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A hybrid evolutionary approach for the protein classification problem

Tsunoda, Denise F. and Lopes, Heitor S. and Freitas, Alex A. (2009) A hybrid evolutionary approach for the protein classification problem. In: Nguyen, Ngoc Thanh and Kowalczyk, Ryszard and Chen, Shyi-Ming, eds. Computational Collective Intelligence. Semantic Web, Social Networks and Multiagent Systems First International Conference. Lecture Notes in Computer Science . Springer, Berlin, Germany, pp. 182-196. ISBN 978-3-642-04440-3. E-ISBN 978-3-642-04441-0. (doi:10.1007/978-3-642-04441-0_55) (The full text of this publication is not currently available from this repository. You may be able to access a copy if URLs are provided)

The full text of this publication is not currently available from this repository. You may be able to access a copy if URLs are provided. (Contact us about this Publication)
Official URL
http://dx.doi.org/10.1007/978-3-642-04441-0_55

Abstract

This paper proposes a hybrid algorithm that combines characteristics of both Genetic Programming (GP) and Genetic Algorithms (GAs), for discovering motifs in proteins and predicting their functional classes, based on the discovered motifs. In this algorithm, individuals are represented as IF-THEN classification rules. The rule antecedent consists of a combination of motifs automatically extracted from protein sequences. The rule consequent consists of the functional class predicted for a protein whose sequence satisfies the combination of motifs in the rule antecedent. The system can be used in two different ways. First, as a stand-alone classification system, where the evolved classification rules are directly used to predict the functional classes of proteins. Second, the system can be used just as an “attribute construction” method, discovering motifs that are given, as predictor attributes, to another classification algorithm. In this usage of the system, a classical decision tree induction algorithm was used as the classifier. The proposed system was evaluated in these two scenarios and compared with another Genetic Algorithm designed specifically for the discovery of motifs – and therefore used only as an attribute construction algorithm. This comparison was performed by mining an enzyme data set extracted from the Protein Data Bank. The best results were obtained when using the proposed hybrid GP/GA as an attribute construction algorithm and performing the classification (using the constructed attributes) with the decision tree induction algorithm.

Item Type: Book section
DOI/Identification number: 10.1007/978-3-642-04441-0_55
Uncontrolled keywords: determinacy analysis; Craig interpolants; bioinformatics; protein classification problem; evolutionary computation; genetic programming; genetic algorithm
Subjects: Q Science > QA Mathematics (inc Computing science) > QA 76 Software, computer programming,
Divisions: Faculties > Sciences > School of Computing > Computational Intelligence Group
Depositing User: Alex Freitas
Date Deposited: 21 Sep 2012 09:49 UTC
Last Modified: 04 Feb 2020 04:04 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/30585 (The current URI for this page, for reference purposes)
Freitas, Alex A.: https://orcid.org/0000-0001-9825-4700
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