key: cord-0829098-qwgp76o9 authors: Āswathy, A. L.; Hareendran, S. Anand; VinodChandra, S. S. title: COVID-19 Diagnosis and Severity Detection from CT-Images Using Transfer Learning and Back Propagation Neural Network date: 2021-07-29 journal: J Infect Public Health DOI: 10.1016/j.jiph.2021.07.015 sha: 6337b39f60fbf7283fb440ccddb834e906bae2e9 doc_id: 829098 cord_uid: qwgp76o9 Background: COVID-19 diagnosis in symptomatic patientsis an important factor for arranging the necessary lifesaving facilities like ICU care and ventilator support. For this purpose, we designed a computer-aided diagnosis and severity detection method by using transfer learning and a back propagation neural network. Method: To increase the learning capability, we used data augmentation. Most of the previously done works in this area concentrate on private datasets, but we used two publicly available datasets. The first section diagnose COVID-19 from the input CT image using the transfer learning of the pre-trained network ResNet-50. We used ResNet-50 and DenseNet-201 pre-trained networks for feature extraction and trained a back propagation neural network to classify it into High, Medium, and Low severity. Results: The proposed method for COVID-19 diagnosis gave an accuracy of 98.5% compared with the state-of-the-art methods. The experimental evaluation shows that combining the ResNet-50 and DenseNet-201 features gave more accurate results with the test data. The proposed system for COVID-19 severity detection gave better average classification accuracy of 97.84% compared with the state-of-the-art methods. This enables medical practitioners to identify the resources and treatment plans correctly. Conclusions: This work is useful in the medical field as a first-line severity risk detection that is helpful for medical personnel to plan patient care and assess the need for ICU facilities and ventilator support. A computer-aided system that is helpful to make a care plan for the huge amount of patient inflow each day is sure to be an asset in these turbulent times. 64 65 Coronaviruses cause infections in the lungs and lead to more severe Middle East Respiratory Syndrome and Severe Acute Respiratory Syndrome cases. The World Health Organization (WHO) announced COVID-19 as a Public Health Emergency of International Concern (PHEIC) on January 31, 2020 [1] . On 23rd April, the COVID-19 update by the WHO announced that globally, there were 144,358,956 confirmed cases of COVID-19, including 3,066,113 deaths. Coronaviruses are zoonotic, which means it can be transmitted between animals and people, and the spreading rate is also high. It is essential to diagnose the disease so that the patient can be isolated as soon as possible. Many methods have been used to confirm the suspected COVID-19 cases by clinicians, like real-time Reverse Transcription Polymerase Chain Reaction (RT-PCR), nonPCR tests such as isothermal nucleic acid amplification technology [2] non-contrast chest Computed Tomography (CT) and radiographs [3] , etc. The RT-PCR test has been widely used to confirm COVID-19. The serial CT imaging is helpful to assess the severity of the lung involvement for COVID-19 patients. Number of works were reported for the detection of COVID-19 from X-Ray image data set. The COVIDX-Net, a deep learning framework was developed by Hemdan * Corresponding author ORCID(s): et al [4] . In this work, they analysed the performance of DenseNet-201,VGG19, InceptionV3, ResNetV2, Inception, Xception ResNetV2, and MobileNetV2. They used the data by [5] and [6] . From the analysis, the results obtained from VGG19 and DenseNet-201 models performed well with an accuracy of 90%. A tailored deep learning-based framework, COVID-Net, was developed by Wang and Wong to detect COVID-19 from chest X-ray images [7] . The architecture consists of 1x1 convolutions, depth-wise and residual architecture. They proposed a multi-classification as normal, viral infection, bacterial infection, and COVID-19 infection. They used the data set provided by [5] and [8] and got an accuracy of 83.5%. A study conducted by Aditya Borakati et al. analyzed the efficiency of common imaging modalities, chest X-ray (CXR) and CT, for diagnosis of COVID-19 [9] . In conclusion, the CT has more diagnostic performance than the CXR for COVID-19. CT should be strongly considered in the initial assessment for suspected COVID-19. There exist many methods for the detection of COVID-19 from the CT images. To diagnose the COVID-19, a Self-supervised learning with transfer learning was proposed by He et al. [10] . Zhao et al. proposed a multi-tasking learning approach for the binary classification for COVID-19 [11] . To avoid the scarcity of the