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• W2996470210 abstract "The type of host that a virus can infect, referred to as host specificity or tropism, influences infectivity and thus is important for disease diagnosis, epidemic response, and prevention. Advances in DNA sequencing technology have enabled rapid metagenomic analyses of viruses, but the prediction of virus phenotype from genome sequences is an active area of research. As such, automatic prediction of host tropism from analysis of genomic information is of considerable utility. Previous research has applied machine learning methods to accomplish this task, although deep learning (particularly deep convolutional neural network, CNN) techniques have not yet been applied. These techniques have the ability to learn how to recognize critical hierarchical structures within the genome in a data-driven manner. We designed deep CNN models to identify host tropism for human and avian influenza A viruses based on protein sequences and performed a detailed analysis of the results. Our findings show that deep CNN techniques work as well as existing approaches (with 99% mean accuracy on the binary prediction task) while performing end-to-end learning of the prediction model (without the need to specify handcrafted features). The findings also show that these models, combined with standard principal component analysis, can be used to quantify and visualize viral strain similarity. Deep learning techniques have the ability to learn how to recognize critical hierarchical structures within the genome in a data-driven manner. The authors designed deep convolutional neural network models to identify host tropism for human and avian influenza A viruses based on protein sequences and performed a detailed analysis of the results. Findings show that deep convolutional neural network techniques work as well as existing approaches while performing end-to-end learning of the prediction model (without the need to specify handcrafted features)." @default.
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• W2996470210 date "2019-12-01" @default.
• W2996470210 modified "2023-10-01" @default.
• W2996470210 title "Predicting Influenza A Tropism with End-to-End Learning of Deep Networks" @default.
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• W2996470210 doi "https://doi.org/10.1089/hs.2019.0055" @default.
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