Probability Distributions.- Linear Models for Regression.- Linear Models for Classification.- Neural Networks.- Kernel Methods.- Sparse Kernel Machines.- Graphical Models.- Mixture Models and EM.- Approximate Inference.- Sampling Methods.- Continuous Latent Variables.- Sequential Data.- Combining Models.

Pattern Recognition and Machine Learning

Statistical Analysis with Missing Data

An overview of the self-organizing map algorithm, on which the papers in this issue are based, is presented in this article.

The Self-Organizing Map

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

Coronavirus disease (COVID-19) is a pandemic disease, which has already caused thousands of causalities and infected several millions of people worldwide. Any technological tool enabling rapid screening of the COVID-19 infection with high accuracy can be crucially helpful to the healthcare professionals. The main clinical tool currently in use for the diagnosis of COVID-19 is the Reverse transcription polymerase chain reaction (RT-PCR), which is expensive, less-sensitive and requires specialized medical personnel. X-ray imaging is an easily accessible tool that can be an excellent alternative in the COVID-19 diagnosis. This research was taken to investigate the utility of artificial intelligence (AI) in the rapid and accurate detection of COVID-19 from chest X-ray images. The aim of this paper is to propose a robust technique for automatic detection of COVID-19 pneumonia from digital chest X-ray images applying pre-trained deep-learning algorithms while maximizing the detection accuracy. A public database was created by the authors combining several public databases and also by collecting images from recently published articles. The database contains a mixture of 423 COVID-19, 1485 viral pneumonia, and 1579 normal chest X-ray images. Transfer learning technique was used with the help of image augmentation to train and validate several pre-trained deep Convolutional Neural Networks (CNNs). The networks were trained to classify two different schemes: i) normal and COVID-19 pneumonia; ii) normal, viral and COVID-19 pneumonia with and without image augmentation. The classification accuracy, precision, sensitivity, and specificity for both the schemes were 99.7%, 99.7%, 99.7% and 99.55% and 97.9%, 97.95%, 97.9%, and 98.8%, respectively. The high accuracy of this computer-aided diagnostic tool can significantly improve the speed and accuracy of COVID-19 diagnosis. This would be extremely useful in this pandemic where disease burden and need for preventive measures are at odds with available resources.

Can AI Help in Screening Viral and COVID-19 Pneumonia?

Chest X-ray is the first imaging technique that plays an important role in the diagnosis of COVID-19 disease. Due to the high availability of large-scale annotated image datasets, great success has been achieved using convolutional neural networks (CNN s) for image recognition and classification. However, due to the limited availability of annotated medical images, the classification of medical images remains the biggest challenge in medical diagnosis. Thanks to transfer learning, an effective mechanism that can provide a promising solution by transferring knowledge from generic object recognition tasks to domain-specific tasks. In this paper, we validate and a deep CNN, called Decompose, Transfer, and Compose (DeTraC), for the classification of COVID-19 chest X-ray images. DeTraC can deal with any irregularities in the image dataset by investigating its class boundaries using a class decomposition mechanism. The experimental results showed the capability of DeTraC in the detection of COVID-19 cases from a comprehensive image dataset collected from several hospitals around the world. High accuracy of 93.1% (with a sensitivity of 100%) was achieved by DeTraC in the detection of COVID-19 X-ray images from normal, and severe acute respiratory syndrome cases.

/pdf/classification-of-covid-19-in-chest-x-ray-images-using-2jfcx6h435.pdf

Classification of COVID-19 in chest X-ray images using DeTraC deep convolutional neural network.

Chest X-ray is the first imaging technique that plays an important role in the diagnosis of COVID-19 disease. Due to the high availability of large-scale annotated image datasets, great success has been achieved using convolutional neural networks (CNNs) for image recognition and classification. However, due to the limited availability of annotated medical images, the classification of medical images remains the biggest challenge in medical diagnosis. Thanks to transfer learning, an effective mechanism that can provide a promising solution by transferring knowledge from generic object recognition tasks to domain-specific tasks. In this paper, we validate and adapt our previously developed CNN, called Decompose, Transfer, and Compose (DeTraC), for the classification of COVID-19 chest X-ray images. DeTraC can deal with any irregularities in the image dataset by investigating its class boundaries using a class decomposition mechanism. The experimental results showed the capability of DeTraC in the detection of COVID-19 cases from a comprehensive image dataset collected from several hospitals around the world. High accuracy of 95.12% (with a sensitivity of 97.91%, a specificity of 91.87%, and a precision of 93.36%) was achieved by DeTraC in the detection of COVID-19 X-ray images from normal, and severe acute respiratory syndrome cases.

https://medrxiv.org/content/10.1101/2020.03.30.20047456v1.full.pdf

Mohammed M. Abdelsamea

Papers

Classification of COVID-19 in chest X-ray images using DeTraC deep convolutional neural network.

Classification of COVID-19 in chest X-ray images using DeTraC deep convolutional neural network

Image-based plant phenotyping with incremental learning and active contours

Artificial intelligence in digital breast pathology: Techniques and applications.

Classification of COVID-19 in chest X-ray images using DeTraC deep convolutional neural network