limited benchmark datasets for COVID-19, especially in chest CT images, Loey et al. proposed a method that uses data augmentation and CGAN to generate more CT images [12] . Liu 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 J o u r n a l P r e -p r o o f : Preprint submitted to Elsevier Page 3 of 12 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 Table 2 . From the experiments, it was observed that ResNet-50 provided the best results. ResNet, can input an image of size 224x224x3 is the short name of Residual Network that supports Residual Learning. Fig 5. shows the detailed architecture of the COVID-19 detection. In ResNet-50, at the first layer, a kernel size of 7 * 7 convolution and 64 different kernels, all with a stride of size two, is used. After that, max-pooling with a stride of size two is used. In the second convolution, there exists a kernel size of 1x1, 3x3, 1x1, 64, 64, and 256 kernels, respectively. These 3 layers are repeated three times, thus getting a 9-layer feature map. The third block consists of a kernel size of 1x1, 128 kernel, 3x3 128 kernels, and 1x1 512 kernels. It is repeated for four times, giving a feature map of 12 layers. The next block has a kernel size of 1x1, 3x3, 1x1, 256, 256, and 1024 kernels. This process is repeated six times, giving a total of 18 layers. Then next block contains 1x1,512 kernels with two more of 3x3,512 and 1x1,2048, which was repeated 3 times, giving us a total of 9 layers. Finally, the network has an average pool followed by a fully connected layer with 1000 nodes and a softmax function. The gradient vanishing problem caused while CNN addresses the complex problem can be solved using skip connections. By using skip connections, the layer activations of a particular layer are added directly to the activation of some other layer that is deeper in the network. There exist more skip connections and the Rectified Linear : Preprint submitted to Elsevier Page 4 of 12 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 If the system diagnosed the input image as a COVID-19, the Severity Detection module processes the CT image. Fig 6. shows the architecture of the severity detection method for COVID-19 patients. Here COVID-19 positive images of various severity levels are given as input. The metadata of 349 images in the dataset are augmented to get a good number of samples. While analyzing, it is observed that the ResNet-50 and DenseNet-201 are giving the most accurate results. So the training sets and the validation sets features are extracted using the well-known ResNet-50 and DenseNet-201. From the fully connected layer 'fc1000' of ResNet-50 we got 1000 features. In DenseNet-201, network connects each layer to every succeeding layer in a feed-forward manner. So, it is referred to as Dense Convolutional Network (DenseNet-201). The feature maps of all the preceding layers are used as input for each succeeding layer. In this network, each layer receiving a 'collective knowledge' from all the preceding layers. In the DenseNet-201, the connection is added from every previous layer. The advantages of the DenseNet are, the vanishing problem is reduced since it contains feature maps of all preceding layers. It strengthens feature propagations, and it also has less number of parameters. For this work, the features are extracted from the fully connected layer 'fc1000'. That is, in total, we got 2000 image features. Since we have many images, and for each image, we extracted 2000 image features, the dimensionality is reduced using Principal Component Analysis (PCA). The reduced feature set is fed as the input to the feed-forward network and is used to classify the input images into High, Medium, and Low severity. The number of hidden layer neurons used is 10, and the activation function used is Sigmoid. Since weights are adjusted in the steepest descent direction, the backpropagation algorithm doesn't guarantee the fastest convergence. To avoid that, in this work, we used the scaled conjugate gradient backpropagation. Because of the searching along with the conjugate directions in this method produce faster convergence. The results of this study indicate that it was possible to construct an accurate model to find the detection and the severity condition of the patients. To measure the prediction performance in this study, we utilized common evaluation metrics such as Specificity, Sensitivity, Accuracy, and F1-Score. Specificity: It is defined as the ratio of true negatives (the classifier returned) to the total negatives and can be calculated as: Sensitivity: It is defined as the ratio of true positives to the total actual positive and can be calculated as: Accuracy: The accuracy will give the