reference for future covid-19 related policy.

During the COVID-19 pandemic, there has been an emerging need for rapid, dedicated, and point-of-care COVID-19 patient disposition techniques to optimize resource utilization and clinical workflow. In view of this need, we present COVID-MobileXpert: a lightweight deep neural network (DNN) based mobile app that can use chest X-ray (CXR) for COVID-19 case screening and radiological trajectory prediction. We design and implement a novel three-player knowledge transfer and distillation (KTD) framework including a pre-trained attending physician (AP) network that extracts CXR imaging features from a large scale of lung disease CXR images, a fine-tuned resident fellow (RF) network that learns the essential CXR imaging features to discriminate COVID-19 from pneumonia and/or normal cases with a small amount of COVID-19 cases, and a trained lightweight medical student (MS) network to perform on-device COVID-19 patient triage and follow-up. To tackle the challenge of vastly similar and dominant fore- and background in medical images, we employ novel loss functions and training schemes for the MS network to learn the robust features. We demonstrate the significant potential of COVID-MobileXpe

Under the global pandemic of COVID-19, the use of artificial intelligence to analyze chest X-ray (CXR) image for COVID-19 diagnosis and patient triage is becoming important. Unfortunately, due to the emergent nature of the COVID-19 pandemic, a systematic collection of the CXR data set for deep neural network training is difficult. To address this problem, here we propose a patch-based convolutional neural network approach with a relatively small number of trainable parameters for COVID-19 diagnosis. The proposed method is inspired by our statistical analysis of the potential imaging biomarkers of the CXR radiographs. Experimental results show that our method achieves state-of-the-art performance and provides clinically interpretable saliency maps, which are useful for COVID-19 diagnosis and patient triage.

The COVID-19 pandemic has inspired unprecedented data collection and computer vision modelling efforts worldwide, focusing on diagnosis and stratification of COVID-19 from medical images. Despite this large-scale research effort, these models have found limited practical application due in part to unproven generalization of these models beyond their source study. This study investigates the generalizability of key published models using the publicly available COVID-19 Computed Tomography data through cross dataset validation. We then assess the predictive ability of these models for COVID-19 severity using an independent new dataset that is stratified for COVID-19 lung involvement. Each inter-dataset study is performed using histogram equalization, and contrast limited adaptive histogram equalization with and without a learning Gabor filter. The study shows high variability in the generalization of models trained on these datasets due to varied sample image provenances and acquisition processes amongst other factors. We show that under certain conditions, an internally consistent dataset can generalize well to an external dataset despite structural differences between these dataset

We present COVID-Q, a set of 1,690 questions about COVID-19 from 13 sources, which we annotate into 15 question categories and 207 question clusters. The most common questions in our dataset asked about transmission, prevention, and societal effects of COVID, and we found that many questions that appeared in multiple sources were not answered by any FAQ websites of reputable organizations such as the CDC and FDA. We post our dataset publicly at https://github.com/JerryWeiAI/COVID-Q. For classifying questions into 15 categories, a BERT baseline scored 58.1% accuracy when trained on 20 examples per category, and for a question clustering task, a BERT + triplet loss baseline achieved 49.5% accuracy. We hope COVID-Q can help either for direct use in developing applied systems or as a domain-specific resource for model evaluation.

Fighting the ongoing COVID-19 infodemic has been declared as one of the most important focus areas by the World Health Organization since the onset of the COVID-19 pandemic. While the information that is consumed and disseminated consists of promoting fake cures, rumors, and conspiracy theories to spreading xenophobia and panic, at the same time there is information (e.g., containing advice, promoting cure) that can help different stakeholders such as policy-makers. Social media platforms enable the infodemic and there has been an effort to curate the content on such platforms, analyze and debunk them. While a majority of the research efforts consider one or two aspects (e.g., detecting factuality) of such information, in this study we focus on a multifaceted approach, including an API,\url{https://app.swaggerhub.com/apis/yifan2019/Tanbih/0.8.0/} and a demo system,\url{https://covid19.tanbih.org}, which we made freely and publicly available. We believe that this will facilitate researchers and different stakeholders. A screencast of the API services and demo is available.\url{https://youtu.be/zhbcSvxEKMk}

We present COVID-SEE, a system for medical literature discovery based on the concept of information exploration, which builds on several distinct text analysis and natural language processing methods to structure and organise information in publications, and augments search by providing a visual overview supporting exploration of a collection to identify key articles of interest. We developed this system over COVID-19 literature to help medical professionals and researchers explore the literature evidence, and improve findability of relevant information. COVID-SEE is available at http://covid-see.com.

