There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

Objective To review and appraise the validity and usefulness of published and preprint reports of prediction models for diagnosing coronavirus disease 2019 (covid-19) in patients with suspected infection, for prognosis of patients with covid-19, and for detecting people in the general population at increased risk of covid-19 infection or being admitted to hospital with the disease. Design Living systematic review and critical appraisal by the COVID-PRECISE (Precise Risk Estimation to optimise covid-19 Care for Infected or Suspected patients in diverse sEttings) group. Data sources PubMed and Embase through Ovid, up to 1 July 2020, supplemented with arXiv, medRxiv, and bioRxiv up to 5 May 2020. Study selection Studies that developed or validated a multivariable covid-19 related prediction model. Data extraction At least two authors independently extracted data using the CHARMS (critical appraisal and data extraction for systematic reviews of prediction modelling studies) checklist; risk of bias was assessed using PROBAST (prediction model risk of bias assessment tool). Results 37 421 titles were screened, and 169 studies describing 232 prediction models were included. The review identified seven models for identifying people at risk in the general population; 118 diagnostic models for detecting covid-19 (75 were based on medical imaging, 10 to diagnose disease severity); and 107 prognostic models for predicting mortality risk, progression to severe disease, intensive care unit admission, ventilation, intubation, or length of hospital stay. The most frequent types of predictors included in the covid-19 prediction models are vital signs, age, comorbidities, and image features. Flu-like symptoms are frequently predictive in diagnostic models, while sex, C reactive protein, and lymphocyte counts are frequent prognostic factors. Reported C index estimates from the strongest form of validation available per model ranged from 0.71 to 0.99 in prediction models for the general population, from 0.65 to more than 0.99 in diagnostic models, and from 0.54 to 0.99 in prognostic models. All models were rated at high or unclear risk of bias, mostly because of non-representative selection of control patients, exclusion of patients who had not experienced the event of interest by the end of the study, high risk of model overfitting, and unclear reporting. Many models did not include a description of the target population (n=27, 12%) or care setting (n=75, 32%), and only 11 (5%) were externally validated by a calibration plot. The Jehi diagnostic model and the 4C mortality score were identified as promising models. Conclusion Prediction models for covid-19 are quickly entering the academic literature to support medical decision making at a time when they are urgently needed. This review indicates that almost all pubished prediction models are poorly reported, and at high risk of bias such that their reported predictive performance is probably optimistic. However, we have identified two (one diagnostic and one prognostic) promising models that should soon be validated in multiple cohorts, preferably through collaborative efforts and data sharing to also allow an investigation of the stability and heterogeneity in their performance across populations and settings. Details on all reviewed models are publicly available at https://www.covprecise.org/. Methodological guidance as provided in this paper should be followed because unreliable predictions could cause more harm than benefit in guiding clinical decisions. Finally, prediction model authors should adhere to the TRIPOD (transparent reporting of a multivariable prediction model for individual prognosis or diagnosis) reporting guideline. Systematic review registration Protocol https://osf.io/ehc47/, registration https://osf.io/wy245. Readers’ note This article is a living systematic review that will be updated to reflect emerging evidence. Updates may occur for up to two years from the date of original publication. This version is update 3 of the original article published on 7 April 2020 (BMJ 2020;369:m1328). Previous updates can be found as data supplements (https://www.bmj.com/content/369/bmj.m1328/related#datasupp). When citing this paper please consider adding the update number and date of access for clarity.

https://www.bmj.com/content/bmj/369/bmj.m1328.full.pdf

Prediction models for diagnosis and prognosis of covid-19: systematic review and critical appraisal

Automated detection of COVID-19 cases using deep neural networks with X-ray images.