recognition rate of the classifier. It is defined as the ratio of the correct predictions by the classifier to the total number of input data and can be calculated as: Accuracy= F1-score: It is another metric to identity the usefulness of a classifier and it considers both the precision and recall. The higher the F1-score better the predictive power of the classification algorithm. It can be calculated as: For COVID-19 detection, we trained the ResNet-50 with various initialization parameters. We tried with 10, 15, 25, and 30 epochs. The performance of COVID-19 detection is analyzed using Specificity, Sensitivity, Accuracy and F1-Score . Fig 7 shows the Convergence graph of Accuracy and loss function using the ResNet-50 model for the 30 ℎ epoch. Table 3 . shows the accuracy, while analyzed the network with the same hyper parameters with various epochs. From the experiments, we identified that the ResNet-50 with 30th iteration gives better performance. Table 4 . shows the outputs we got from the first section of the proposed method. The method gives a better accuracy 98.5%. Fig 8. shows the corresponding confusion matrix. Here out of 212 COVID-19 images, 209 images are classified into the corresponding class, and only 3 of them are misclassified in the Non-COVID-19 class, thus getting a precision of 98.58%. And from a total of 188 Non-COVID-19 images, only 3 of them are misclassified. The ROC curve corresponding to the output is shown in Fig 9. The value of Area Under the Curve (AUC) is 99.19%, which measures a classifier's performance. Based on the literature and the survey conducted by Ozsahin et.al. [20] several works are reported. Table 5 shows a comparison of the proposed method with the state-of-theart methods. Various methods used a different number of images for training and testing. He et al. used transfer learning approach and the COVID-19 CT dataset, which contains 349 positive CT scans with clinical findings of COVID-19 and 397 negative images and gets an accuracy of 86% [10] . Zhao et al. created a COVID-19 data set and proposed a multitasking learning approach for the binary classification of COVID-19 [11] . They got an accuracy of 89%. Loey et al. explored five different CNN models, namely, VGG16, AlexNet, VGG19, ResNet-50, and GoogleNet used 349 COVID CT scans and 397 Non-COVID CT scans [12] . By analysis, they identified that ResNet-50 is the best performing model and achieved an accuracy of 82.91%. LA-DNN proposed by Liu et al. used 746 public chest positive CT images [13] . Here they performed a binary classification and a description of five lesions on the CT images associated with the positive cases. They got an accuracy of 88.6%. The work proposed by Wang et al. used 3D CT volumes for COVID-19 classification [15] . Each patient's lung region is extracted using a trained UNet and inputted to a 3D deep neural network to predict the probability of COVID-19 infected portions. Here 499 CT volumes were used for training, and 131 CT volumes were used for testing, got an accuracy of 90.1%. Pathak et al. used the ResNet-50 and a 2D CNN for the classification [16] . Additionally, a top-2 smooth loss function with cost-sensitive attributes is also utilized to handle noisy and imbalanced COVID-19 dataset kind of problems. They got an accuracy of 93.02% In the work proposed by Han et al., each 3D chest CT was assigned a patient-level label [17] . 3D instances of all infection areas semantically generated by AD3D-MIL. The AD3D-MIL learned Bernoulli distributions of the bag level labels. They got an accuracy of 97.9%. The work by Harmon et al. the lung segmentation model was trained using AH-Net architecture [18] . The network trained with LIDC dataset consisting of 1018 images and 95 in-house CT volumes. DenseNet-121 architecture is used for classification purposes. They got an accuracy of 90.8%. Jin et al. proposed a method based on CNN and they achieved an accuracy of 94.98% with a data set of 496 COVID-19 and 1385 non-COVID 19 images [21] . Ahuja et al. used data augmentation and used ResNet-18 for the classification [22] . They got an accuracy of 99.4% with a data set of 349 COVID-19 and 397 non-COVID-19 images. The proposed method used publicly available datasets and got an accuracy of 98.5% for the COVID-19 diagnosis. Every hospital has a limited number of ICU facilities and ventilators and hence, the detection of the severity of lung involvement and subsequent need for advanced life support : Preprint submitted to Elsevier Page 7 of 12 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 care is extremely important. With the staggering number of people being admitted into hospitals each day, a system which can assess patient condition