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Structural classification of proteins through amino acid sequence using interval type-2 fuzzy logic system

Version 2 2024-06-05, 11:47
Version 1 2023-10-26, 04:17
conference contribution
posted on 2024-06-05, 11:47 authored by T Nguyen, Abbas KhosraviAbbas Khosravi, Douglas CreightonDouglas Creighton, S Nahavandi
This paper introduces a new multi-output interval type-2 fuzzy logic system (MOIT2FLS) that is automatically constructed from unsupervised data clustering method and trained using heuristic genetic algorithm for a protein secondary structure classification. Three structure classes are distinguished including helix, strand (sheet) and coil which correspond to three outputs of the MOIT2FLS. Quantitative properties of amino acids are used to characterize the twenty amino acids rather than the widely used computationally expensive binary encoding scheme. Amino acid sequences are parsed into learnable patterns using a local moving window strategy. Three clustering tasks are performed using the adaptive vector quantization method to derive an equal number of initial rules for each type of secondary structure. Genetic algorithm is applied to optimally adjust parameters of the MOIT2FLS with the purpose of maximizing the Q3 measure. Comprehensive experimental results demonstrate the strong superiority of the proposed approach over the traditional methods including Chou-Fasman method, Garnier-Osguthorpe-Robson method, and artificial neural network models.

History

Pagination

1123-1130

Location

Beijing, China

Start date

2014-07-06

End date

2014-07-11

ISSN

1098-7584

ISBN-13

9781479920723

Language

eng

Publication classification

E Conference publication, E1 Full written paper - refereed

Copyright notice

2014, IEEE

Title of proceedings

Proceedings of the 2014 IEEE International Conference on Fuzzy Systems: FUZZ-IEEE 2014

Event

IEEE International Conference on Fuzzy Systems (2014: Beijing, China)

Publisher

Institute of Electrical and Electronics Engineers Inc.

Place of publication

Beijing, China

Series

IEEE International Conference on Fuzzy Systems

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