Various viral epidemics have been detected such as the severe acute respiratory syndrome coronavirus and the Middle East respiratory syndrome coronavirus in the last two decades. The coronavirus disease 2019 (COVID-19) is a pandemic caused by a novel betacoronavirus called severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). After the rapid spread of COVID-19, many researchers have investigated diagnosis and treatment for this terrifying disease quickly. Identifying COVID-19 from the other types of coronaviruses is a difficult problem due to their genetic similarity. In this study, we propose a new efficient COVID-19 detection method based on the K-nearest neighbors (KNN) classifier using the complete genome sequences of human coronaviruses in the dataset recorded in 2019 Novel Coronavirus Resource. We also describe two features based on CpG island that efficiently detect COVID-19 cases. Thus, genome sequences including approximately 30,000 nucleotides can be represented by only two real numbers. The KNN method is a simple and effective non-parametric technique for solving classification problems. However, performance of the KNN depends on the distance measure used. We perform 19 distance metrics investigated in five categories to improve the performance of the KNN algorithm. Some efficient performance parameters are computed to evaluate the proposed method. The proposed method achieves 98.4% precision, 99.2% recall, 98.8% F-measure, and 98.4% accuracy in a few seconds when any type metric is used as a distance measure in the KNN.

Accurate identification of COVID-19 is now a critical task since it has seriously damaged daily life, public health, and the economy. It is essential to identify the infected people to prevent the further spread of the pandemic and to treat infected patients quickly. Machine learning techniques have a significant role in predicting of COVID-19. In this study, we performed binary classification (COVID-19 vs. other types of coronavirus) by extracting features from genome sequences. Support vector machines, naive Bayes, K-nearest neighbor, and random forest methods were used for classification. We used viral gene sequences from the 2019 Novel Coronavirus Resource Database. Experimental results presented show that a decision tree method achieved 93% accuracy.

This paper proposes an efficient and accurate method to predict coronavirus disease 19 (COVID-19) based on the genome similarity of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and a bat SARS-CoV-like coronavirus. We introduce similarity features to distinguish COVID-19 from other human coronaviruses by comparing human coronaviruses with a bat SARS-CoV-like coronavirus. In the proposed method each human coronavirus sequence is assigned to three similarity scores considering nucleotide similarities and mutations that lead to the strong absence of cytosine and guanine nucleotides. Next the proposed features are integrated with CpG island features of the genome sequences to improve COVID-19 prediction. Thus each genome sequence is represented by five real numbers. We exhibit the effectiveness of the proposed features using six machine learning classifiers on a dataset including the genome sequences of human coronaviruses similar to SARS-CoV-2. The performances of the machine learning classifiers are close to each other and k-nearest neighbor classifier with similarity features achieves the best results with an accuracy of 99.2%. Moreover, k-nearest neighbor classifier with the integration of CpG based and similarity features has an admirable performance and achieves an accuracy of 99.8%. Experimental results demonstrate that similarity features remarkably decreases the number of false negatives and significantly improve the overall performance. The superiority of the proposed method is also highlighted by comparing with the state-of-the-art studies detecting COVID-19 from genome sequences.

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The single-source shortest path problem arises in many applications, such as roads, social applications, and computer networks. Finding the shortest path is challenging, especially for graphs that contain a large number of vertices and edges. In this work, we propose a novel hybrid method that first sparsifies a given graph by removing most edges that cannot form the shortest path tree and then applies a classical shortest path algorithm to the sparser graph. Removing all the edges that cannot form the shortest path tree would be expensive since it is equivalent to solving the original problem. Therefore, we propose an iterative bioinspired algorithm, namely the Physarum algorithm, as the first stage to sparsify the graph. We prove that the resulting sparser graph always contains the shortest path tree of the original graph. Next, a state-of-the-art algorithm such as Dijkstra's is applied to find the single-source shortest path on the resulting graph. The proposed method is therefore a two-stage hybrid algorithm and it computes the single-source shortest path exactly. We compare the accuracy and solution time of the proposed hybrid method against state-of-the-art implementation of Dijkstra's algorithm and the BFS algorithm on directed weighted and unweighted graphs, respectively, as a baseline. The results show that the proposed hybrid method achieves a significant speed improvement compared to the baseline.