and make a calculated risk analysis has become the need of the hour. Since this study's main objective is to classify the severity level of patients, various statistical measures like confusion matrix, specificity, sensitivity, F1-score, and accuracy is employed for this purpose. The results obtained for severity detection are shown in Table 6 . Since it is a multiclass problem, the performance measures are calculated for each of the classes. Confusion matrix obtained from the Back propagation Neural Network shown in Fig 10 . The method achieved a good result with an overall average accuracy of 97.84%. Here class 1 is High severity, class 2 is Medium severity, and class 3 is low severity. Out of 45 class1 (High) test data, 44 are classified correctly. Out of 61 samples from class2 (Medium), one is classified in Class 1 (High), and 4 is classified in class 3 (Low). For class 3, from a total of 103 images, four images are misclassified into class2 (Medium).The ROC curve corresponding to the output shown in Fig. 11 . : Preprint submitted to Elsevier Page 8 of 12 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 Most of the existing works in this area have not used standard datasets. Table 7 . compares the proposed work with the state-of-the-art methods. To the best of our knowledge, this is the first work that evaluates the accuracy of the severity detection method in a standard data set and detects three types of severity (High, Low, Medium). To find out the severity, Changati et al. used a Dense-UNet with anisotropic kernels for segmenting the infected regions [2] . The severity of lung and lobe involvement was measured in this study. For the COVID-19 cases, the Pearson Correlation Coefficient between prediction and ground truth is calculated. Percentage of Opacity (PO), Percentage of High Opacity (PHO), Lung Severity Score (LSS), and Lung High Opacity Score (LHOS) are calculated. The method proposed by Shen et al. used thresholding and adaptive region growing for segmenting the lung volume [26] . Then the pulmonary vessels are segmented and subtracted from the lung region. After that the detection of : Preprint submitted to Elsevier Page 9 of 12 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 Accuracy 87.5% Pu et al. used UNet architecture to first segment the lung boundary and the major vessels; then these two images are registered with the help of bidirectional elastic registration algorithm [25] . To detect the regions associated with pneumonia, a threshold is calculated by finding out the average density of the middle of the lungs. They used a private data set that consists of 72 COVID-19 and 120 other images. He achieved a sensitivity of 95% and specificity of 84%. Tang et al. explore the machine learning algorithm, Random forest, for detecting the severity of COVID-19 patients as severe or non-severe, got an accuracy of 87.5% [28] . The proposed method classified the COVID-19 CT image data set into High, Medium, and Low severity and attained an excellent classification accuracy of 97.84%. As we are aware, the world is now struggling to contain the spread of the new mutant strain of the COVID-19 virus, theoretically supposed to have a 70% more transmission rate. By this work, we are proposing a computer-aided system for rapid diagnosis and prognosis of a large number of CT samples in the shortest possible time. Here we have used the effectiveness of the pre-trained model ResNet-50 for COVID-19 detection and feature extraction by ResNet-50 and DenseNet-201 to estimate the severity of the patients. This is the first model of its kind that can, in a single architecture, both detect and assess the severity of the condition. Earlier works in this area have built models using a significantly less number of datasets. But we have taken a large number of datasets and also yielded an impactful result from the same. The proposed method gave an accuracy of 98.5% with a sensitivity of 98.58% of positivity detection. Similarly, we got an average accuracy of 97.84% for severity detection, which is a highly superlative result compared to earlier works in the field. The proposed work can have profound use in the medical field as a first-line severity risk detection method that can help medical personnel plan patient care, assess the need for ICU facilities and ventilator support. A computer-aided system that can help make a care plan for the huge amount of patient inflow each day is sure to be an asset in these turbulent times. A future scope that we see for this proposed work is a comparison study between the rate of transmission, the severity of lung involvement, and prognosis of patients affected with a new mutant strain of COVID-19 and patients