Prediction of pandemic risk for animal-origin coronavirus using a deep learning method.

BACKGROUND: Coronaviruses can be isolated from bats, civets, pangolins, birds and other wild animals. As an animal-origin pathogen, coronavirus can cross species barrier and cause pandemic in humans. In this study, a deep learning model for early prediction of pandemic risk was proposed based on the sequences of viral genomes. METHODS: A total of 3257 genomes were downloaded from the Coronavirus Genome Resource Library. We present a deep learning model of cross-species coronavirus infection that combines a bidirectional gated recurrent unit network with a one-dimensional convolution. The genome sequence of animal-origin coronavirus was directly input to extract features and predict pandemic risk. The best performances were explored with the use of pre-trained DNA vector and attention mechanism. The area under the receiver operating characteristic curve (AUROC) and the area under precision-recall curve (AUPR) were used to evaluate the predictive models. RESULTS: The six specific models achieved good performances for the corresponding virus groups (1 for AUROC and 1 for AUPR). The general model with pre-training vector and attention mechanism provided excellent predictions for all virus groups (1 for AUROC and 1 for AUPR) while those without pre-training vector or attention mechanism had obviously reduction of performance (about 5-25%). Re-training experiments showed that the general model has good capabilities of transfer learning (average for six groups: 0.968 for AUROC and 0.942 for AUPR) and should give reasonable prediction for potential pathogen of next pandemic. The artificial negative data with the replacement of the coding region of the spike protein were also predicted correctly (100% accuracy). With the application of the Python programming language, an easy-to-use tool was created to implements our predictor. CONCLUSIONS: Robust deep learning model with pre-training vector and attention mechanism mastered the features from the whole genomes of animal-origin coronaviruses and could predict the risk of cross-species infection for early warning of next pandemic.

A Study on Domination in Vague Incidence Graph and Its Application in Medical Sciences

Fuzzy graphs (FGs), broadly known as fuzzy incidence graphs (FIGs), have been acknowledged as being an applicable and well-organized tool to epitomize and solve many multifarious real-world problems in which vague data and information are essential. Owing to unpredictable and unspecified information being an integral component in real-life problems that are often uncertain, it is highly challenging for an expert to illustrate those problems through a fuzzy graph. Therefore, resolving the uncertainty accompanying the unpredictable and unspecified information of any real-world problem can be done by applying a vague incidence graph (VIG), based on which the FGs may not engender satisfactory results. Similarly, VIGs are outstandingly practical tools for analyzing different computer science domains such as networking, clustering, and also other issues such as medical sciences, and traffic planning. Dominating sets (DSs) enjoy practical interest in several areas. In wireless networking, DSs are being used to find efficient routes with ad-hoc mobile networks. They have also been employed in document summarization, and in secure systems designs for electrical grids;consequently, in this paper, we extend the concept of the FIG to the VIG, and show some of its important properties. In particular, we discuss the well-known problems of vague incidence dominating set, valid degree, isolated vertex, vague incidence irredundant set and their cardinalities related to the dominating, etc. Finally, a DS application for VIG to properly manage the COVID-19 testing facility is introduced.