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Authors: Vojtěch Bystrý and Matej Lexa

Affiliation: Masaryk University, Czech Republic

ISBN: 978-989-8425-90-4

Keyword(s): Bioinformatics, Data-mining, Hidden markov models.

Related Ontology Subjects/Areas/Topics: Bioinformatics ; Biomedical Engineering ; Data Mining and Machine Learning ; Model Design and Evaluation ; Pattern Recognition, Clustering and Classification ; Sequence Analysis

Abstract: In this work we created a sequence model that goes beyond simple linear patterns to model a specific type of higher-order relationship possible in biological sequences. Particularly, we seek models that can account for partially overlaid and interleaved patterns in biological sequences. Our proposed context-switching model (cswHMM) is designed as a variable-order hidden Markov model (HMM) with a specific structure that allows switching control between two or more sub-models. An important feature of our model is the ability of its sub-models to store their last active state, so when each sub-model resumes control it can continue uninterrupted. This is a fundamental variation on the closely related jumping HMMs. A combination of as few as two simple linear HMMs can describe sequences with complicated mixed dependencies. Tests of this approach suggest that a combination of HMMs for protein sequence analysis, such as pattern mining based HMMs or profile HMMs, with the context-switching ap proach can improve the descriptive ability and performance of the models. (More)

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Paper citation in several formats:
Bystrý, V. and Lexa, M. (2012). cswHMM: A NOVEL CONTEXT SWITCHING HIDDEN MARKOV MODEL FOR BIOLOGICAL SEQUENCE ANALYSIS.In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012) ISBN 978-989-8425-90-4, pages 208-213. DOI: 10.5220/0003780902080213

@conference{bioinformatics12,
author={Vojtěch Bystrý. and Matej Lexa.},
title={cswHMM: A NOVEL CONTEXT SWITCHING HIDDEN MARKOV MODEL FOR BIOLOGICAL SEQUENCE ANALYSIS},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)},
year={2012},
pages={208-213},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003780902080213},
isbn={978-989-8425-90-4},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)
TI - cswHMM: A NOVEL CONTEXT SWITCHING HIDDEN MARKOV MODEL FOR BIOLOGICAL SEQUENCE ANALYSIS
SN - 978-989-8425-90-4
AU - Bystrý, V.
AU - Lexa, M.
PY - 2012
SP - 208
EP - 213
DO - 10.5220/0003780902080213

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