affected with an older strain. In this study, authors have used ResNet-50 architecture which has an image input size of 224x224 for the covid-19 detection. The combined features of ResNet-50 and DensNet-201 are used to detect the severity condition of the patient. DenseNet-201 also has an input processing capability of 224x224. By reducing the input images' size to give as input to the pre-trained network, there is a chance of losing image information. Improved image warping packages has been used while manipulating the images which has helped to minimise such information mislays. Another issue while dealing with the severity detection was the number of samples with the ground truth this has been solved to a great extend by data augmentation. A possible extension or future enhancement of this work can be focusing on severity detection from 3D CT volumes. Authors hereby confirm that there is no conflict of interest or competing interest for this work submitted in this journal. We also confirm that no Funding/Research Grants has been obtained for this work. In addition to this, Non-financial interests like personal relationships or personal beliefs, position on editorial board, advisory board or board of directors or other type of management relationships, writing and/or consulting for educational purposes, expert witness, mentoring relations has not been utilised. Authors have no financial or proprietary interests in any material discussed in this article. This article does not contain any studies with human participants or animals performed by the author. [6]Adrian Rosebrock, "Detecting COVID-19 in X-ray images with Keras, TensorFlow, and Deep Learning", 2020. [7]L. Wang, A. Wong, "Covid-net: A tailored deep convolutional neural network design for detection of COVID-19 cases from chest radiography images", 2020. [8]Kaggle, Kaggle's Chest X-Ray Images (Pneumonia) dataset, 2020. [9]A Borakati, A Perera, J Johnson, T Sood, "Diagnostic accuracy of X-ray versus CT in COVID-19: a propensitymatched database study", BMJ open, vol.10, 2020. [10]He X, Yang X, Zhang S, Zhao J, Zhang Y, Xing E, Xie P, "Sample-efficient deep learning for COVID-19 diagnosis based on CT scans", MedRxiv, 2020. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 Method: To increase the learning capability, we used data augmentation. Most of the previously done works in this area concentrate on private datasets, but we used two publicly available datasets. The first section diagnoses COVID-19 from the input CT image using the transfer learning of the pre-trained network ResNet-50. We used ResNet-50 and DenseNet-201 pre-trained networks for feature extraction and trained a back propagation neural network to classify it into High, Medium, and Low severity. The proposed method for COVID-19 diagnosis gave an accuracy of 98.7% com- Old Manuscript Click here to access/download;Manuscript;elsarticle-template.tex Click here to view linked References 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 Conclusions: This work is useful in the medical field as a first-line severity risk detection that is helpful for medical personnel to plan patient care and assess the need for ICU facilities and ventilator support. A computer-aided system that is helpful to make a care plan for the huge amount of patient inflow each day is sure to be an asset in these turbulent times. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 J o u r n a l P r e -p r o o f imaging is helpful to assess the severity of the lung involvement for COVID-19 patients. Number of works were reported for the detection of COVID-19 from X-Ray image data set. The COVIDX-Net, a deep learning framework was developed by Hemdan et al [4] . In this work, they analysed the performance of DenseNet-201,VGG19, InceptionV3, ResNetV2, Inception, Xception ResNetV2, 20 and MobileNetV2. They used the data by [5] and [6] . From the analysis, the results obtained from VGG19 and DenseNet-201 models performed well with an accuracy of 90%. A tailored deep learning-based framework, COVID-Net, was developed by Wang and Wong to detect COVID-19 from chest X-ray images [7] . The architecture consists of 1x1 convolutions, depth-wise and residual architec- analyzed the efficiency of common imaging modalities, chest X-ray (CXR) and CT, for diagnosis of COVID-19 [9] . In conclusion, the CT has more diagnostic 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 CT-scan dataset [19] and the COVID CT data set [11] . To avoid the gradient vanishing problem, we used the ResNet-50 and the DenseNet-201 architecture. The results obtained are totally in-line with the CO-RADS clinical finding, which provides emphasis to our proposal. 