Abstract:
:The rapid evolution of influenza A viruses poses a great challenge to vaccine development. Analytical and machine learning models have been applied to facilitate the process of antigenicity determination. In this study, we designed deep convolutional neural networks (CNNs) to predict Influenza antigenicity. Our model is the first that systematically analyzed 566 amino acid properties and 141 amino acid substitution matrices for their predictability. We then optimized the structure of the CNNs using particle swarm optimization. The optimal neural networks outperform other predictive models with a blind validation accuracy of 95.8%. Further, we applied our model to vaccine recommendations in the period 1997 to 2011 and contrasted the performance of previous vaccine recommendations using traditional experimental approaches. The results show that our model outperforms the WHO recommendation and other existing models and could potentially improve the vaccine recommendation process. Our results show that WHO often selects virus strains with small variation from year to year and learns slowly and recovers once coverage dips very low. In contrast, the influenza strains selected via our CNN model can differ quite drastically from year to year and exhibit consistently good coverage. In summary, we have designed a comprehensive computational pipeline for optimizing a CNN in the modeling of Influenza A antigenicity and vaccine recommendation. It is more cost and time-effective when compared to traditional hemagglutination inhibition assay analysis. The modeling framework is flexible and can be adopted to study other type of viruses.
journal_name
Hum Vaccin Immunotherjournal_title
Human vaccines & immunotherapeuticsauthors
Lee EK,Tian H,Nakaya HIdoi
10.1080/21645515.2020.1734397subject
Has Abstractpub_date
2020-11-01 00:00:00pages
2690-2708issue
11eissn
2164-5515issn
2164-554Xjournal_volume
16pub_type
杂志文章abstract::Background: Rotavirus (RV) is worldwide an important cause of acute gastroenteritis (AGE) in infants and young children. There is no specific treatment for AGE caused by RV (RVGE) but since 2006 two safe and effective vaccines have been available. RV vaccination was included in the national immunization program (NIP) ...
journal_title:Human vaccines & immunotherapeutics
pub_type: 杂志文章
doi:10.1080/21645515.2018.1534515
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journal_title:Human vaccines & immunotherapeutics
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journal_title:Human vaccines & immunotherapeutics
pub_type: 杂志文章,评审
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journal_title:Human vaccines & immunotherapeutics
pub_type: 杂志文章,评审
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journal_title:Human vaccines & immunotherapeutics
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journal_title:Human vaccines & immunotherapeutics
pub_type: 杂志文章,评审
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journal_title:Human vaccines & immunotherapeutics
pub_type: 杂志文章
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journal_title:Human vaccines & immunotherapeutics
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journal_title:Human vaccines & immunotherapeutics
pub_type: 杂志文章
doi:10.4161/hv.36168
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journal_title:Human vaccines & immunotherapeutics
pub_type: 杂志文章,评审
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journal_title:Human vaccines & immunotherapeutics
pub_type: 杂志文章
doi:10.1080/21645515.2020.1791509
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journal_title:Human vaccines & immunotherapeutics
pub_type: 杂志文章
doi:10.4161/hv.24250
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journal_title:Human vaccines & immunotherapeutics
pub_type: 杂志文章,随机对照试验
doi:10.4161/hv.20211
更新日期:2012-07-01 00:00:00
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journal_title:Human vaccines & immunotherapeutics
pub_type: 杂志文章
doi:10.4161/hv.34407
更新日期:2014-01-01 00:00:00
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journal_title:Human vaccines & immunotherapeutics
pub_type: 杂志文章
doi:10.1080/21645515.2020.1737456
更新日期:2020-11-01 00:00:00
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journal_title:Human vaccines & immunotherapeutics
pub_type: 杂志文章,评审
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journal_title:Human vaccines & immunotherapeutics
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journal_title:Human vaccines & immunotherapeutics
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doi:10.1080/21645515.2018.1448328
更新日期:2018-07-03 00:00:00
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journal_title:Human vaccines & immunotherapeutics
pub_type: 杂志文章
doi:10.1080/21645515.2017.1299837
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journal_title:Human vaccines & immunotherapeutics
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journal_title:Human vaccines & immunotherapeutics
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journal_title:Human vaccines & immunotherapeutics
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doi:10.4161/21645515.2014.980684
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journal_title:Human vaccines & immunotherapeutics
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pub_type: 杂志文章,评审
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abstract::The effective protective HIV vaccine should elicit either protective antibodies or effective T cell response, or both. To improve the efficacy of HIV-1 vaccines, HLA polymorphism and HIV-1 diversity are 2 key factors to be considered for vaccine development. In this study, we expressed a recombinant multi-epitope prot...
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