Comprehensive decision tree models in bioinformatics.

<h4>Purpose</h4>Classification is an important and widely used machine learning technique in bioinformatics. Researchers and other end-users of machine learning software often prefer to work with comprehensible models where knowledge extraction and explanation of reasoning behind the cla...

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Autores principales:	Gregor Stiglic, Simon Kocbek, Igor Pernek, Peter Kokol
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/782c508894924c779893ef1e028a65c0
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spelling	oai:doaj.org-article:782c508894924c779893ef1e028a65c02021-11-18T07:23:41ZComprehensive decision tree models in bioinformatics.1932-620310.1371/journal.pone.0033812https://doaj.org/article/782c508894924c779893ef1e028a65c02012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22479449/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Purpose</h4>Classification is an important and widely used machine learning technique in bioinformatics. Researchers and other end-users of machine learning software often prefer to work with comprehensible models where knowledge extraction and explanation of reasoning behind the classification model are possible.<h4>Methods</h4>This paper presents an extension to an existing machine learning environment and a study on visual tuning of decision tree classifiers. The motivation for this research comes from the need to build effective and easily interpretable decision tree models by so called one-button data mining approach where no parameter tuning is needed. To avoid bias in classification, no classification performance measure is used during the tuning of the model that is constrained exclusively by the dimensions of the produced decision tree.<h4>Results</h4>The proposed visual tuning of decision trees was evaluated on 40 datasets containing classical machine learning problems and 31 datasets from the field of bioinformatics. Although we did not expected significant differences in classification performance, the results demonstrate a significant increase of accuracy in less complex visually tuned decision trees. In contrast to classical machine learning benchmarking datasets, we observe higher accuracy gains in bioinformatics datasets. Additionally, a user study was carried out to confirm the assumption that the tree tuning times are significantly lower for the proposed method in comparison to manual tuning of the decision tree.<h4>Conclusions</h4>The empirical results demonstrate that by building simple models constrained by predefined visual boundaries, one not only achieves good comprehensibility, but also very good classification performance that does not differ from usually more complex models built using default settings of the classical decision tree algorithm. In addition, our study demonstrates the suitability of visually tuned decision trees for datasets with binary class attributes and a high number of possibly redundant attributes that are very common in bioinformatics.Gregor StiglicSimon KocbekIgor PernekPeter KokolPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 3, p e33812 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Gregor Stiglic Simon Kocbek Igor Pernek Peter Kokol Comprehensive decision tree models in bioinformatics.
description	<h4>Purpose</h4>Classification is an important and widely used machine learning technique in bioinformatics. Researchers and other end-users of machine learning software often prefer to work with comprehensible models where knowledge extraction and explanation of reasoning behind the classification model are possible.<h4>Methods</h4>This paper presents an extension to an existing machine learning environment and a study on visual tuning of decision tree classifiers. The motivation for this research comes from the need to build effective and easily interpretable decision tree models by so called one-button data mining approach where no parameter tuning is needed. To avoid bias in classification, no classification performance measure is used during the tuning of the model that is constrained exclusively by the dimensions of the produced decision tree.<h4>Results</h4>The proposed visual tuning of decision trees was evaluated on 40 datasets containing classical machine learning problems and 31 datasets from the field of bioinformatics. Although we did not expected significant differences in classification performance, the results demonstrate a significant increase of accuracy in less complex visually tuned decision trees. In contrast to classical machine learning benchmarking datasets, we observe higher accuracy gains in bioinformatics datasets. Additionally, a user study was carried out to confirm the assumption that the tree tuning times are significantly lower for the proposed method in comparison to manual tuning of the decision tree.<h4>Conclusions</h4>The empirical results demonstrate that by building simple models constrained by predefined visual boundaries, one not only achieves good comprehensibility, but also very good classification performance that does not differ from usually more complex models built using default settings of the classical decision tree algorithm. In addition, our study demonstrates the suitability of visually tuned decision trees for datasets with binary class attributes and a high number of possibly redundant attributes that are very common in bioinformatics.
format	article
author	Gregor Stiglic Simon Kocbek Igor Pernek Peter Kokol
author_facet	Gregor Stiglic Simon Kocbek Igor Pernek Peter Kokol
author_sort	Gregor Stiglic
title	Comprehensive decision tree models in bioinformatics.
title_short	Comprehensive decision tree models in bioinformatics.
title_full	Comprehensive decision tree models in bioinformatics.
title_fullStr	Comprehensive decision tree models in bioinformatics.
title_full_unstemmed	Comprehensive decision tree models in bioinformatics.
title_sort	comprehensive decision tree models in bioinformatics.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/782c508894924c779893ef1e028a65c0
work_keys_str_mv	AT gregorstiglic comprehensivedecisiontreemodelsinbioinformatics AT simonkocbek comprehensivedecisiontreemodelsinbioinformatics AT igorpernek comprehensivedecisiontreemodelsinbioinformatics AT peterkokol comprehensivedecisiontreemodelsinbioinformatics
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Comprehensive decision tree models in bioinformatics.

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