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Use of a Novel Grammatical Inference Approach in Classification of Amyloidogenic Hexapeptides


Affiliations
1 University of Silesia, Ulica Zytnia 12, 41-200 Sosnowiec, Poland
2 Department of Computer Engineering, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
 

The present paper is a novel contribution to the field of bioinformatics by using grammatical inference in the analysis of data.We developed an algorithm for generating star-free regular expressions which turned out to be good recommendation tools, as they are characterized by a relatively high correlation coefficient between the observed and predicted binary classifications. The experiments have been performed for three datasets of amyloidogenic hexapeptides, and our results are compared with those obtained using the graph approaches, the current state-of-the-art methods in heuristic automata induction, and the support vector machine.The results showed the superior performance of the new grammatical inference algorithm on fixed-length amyloid datasets.
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  • Use of a Novel Grammatical Inference Approach in Classification of Amyloidogenic Hexapeptides

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Authors

Wojciech Wieczorek
University of Silesia, Ulica Zytnia 12, 41-200 Sosnowiec, Poland
Olgierd Unold
Department of Computer Engineering, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland

Abstract


The present paper is a novel contribution to the field of bioinformatics by using grammatical inference in the analysis of data.We developed an algorithm for generating star-free regular expressions which turned out to be good recommendation tools, as they are characterized by a relatively high correlation coefficient between the observed and predicted binary classifications. The experiments have been performed for three datasets of amyloidogenic hexapeptides, and our results are compared with those obtained using the graph approaches, the current state-of-the-art methods in heuristic automata induction, and the support vector machine.The results showed the superior performance of the new grammatical inference algorithm on fixed-length amyloid datasets.