4 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 J o u r n a l P r e -p r o o f For the COVID-19 Severity detection, the metadata of the patient's CT 75 images is also needed. So here we used two publically available data set which was really prooven. The SARS-CoV-2 CT-scan dataset [19] contains both positive and negative data; the data is collected from both males and females. The data set consists 80 of 2482 CT scans, 1252 images are positive, and 1230 images are negative. The images have no standard size. Fig 1. shows a sample image from this data set. This data set consists of 349 CT images. The authors [11] used PyMuPDF software to extract images of patients infected with COVID-19 from scientific 85 articles, and images were collected from hospitals. Metadata were manually extracted and associated with each image: patient age, gender, location, medical history, scan time, the severity of COVID-19, and medical report. The data set 5 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 J o u r n a l P r e -p r o o f Comparing with the SARS-CoV-2 CT-scan dataset, the non-COVID CT images are more complex, and it is really a challenging task to distinguish as either COVID or non-COVID. Fig.2 . shows the sample COVID-19 and non-COVID -19 images. The proposed work aims to find whether a person is COVID positive and 95 assess the patient's severity condition so that the medical team can prepare the facilities needed in advance, such as a ventilator, availability of oxygen, etc. The [11] contains 349 COVID-19 images with the details to predict each patient's severity condition. To build a fully automatic system, we consider the data set [12] and [19] . Since the metadata regarding the COVID-19 severity is available 100 with [11] , we took the data from the COVID-CT dataset for COVID-19 severity detection, and augmentation is applied to get many samples. We used the data Table 1 shows the splitting up of data for the training, validation, and testing. We developed a two-stage architecture for the severity detection of COVID- In the COVID-19 detection, after preprocessing from the input images, a 7 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 J o u r n a l P r e -p r o o f ResNet-50 architecture is used to identify COVID-19. In the COVID-19 severity detection system, we utilize two pre-trained networks, Resnet-50, DenseNet-201, and a backpropagation network, to determine the severity of the COVID-19. The data is divided into 70% for training and 15% for validation, and 15% for testing. The preprocessing is carried out to make the input images are of same size and same bit depth. The images are resized to the corresponding CNN's input 130 size. Deep 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 J o u r n a l P r e -p r o o f 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 J o u r n a l P r e -p r o o f ResNet, can input an image of size 224x224x3 is the short name of Residual Network that supports Residual Learning. Fig 5. shows the detailed architecture of the COVID-19 detection. In ResNet-50, at the first layer, a kernel size 150 of 7 * 7 convolution and 64 different kernels, all with a stride of size two, is used. After that, max-pooling with a stride of size two is used. In the second convolution, there exists a kernel size of 1x1, 3x3, 1x1, 64, 64, and 256 kernels, respectively. These 3 layers are repeated three times, thus getting a 9-layer feature map. The third block consists of a kernel size of 1x1, 128 kernel, 3x3 155 128 kernels, and 1x1 512 kernels. It is repeated for four times, giving a feature map of 12 layers. The next block has a kernel size of 1x1, 3x3, 1x1, 256, 256, and 1024 kernels. This process is repeated six times, giving a total of 18 layers. Then next block contains 1x1,512 kernels with two more of 3x3,512 and 1x1,2048, which was repeated 3 times, giving us a total of 9 layers. Finally, 160 the network has an average pool followed by a fully connected layer with 1000 nodes and a softmax function. The gradient vanishing problem caused while CNN addresses the complex problem can be solved using skip connections. By 10 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 J o u r n a l P r e -p r o o f 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 J o u r n a l P r e -p r o o f 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 The results of this study indicate that it was possible to construct an accurate model to find the detection and the severity condition of the patients. To 200 measure the prediction performance in this study, we utilized common evaluation metrics such as Specificity, Sensitivity, Accuracy, and F1-Score. Specificity: It is defined as the ratio of true negatives (the classifier returned) to