Fast Fourier Transform

The 2019 novel coronavirus disease (COVID-19), with a starting point in China, has spread rapidly among people living in other countries, and is approaching approximately 34,986,502 cases worldwide according to the statistics of European Centre for Disease Prevention and Control. There are a limited number of COVID-19 test kits available in hospitals due to the increasing cases daily. Therefore, it is necessary to implement an automatic detection system as a quick alternative diagnosis option to prevent COVID-19 spreading among people. In this study, five pre-trained convolutional neural network based models (ResNet50, ResNet101, ResNet152, InceptionV3 and Inception-ResNetV2) have been proposed for the detection of coronavirus pneumonia infected patient using chest X-ray radiographs. We have implemented three different binary classifications with four classes (COVID-19, normal (healthy), viral pneumonia and bacterial pneumonia) by using 5-fold cross validation. Considering the performance results obtained, it has seen that the pre-trained ResNet50 model provides the highest classification performance (96.1% accuracy for Dataset-1, 99.5% accuracy for Dataset-2 and 99.7% accuracy for Dataset-3) among other four used models.

/pdf/automatic-detection-of-coronavirus-disease-covid-19-using-x-562zky4j2h.pdf

Automatic Detection of Coronavirus Disease (COVID-19) Using X-ray Images and Deep Convolutional Neural Networks

This study presents early phase detection of Coronavirus (COVID-19), which is named by World Health Organization (WHO), by machine learning methods. The detection process was implemented on abdominal Computed Tomography (CT) images. The expert radiologists detected from CT images that COVID-19 shows different behaviours from other viral pneumonia. Therefore, the clinical experts specify that COVID-19 virus needs to be diagnosed in early phase. For detection of the COVID-19, four different datasets were formed by taking patches sized as 16x16, 32x32, 48x48, 64x64 from 150 CT images. The feature extraction process was applied to patches to increase the classification performance. Grey Level Co-occurrence Matrix (GLCM), Local Directional Pattern (LDP), Grey Level Run Length Matrix (GLRLM), Grey-Level Size Zone Matrix (GLSZM), and Discrete Wavelet Transform (DWT) algorithms were used as feature extraction methods. Support Vector Machines (SVM) classified the extracted features. 2-fold, 5-fold and 10-fold cross-validations were implemented during the classification process. Sensitivity, specificity, accuracy, precision, and F-score metrics were used to evaluate the classification performance. The best classification accuracy was obtained as 99.68% with 10-fold cross-validation and GLSZM feature extraction method.

Coronavirus (COVID-19) Classification using CT Images by Machine Learning Methods

Coronavirus (COVID-19) emerged towards the end of 2019. World Health Organization (WHO) was identified it as a global epidemic. Consensus occurred in the opinion that using Computerized Tomography (CT) techniques for early diagnosis of pandemic disease gives both fast and accurate results. It was stated by expert radiologists that COVID-19 displays different behaviours in CT images. In this study, a novel method was proposed as fusing and ranking deep features to detect COVID-19 in early phase. 16x16 (Subset-1) and 32x32 (Subset-2) patches were obtained from 150 CT images to generate sub-datasets. Within the scope of the proposed method, 3000 patch images have been labelled as CoVID-19 and No finding for using in training and testing phase. Feature fusion and ranking method have been applied in order to increase the performance of the proposed method. Then, the processed data was classified with a Support Vector Machine (SVM). According to other pre-trained Convolutional Neural Network (CNN) models used in transfer learning, the proposed method shows high performance on Subset-2 with 98.27% accuracy, 98.93% sensitivity, 97.60% specificity, 97.63% precision, 98.28% F1-score and 96.54% Matthews Correlation Coefficient (MCC) metrics.

Coronavirus (COVID-19) Classification using Deep Features Fusion and Ranking Technique

