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Application of support vector machines in viral biology

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TLDR
This chapter provides lucid and easy to understand details of SVM algorithms along with applications in virology, one such robust tool based rigorously on statistical learning theory.
Abstract
Novel experimental and sequencing techniques have led to an exponential explosion and spiraling of data in viral genomics. To analyse such data, rapidly gain information, and transform this information to knowledge, interdisciplinary approaches involving several different types of expertise are necessary. Machine learning has been in the forefront of providing models with increasing accuracy due to development of newer paradigms with strong fundamental bases. Support Vector Machines (SVM) is one such robust tool, based rigorously on statistical learning theory. SVM provides very high quality and robust solutions to classification and regression problems. Several studies in virology employ high performance tools including SVM for identification of potentially important gene and protein functions. This is mainly due to the highly beneficial aspects of SVM. In this chapter we briefly provide lucid and easy to understand details of SVM algorithms along with applications in virology.

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References
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Journal Article

Assembly and characterization of pandemic influenza A H1N1 genome in nasopharyngeal swabs using high-throughput pyrosequencing

TL;DR: De novo high-throughput pyrosequencing was used to detect and characterize 2009 pandemic influenza A (H1N1) virus directly in nasopharyngeal swabs in the context of the microbial community, and could be of great value in identifying possibly new reassortants that may occur in the near future.
Journal ArticleDOI

QSAR studies of the bioactivity of hepatitis C virus (HCV) NS3/4A protease inhibitors by multiple linear regression (MLR) and support vector machine (SVM).

TL;DR: The combination of the best sub- and whole dataset SVM models can be used as reliable lead designing tools for new NS3/4A protease inhibitors scaffolds in a drug discovery pipeline.
Journal ArticleDOI

Enhancement of hepatitis virus immunoassay outcome predictions in imbalanced routine pathology data by data balancing and feature selection before the application of support vector machines.

TL;DR: Laboratories looking to include machine learning via SVM as part of their decision support need to be aware that the balancing method, predictor variable selection and the virus type interact to affect the laboratory diagnosis of hepatitis virus infection with routine pathology laboratory variables in different ways depending on which combination is being studied.
Journal ArticleDOI

Hybrid biogeography based simultaneous feature selection and MHC class I peptide binding prediction using support vector machines and random forests.

TL;DR: This work proposes the application of a hybrid filter-wrapper algorithm employing concepts from the recently developed biogeography based optimization algorithm, in conjunction with SVM and Random Forests for identification of MHC-I binding peptides, and demonstrates the effectiveness of this evolutionary technique, coupled with weighted heuristics, for the construction of improved prediction models.
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Trending Questions (1)
What are the potential applications of machine learning in virology?

Machine learning, specifically Support Vector Machines (SVM), is used in virology for tasks such as epitope prediction, virus-host interaction detection, and influenza host prediction.