Comparing artificial neural networks, general linear models and support vector machines in building predictive models for small interfering RNAs.

<h4>Background</h4>Exogenous short interfering RNAs (siRNAs) induce a gene knockdown effect in cells by interacting with naturally occurring RNA processing machinery. However not all siRNAs induce this effect equally. Several heterogeneous kinds of machine learning techniques and feature...

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Autores principales:	Kyle A McQuisten, Andrew S Peek
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2009
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/54a6ebf42aa84d0aa39f142f1ab115e5
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spelling	oai:doaj.org-article:54a6ebf42aa84d0aa39f142f1ab115e52021-11-25T06:28:35ZComparing artificial neural networks, general linear models and support vector machines in building predictive models for small interfering RNAs.1932-620310.1371/journal.pone.0007522https://doaj.org/article/54a6ebf42aa84d0aa39f142f1ab115e52009-10-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19847297/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Exogenous short interfering RNAs (siRNAs) induce a gene knockdown effect in cells by interacting with naturally occurring RNA processing machinery. However not all siRNAs induce this effect equally. Several heterogeneous kinds of machine learning techniques and feature sets have been applied to modeling siRNAs and their abilities to induce knockdown. There is some growing agreement to which techniques produce maximally predictive models and yet there is little consensus for methods to compare among predictive models. Also, there are few comparative studies that address what the effect of choosing learning technique, feature set or cross validation approach has on finding and discriminating among predictive models.<h4>Principal findings</h4>Three learning techniques were used to develop predictive models for effective siRNA sequences including Artificial Neural Networks (ANNs), General Linear Models (GLMs) and Support Vector Machines (SVMs). Five feature mapping methods were also used to generate models of siRNA activities. The 2 factors of learning technique and feature mapping were evaluated by complete 3x5 factorial ANOVA. Overall, both learning techniques and feature mapping contributed significantly to the observed variance in predictive models, but to differing degrees for precision and accuracy as well as across different kinds and levels of model cross-validation.<h4>Conclusions</h4>The methods presented here provide a robust statistical framework to compare among models developed under distinct learning techniques and feature sets for siRNAs. Further comparisons among current or future modeling approaches should apply these or other suitable statistically equivalent methods to critically evaluate the performance of proposed models. ANN and GLM techniques tend to be more sensitive to the inclusion of noisy features, but the SVM technique is more robust under large numbers of features for measures of model precision and accuracy. Features found to result in maximally predictive models are not consistent across learning techniques, suggesting care should be taken in the interpretation of feature relevance. In the models developed here, there are statistically differentiable combinations of learning techniques and feature mapping methods where the SVM technique under a specific combination of features significantly outperforms all the best combinations of features within the ANN and GLM techniques.Kyle A McQuistenAndrew S PeekPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 4, Iss 10, p e7522 (2009)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Kyle A McQuisten Andrew S Peek Comparing artificial neural networks, general linear models and support vector machines in building predictive models for small interfering RNAs.
description	<h4>Background</h4>Exogenous short interfering RNAs (siRNAs) induce a gene knockdown effect in cells by interacting with naturally occurring RNA processing machinery. However not all siRNAs induce this effect equally. Several heterogeneous kinds of machine learning techniques and feature sets have been applied to modeling siRNAs and their abilities to induce knockdown. There is some growing agreement to which techniques produce maximally predictive models and yet there is little consensus for methods to compare among predictive models. Also, there are few comparative studies that address what the effect of choosing learning technique, feature set or cross validation approach has on finding and discriminating among predictive models.<h4>Principal findings</h4>Three learning techniques were used to develop predictive models for effective siRNA sequences including Artificial Neural Networks (ANNs), General Linear Models (GLMs) and Support Vector Machines (SVMs). Five feature mapping methods were also used to generate models of siRNA activities. The 2 factors of learning technique and feature mapping were evaluated by complete 3x5 factorial ANOVA. Overall, both learning techniques and feature mapping contributed significantly to the observed variance in predictive models, but to differing degrees for precision and accuracy as well as across different kinds and levels of model cross-validation.<h4>Conclusions</h4>The methods presented here provide a robust statistical framework to compare among models developed under distinct learning techniques and feature sets for siRNAs. Further comparisons among current or future modeling approaches should apply these or other suitable statistically equivalent methods to critically evaluate the performance of proposed models. ANN and GLM techniques tend to be more sensitive to the inclusion of noisy features, but the SVM technique is more robust under large numbers of features for measures of model precision and accuracy. Features found to result in maximally predictive models are not consistent across learning techniques, suggesting care should be taken in the interpretation of feature relevance. In the models developed here, there are statistically differentiable combinations of learning techniques and feature mapping methods where the SVM technique under a specific combination of features significantly outperforms all the best combinations of features within the ANN and GLM techniques.
format	article
author	Kyle A McQuisten Andrew S Peek
author_facet	Kyle A McQuisten Andrew S Peek
author_sort	Kyle A McQuisten
title	Comparing artificial neural networks, general linear models and support vector machines in building predictive models for small interfering RNAs.
title_short	Comparing artificial neural networks, general linear models and support vector machines in building predictive models for small interfering RNAs.
title_full	Comparing artificial neural networks, general linear models and support vector machines in building predictive models for small interfering RNAs.
title_fullStr	Comparing artificial neural networks, general linear models and support vector machines in building predictive models for small interfering RNAs.
title_full_unstemmed	Comparing artificial neural networks, general linear models and support vector machines in building predictive models for small interfering RNAs.
title_sort	comparing artificial neural networks, general linear models and support vector machines in building predictive models for small interfering rnas.
publisher	Public Library of Science (PLoS)
publishDate	2009
url	https://doaj.org/article/54a6ebf42aa84d0aa39f142f1ab115e5
work_keys_str_mv	AT kyleamcquisten comparingartificialneuralnetworksgenerallinearmodelsandsupportvectormachinesinbuildingpredictivemodelsforsmallinterferingrnas AT andrewspeek comparingartificialneuralnetworksgenerallinearmodelsandsupportvectormachinesinbuildingpredictivemodelsforsmallinterferingrnas
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Comparing artificial neural networks, general linear models and support vector machines in building predictive models for small interfering RNAs.

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