Necessary screenings must be performed to control the spread of the COVID-19 in daily life and to make a preliminary diagnosis of suspicious cases. The long duration of pathological laboratory tests and the suspicious test results led the researchers to focus on different fields. Fast and accurate diagnoses are essential for effective interventions for COVID-19. The information obtained by using X-ray and Computed Tomography (CT) images is vital in making clinical diagnoses. Therefore it is aimed to develop a machine learning method for the detection of viral epidemics by analyzing X-ray and CT images. In this study, images belonging to six situations, including coronavirus images, are classified using a two-stage data enhancement approach. Since the number of images in the dataset is deficient and unbalanced, a shallow image augmentation approach was used in the first phase. It is more convenient to analyze these images with hand-crafted feature extraction methods because the dataset newly created is still insufficient to train a deep architecture. Therefore, the Synthetic minority over-sampling technique algorithm is the second data enhancement step of this study. Finally, the feature vector is reduced in size by using a stacked auto-encoder and principal component analysis methods to remove interconnected features in the feature vector. According to the obtained results, it is seen that the proposed method has leveraging performance, especially to make the diagnosis of COVID-19 in a short time and effectively. Also, it is thought to be a source of inspiration for future studies for deficient and unbalanced datasets.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/ima.22469

Classification of Coronavirus (COVID-19) from X-ray and CT images using shrunken features.

Recently, the incidence of skin cancer has increased considerably and is seriously threatening human health. Automatic detection of this disease, where early detection is critical to human life, is quite challenging. Factors such as undesirable residues (hair, ruler markers), indistinct boundaries, variable contrast, shape differences, and color differences in the skin lesion images make automatic analysis quite difficult. To overcome these challenges, a highly effective segmentation method based on a fully convolutional network (FCN) is presented in this paper. The proposed improved FCN (iFCN) architecture is used for the segmentation of full-resolution skin lesion images without any pre- or post-processing. It is to support the residual structure of the FCN architecture with spatial information. This situation, which creates a more advanced residual system, enables more precise detection of details on the edges of the lesion, and an analysis independent of skin color can be performed. It offers two contributions: determining the center of the lesion and clarifying the edge details despite the undesirable effects. Two publicly available datasets, the IEEE International Symposium on Biomedical Imaging (ISBI) 2017 Challenge and PH2 datasets, are used to evaluate the performance of the iFCN method. The mean Jaccard index is 78.34%, the mean Dice score is 88.64%, and the mean accuracy value is 95.30% for the proposed method for the ISBI 2017 test dataset. Furthermore, the mean Jaccard index is 87.1%, the mean Dice score is 93.02%, and the mean accuracy value is 96.92% for the proposed method for the PH2 test dataset.

https://link.springer.com/content/pdf/10.1007/s10278-020-00343-z.pdf

Skin Lesion Segmentation with Improved Convolutional Neural Network.

COVID-19, which appeared towards the end of 2019, has become a huge threat to public health The solution to this threat, which is defined as a global epidemic by the World Health Organization (WHO), is currently undergoing very intensive studies There is a consensus that the use of Computed Tomography (CT) techniques for early diagnosis of pandemic disease gives both fast and accurate results This study provides an automated and highly effective method for detecting COVID-19 at an early stage CT image features are extracted using the convolutional neural network (CNN) architecture, which is the most successful image processing tool of today, for the detection of COVID-19, where early detection is vital for human life Representation power is increased by combining features from the output of four CNN architectures with data fusion Finally, the features combined with the feature ranking method are sorted, and their length is reduced In this way, the dimensional curse is saved From 150 CT images, 16 × 16 (Subset-1) and 32 × 32 (Subset-2) patches were obtained to create a subset Within the scope of the proposed method, 3000 patch images are labeled as “COVID-19 (coronavirus)” or “No finding” for use in training and test stages The Support Vector Machine (SVM) method then classified the processed data The proposed method shows high performance in Subset-2 with 9827% accuracy, 9893% sensitivity, 9760% specificity, 9763% sensitivity, 9828% F1 score and 9654% Matthews Correlation Coefficient (MCC) metrics

Umut Özkaya

Papers

Coronavirus (COVID-19) Classification using CT Images by Machine Learning Methods

Coronavirus (COVID-19) Classification using Deep Features Fusion and Ranking Technique

Classification of Coronavirus (COVID-19) from X-ray and CT images using shrunken features.

Skin Lesion Segmentation with Improved Convolutional Neural Network.

Coronavirus (COVID-19) Classification Using Deep Features Fusion and Ranking Technique