Predicting Influenza A Tropism with End-to-End Learning of Deep Networks
| Autor: | Brian A. Telfer, Daniel Scarafoni, James Comolli, Darrell O. Ricke, Jason Thornton |
|---|---|
| Rok vydání: | 2019 |
| Předmět: |
Health (social science)
Genotype viruses Health Toxicology and Mutagenesis 030231 tropical medicine Disease Management Monitoring Policy and Law Biology medicine.disease_cause Models Biological Virus Birds Machine Learning 03 medical and health sciences 0302 clinical medicine Influenza Human medicine Animals Humans Computer Simulation 030212 general & internal medicine Tropism Infectivity business.industry Host (biology) Deep learning fungi Public Health Environmental and Occupational Health food and beverages Influenza a Virology Influenza A virus subtype H5N1 Viral Tropism Phenotype Influenza A virus Influenza in Birds Emergency Medicine Artificial intelligence Neural Networks Computer business Safety Research |
| Zdroj: | Health security. 17(6) |
| ISSN: | 2326-5108 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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