Novel Coronavirus (COVID-19) has drastically overwhelmed more than 200 countries affecting millions and claiming almost 2 million lives, since its emergence in late 2019. This highly contagious disease can easily spread, and if not controlled in a timely fashion, can rapidly incapacitate healthcare systems. The current standard diagnosis method, the Reverse Transcription Polymerase Chain Reaction (RT- PCR), is time consuming, and subject to low sensitivity. Chest Radiograph (CXR), the first imaging modality to be used, is readily available and gives immediate results. However, it has notoriously lower sensitivity than Computed Tomography (CT), which can be used efficiently to complement other diagnostic methods. This paper introduces a new COVID-19 CT scan dataset, referred to as COVID-CT-MD, consisting of not only COVID-19 cases, but also healthy and participants infected by Community Acquired Pneumonia (CAP). COVID-CT-MD dataset, which is accompanied with lobe-level, slice-level and patient-level labels, has the potential to facilitate the COVID-19 research, in particular COVID-CT-MD can assist in development of advanced Machine Learning (ML) and Deep Neural Network (DNN) based solutions.

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 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.

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The unprecedented COVID-19 pandemic has been remarkably impacting the world and influencing a broad aspect of people's lives since its first emergence in late 2019. The highly contagious nature of the COVID-19 has raised the necessity of developing deep learning-based diagnostic tools to identify the infected cases in the early stages. Recently, we proposed a fully-automated framework based on Capsule Networks, referred to as the CT-CAPS, to distinguish COVID-19 infection from normal and Community Acquired Pneumonia (CAP) cases using chest Computed Tomography (CT) scans. Although CT scans can provide a comprehensive illustration of the lung abnormalities, COVID-19 lung manifestations highly overlap with the CAP findings making their identification challenging even for experienced radiologists. Here, the CT-CAPS is augmented with a wide range of clinical/demographic data, including patients' gender, age, weight and symptoms. More specifically, we propose a hybrid deep learning model that utilizes both clinical/demographic data and CT scans to classify COVID-19 and non-COVID cases using a Random Forest Classifier. The proposed hybrid model specifies the most important predictive factors increasing the explainability of the model. The experimental results show that the proposed hybrid model improves the CT-CAPS performance, achieving accuracy of 90.8%, sensitivity of 94.5% and specificity of 86.0%.

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