COVID-19 has fundamentally disrupted the way we live. Government bodies, universities, and companies worldwide are rapidly developing technologies to combat the COVID-19 pandemic and safely reopen society. Essential analytics tools such as contact tracing, super-spreader event detection, and exposure mapping require collecting and analyzing sensitive user information. The increasing use of such powerful data-driven applications necessitates a secure, privacy-preserving infrastructure for computation on personal data. In this paper, we analyze two such computing infrastructures under development at the University of Illinois at Urbana-Champaign to track and mitigate the spread of COVID-19. First, we present Safer Illinois, a system for decentralized health analytics supporting two applications currently deployed with widespread adoption: digital contact tracing and COVID-19 status cards. Second, we introduce the RokWall architecture for privacy-preserving centralized data analytics on sensitive user data. We discuss the architecture of these systems, design choices, threat models considered, and the challenges we experienced in developing production-ready systems for sensitive data

We present CAiRE-COVID, a real-time question answering (QA) and multi-document summarization system, which won one of the 10 tasks in the Kaggle COVID-19 Open Research Dataset Challenge, judged by medical experts. Our system aims to tackle the recent challenge of mining the numerous scientific articles being published on COVID-19 by answering high priority questions from the community and summarizing salient question-related information. It combines information extraction with state-of-the-art QA and query-focused multi-document summarization techniques, selecting and highlighting evidence snippets from existing literature given a query. We also propose query-focused abstractive and extractive multi-document summarization methods, to provide more relevant information related to the question. We further conduct quantitative experiments that show consistent improvements on various metrics for each module. We have launched our website CAiRE-COVID for broader use by the medical community, and have open-sourced the code for our system, to bootstrap further study by other researches.

The COVID-19 Open Research Dataset (CORD-19) is a growing resource of scientific papers on COVID-19 and related historical coronavirus research. CORD-19 is designed to facilitate the development of text mining and information retrieval systems over its rich collection of metadata and structured full text papers. Since its release, CORD-19 has been downloaded over 200K times and has served as the basis of many COVID-19 text mining and discovery systems. In this article, we describe the mechanics of dataset construction, highlighting challenges and key design decisions, provide an overview of how CORD-19 has been used, and describe several shared tasks built around the dataset. We hope this resource will continue to bring together the computing community, biomedical experts, and policy makers in the search for effective treatments and management policies for COVID-19.

Clinicians in the frontline need to assess quickly whether a patient with symptoms indeed has COVID-19 or not. The difficulty of this task is exacerbated in low resource settings that may not have access to biotechnology tests. Furthermore, Tuberculosis (TB) remains a major health problem in several low- and middle-income countries and its common symptoms include fever, cough and tiredness, similarly to COVID-19. In order to help in the detection of COVID-19, we propose the extraction of deep features (DF) from chest X-ray images, a technology available in most hospitals, and their subsequent classification using machine learning methods that do not require large computational resources. We compiled a five-class dataset of X-ray chest images including a balanced number of COVID-19, viral pneumonia, bacterial pneumonia, TB, and healthy cases. We compared the performance of pipelines combining 14 individual state-of-the-art pre-trained deep networks for DF extraction with traditional machine learning classifiers. A pipeline consisting of ResNet-50 for DF computation and ensemble of subspace discriminant classifier was the best performer in the classification of the five classes, achi

The global pandemic of COVID-19 has made the public pay close attention to related news, covering various domains, such as sanitation, treatment, and effects on education. Meanwhile, the COVID-19 condition is very different among the countries (e.g., policies and development of the epidemic), and thus citizens would be interested in news in foreign countries. We build a system for worldwide COVID-19 information aggregation containing reliable articles from 10 regions in 7 languages sorted by topics. Our reliable COVID-19 related website dataset collected through crowdsourcing ensures the quality of the articles. A neural machine translation module translates articles in other languages into Japanese and English. A BERT-based topic-classifier trained on our article-topic pair dataset helps users find their interested information efficiently by putting articles into different categories.

TREC-COVID is a community evaluation designed to build a test collection that captures the information needs of biomedical researchers using the scientific literature during a pandemic. One of the key characteristics of pandemic search is the accelerated rate of change: the topics of interest evolve as the pandemic progresses and the scientific literature in the area explodes. The COVID-19 pandemic provides an opportunity to capture this progression as it happens. TREC-COVID, in creating a test collection around COVID-19 literature, is building infrastructure to support new research and technologies in pandemic search.