Comprehensive decision tree models in bioinformatics

Gregor Štiglic (Author), Simon Kocbek (Author), Igor Pernek (Author), Peter Kokol (Author)

Abstract

Purpose 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. Methods 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. Results 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 notexpected significant differences in classification performance, the resultsdemonstrate a significant increase of accuracy in less complex visuallytuned 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 assumptionthat the tree tuning times are significantly lower for the proposed method in comparison to manual tuning of the decision tree. Conclusions 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 anda high number of possibly redundant attributes that are very common in bioinformatics.

Keywords

decision tree models;machine learning technique;visual tuning;bioinformatics;

Data

Language:	English
Year of publishing:	2012
Typology:	1.01 - Original Scientific Article
Organization:	UM FZV - Faculty of Health Sciences
UDC:	004.8:575.112
COBISS:	1788068
ISSN:	1932-6203
Views:	1537
Downloads:	291
Average score:	0 (0 votes)
Metadata:

Other data

Secondary language:	Slovenian
Secondary keywords:	drevo odločanja;strojno učenje;vizualno uravnavanje;bioinformatika;
URN:	URN:SI:UM:
Type (COBISS):	Scientific work
Pages:	str. [1-14], e33812
Volume:	ǂVol. ǂ7
Issue:	ǂiss. ǂ3
Chronology:	2012
DOI:	10.1371/journal.pone.0033812
ID:	8720360