the total negatives and can be calculated as: Sensitivity: It is defined as the ratio of true positives to the total actual positive and can be calculated as: Accuracy: The accuracy will give the recognition rate of the classifier. It is defined as the ratio of the correct predictions by the classifier to the total number 210 of input data and can be calculated as: Accuracy= T P +T N T P +T N +F P +F N (3) F-score: It is another metric to identity the usefulness of a classifier and it considers both the precision and recall. The higher the F-score better the predictive power of the classification algorithm. It can be calculated as: For COVID-19 detection, we trained the ResNet-50 with various initialization parameters. We tried with 10, 15, 25, and 30 epochs. The performance 220 of COVID-19 detection is analyzed using Specificity, Sensitivity, Accuracy and 14 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 J o u r n a l P r e -p r o o f Based on the literature and the survey conducted by Ozsahinet. al. [20] 235 several works are reported. Table 5 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 J o u r n a l P r e -p r o o f 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 J o u r n a l P r e -p r o o f 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 J o u r n a l P r e -p r o o f classification [15] . Each patient's lung region is extracted using a trained UNet and inputted to a 3D deep neural network to predict the probability of COVID-19 infected portions. Here 499 CT volumes were used for training, and 131 CT volumes were used for testing, got an accuracy of 90.1%. Pathak et al. used the ResNet-50 and a 2D CNN for the classification [16] . Additionally, a top-2 smooth loss function with cost-sensitive attributes is also utilized to handle noisy and imbalanced COVID-19 dataset kind of problems. They got an accuracy of 93.02% In the work proposed by Han et al., each 3D chest CT was assigned a patientlevel label [17] . 3D instances of all infection areas semantically generated by images. The proposed method used publically available large datasets and got an excellent accuracy of 98.8% for the COVID-19 diagnosis. Every hospital has a limited number of ICU facilities and ventilators and hence, the detection of the severity of lung involvement and subsequent need 280 for advanced life support care is extremely important. With the staggering number of people being admitted into hospitals each day, a system which can assess patient condition and make a calculated risk analysis has become the need of the hour. Since this study's main objective is to classify the severity 19 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 J o u r n a l P r e -p r o o f 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 J o u r n a l P r e -p r o o f sensitivity, F1-score, and accuracy is employed for this purpose. The results obtained for severity detection are shown in Table 6 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 J o u r n a l P r e -p r o o f Most of the existing works in this area have not used standard datasets. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 J o u r n a l P r e -p r o o f 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 and 120 other images. He achieved a sensitivity of 95% and specificity of 84%. Tang et al. explore the machine learning algorithm, Random forest, for detecting the severity of COVID-19 patients as severe or non-severe, got an accuracy of 87.5% [28] . The proposed method classified the COVID-19 CT image data set into High, Medium, and Low severity and attained an excellent classification accuracy of 97.84%. As we are aware, the world is now struggling to contain the spread of the 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 J o u r n a l P r e -p r o o f 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 Authors hereby confirm that there is no conflict of interest or competing interest for the article and work submitted in this journal. All Ethical norms 365 are being followed during each and every phase of the work from the inception to the submission of the manuscript. We also confirm that no Funding/Research Grants has been obtained for this work. • The authors did not receive support from any organization for the submitted work. • No funding, grants was received for conducting this study. 26 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 J o u r n a l P r e -p r o o f 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 Molecular immune pathogenesis and diagnosis of COVID-19 Quantification of tomographic patterns associated with covid-19 from chest ct COVID-19 Pneumonia: What Has CT Taught Us? 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