A deep learning model and machine learning methods for the classification of potential coronavirus treatments on a single human cell

Machine learning-based IoT system for COVID-19 epidemics

The planet earth has been facing COVID-19 epidemic as a challenge in recent time. It is predictable that the world will be fighting the pandemic by taking precautions steps before an operative vaccine is found. The IoT produces huge data volumes, whether private or public, through the invention of IoT devices in the form of smart devices with an improved rate of IoT data generation. A lot of devices interact with each other in the IoT ecosystem through the cloud or servers. Various techniques have been presented in recent time, using data mining approach have proven help detect possible cases of coronaviruses. Therefore, this study uses machine learning technique (ABC and SVM) to predict COVID-19 for IoT data system. The system used two machine learning techniques which are Artificial Bee Colony algorithm with Support Vector Machine classifier on a San Francisco COVID-19 dataset. The system was evaluated using confusion matrix and had a 95% accuracy, 95% sensitivity, 95% specificity, 97% precision, 96% F1 score, 89% Matthews correlation coefficient for ABC-L-SVM and 97% accuracy, 95% sensitivity, 100% specificity, 100% precision, 97% F1 score, 93.1% Matthews correlation coefficient for ABC-Q-SVM. In conclusion, the system shows that the process of dimensionality reduction utilizing ABC feature extraction techniques can boost the classification production for SVM. It was observed that fetching relevant information from IoT systems before classification is relatively beneficial.

Biased, wrong and counterfeited evidences published during the COVID-19 pandemic, a systematic review of retracted COVID-19 papers

In 2020 COVID-19 led to an unprecedented stream of papers being submitted to journals. Scientists and physicians all around the globe were in need for information about this new disease. In this climate, many articles were accepted after extremely fast peer-reviews to provide the scientific community with the latest discoveries and knowledge. Unfortunately, this also led to articles retraction due to authors' misconduct or errors in methodology and/or conclusions. The aim of this study is to investigate the number and characteristics of retracted papers, and to explore the main causes that led to retraction. We conducted a systematic review on retracted articles, using PubMed as data source. Our inclusion criteria were the following: English-language retracted articles that reported original data, results, opinions or hypotheses on COVID-19 and Sars-CoV-2. Twenty-seven retracted articles were identified, mainly reporting observational studies and opinion pieces. Many articles published during the first year of the pandemic have been retracted, mainly due to the authors' scientific misconduct. Duplications, plagiarism, frauds and absence of consent, were the main reasons for retractions. In modern medicine, researchers are required to publish frequently, and, especially during situations like the COVID-19 pandemic, when articles were rapidly published, gaps in peer-reviews system and in the path to scientific publication arose.

A contemporary review on the important role of in silico approaches for managing different aspects of COVID-19 crisis

In the last century, the emergence of in silico tools has improved the quality of healthcare studies by providing high quality predictions. In the case of COVID-19, these tools have been advantageous for bioinformatics analysis of SARS-CoV-2 structures, studying potential drugs and introducing drug targets, investigating the efficacy of potential natural product components at suppressing COVID-19 infection, designing peptide-mimetic and optimizing their structure to provide a better clinical outcome, and repurposing of the previously known therapeutics. These methods have also helped medical biotechnologists to design various vaccines; such as multi-epitope vaccines using reverse vaccinology and immunoinformatics methods, among which some of them have showed promising results through in vitro, in vivo and clinical trial studies. Moreover, emergence of artificial intelligence and machine learning algorithms have helped to classify the previously known data and use them to provide precise predictions and make plan for future of the pandemic condition. At this contemporary review, by collecting related information from the collected literature on valuable data sources; such as PubMed, Scopus, and Web of Science, we tried to provide a brief outlook regarding the importance of in silico tools in managing different aspects of COVID-19 pandemic infection and how these methods have been helpful to biomedical researchers.

Deep Learning for Drug Discovery: A Study of Identifying High Efficacy Drug Compounds Using a Cascade Transfer Learning Approach

In this research, we applied deep learning to rank the effectiveness of candidate drug compounds in combating viral cells, in particular, SARS-Cov-2 viral cells. For this purpose, two different datasets from Recursion Pharmaceuticals, a siRNA image dataset (RxRx1), which were used to build and calibrate our model for feature extraction, and a SARS-CoV-2 dataset (RxRx19a) was used to train our model for ranking efficacy of candidate drug compounds. The SARS-CoV-2 dataset contained healthy, uninfected control or “mock” cells, as well as “active viral” cells (cells infected with COVID-19), which were the two cell types used to train our deep learning model. In addition, it contains viral cells treated with different drug compounds, which were the cells not used to train but test our model. We devised a new cascade transfer learning strategy to construct our model. We first trained a deep learning model, the DenseNet, with the siRNA set, a dataset with characteristics similar to the SARS-CoV-2 dataset, for feature extraction. We then added additional layers, including a SoftMax layer as an output layer, and retrained the model with active viral cells and mock cells from the SARS-CoV-2 dataset. In the test phase, the SoftMax layer outputs probability (equivalently, efficacy) scores which allows us to rank candidate compounds, and to study the performance of each candidate compound statistically. With this approach, we identified several compounds with high efficacy scores which are promising for the therapeutic treatment of COVID-19. The compounds showing the most promise were GS-441524 and then Remdesivir, which overlapped with these reported in the literature and with these drugs that are approved by FDA, or going through clinical trials and preclinical trials. This study shows the potential of deep learning in its ability to identify promising compounds to aid rapid responses to future pandemic outbreaks.

COVID-19 Detection from Chest X-ray Images Using Feature Fusion and Deep Learning

Currently, COVID-19 is considered to be the most dangerous and deadly disease for the human body caused by the novel coronavirus. In December 2019, the coronavirus spread rapidly around the world, thought to be originated from Wuhan in China and is responsible for a large number of deaths. Earlier detection of the COVID-19 through accurate diagnosis, particularly for the cases with no obvious symptoms, may decrease the patient's death rate. Chest X-ray images are primarily used for the diagnosis of this disease. This research has proposed a machine vision approach to detect COVID-19 from the chest X-ray images. The features extracted by the histogram-oriented gradient (HOG) and convolutional neural network (CNN) from X-ray images were fused to develop the classification model through training by CNN (VGGNet). Modified anisotropic diffusion filtering (MADF) technique was employed for better edge preservation and reduced noise from the images. A watershed segmentation algorithm was used in order to mark the significant fracture region in the input X-ray images. The testing stage considered generalized data for performance evaluation of the model. Cross-validation analysis revealed that a 5-fold strategy could successfully impair the overfitting problem. This proposed feature fusion using the deep learning technique assured a satisfactory performance in terms of identifying COVID-19 compared to the immediate, relevant works with a testing accuracy of 99.49%, specificity of 95.7% and sensitivity of 93.65%. When compared to other classification techniques, such as ANN, KNN, and SVM, the CNN technique used in this study showed better classification performance. K-fold cross-validation demonstrated that the proposed feature fusion technique (98.36%) provided higher accuracy than the individual feature extraction methods, such as HOG (87.34%) or CNN (93.64%).