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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 ArticleDOI

A binary QSAR model for classifying neuraminidase inhibitors of influenza A viruses (H1N1) using the combined minimum redundancy maximum relevancy criterion with the sparse support vector machine.

TL;DR: A two-stage classification approach is proposed by combining the minimum redundancy maximum relevancy criterion with the sparse support vector machine and the experimental results show that the proposed method is able to effectively outperform other sparse alternatives methods in terms of classification performance and the number of selected descriptors.
Journal ArticleDOI

HIVprotI: an integrated web based platform for prediction and design of HIV proteins inhibitors

TL;DR: Support vector machine based regression models are developed using experimentally validated data from ChEMBL repository for predicting inhibition activity of a compound against HIV proteins namely protease (PR), reverse transcriptase (RT) and integrase (IN).
Journal ArticleDOI

An improved method for predicting interactions between virus and human proteins.

TL;DR: A method that represents key features of virus and human proteins of variable length into a feature vector of fixed length and uses the SVM model with gene ontology annotations of proteins to predict new HPV-human PPIs is developed.
Journal ArticleDOI

Identification of Amino Acid Propensities That Are Strong Determinants of Linear B-cell Epitope Using Neural Networks

TL;DR: A novel Group Feature Selecting Multilayered Perceptron, GFSMLP is used, which treats a group of related information as a single entity and selects useful propensities related to linear B-cell epitopes, and uses them to predict epitopes and confirms the effectiveness of active (group) feature selection by GFS MLP over the traditional passive approaches of evaluating various combinations of propensity.
Journal ArticleDOI

Predicting the host of influenza viruses based on the word vector.

TL;DR: This work attempted to predict the host of influenza viruses using the Support Vector Machine (SVM) classifier based on the word vector, a new representation and feature extraction method for biological sequences, and found the best performance was achieved when the model was built on the HA gene based on word vectors generated from DNA sequences of the influenza virus.
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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.