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Authors: Vladimir Nikulin and Geoffrey J. McLachlan

Affiliation: University of Queensland, Australia

ISBN: 978-989-674-019-1

Keyword(s): Matrix factorisation, Gradient-based optimisation, Cross-validation, Gene expression data.

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Artificial Intelligence ; Bioinformatics ; Biomedical Engineering ; Biostatistics and Stochastic Models ; Computational Intelligence ; Data Mining and Machine Learning ; Soft Computing

Abstract: The high dimensionality of microarray data, the expressions of thousands of genes in a much smaller number of samples, presents challenges that affect the applicability of the analytical results. In principle, it would be better to describe the data in terms of a small number of metagenes, derived as a result of matrix factorisation, which could reduce noise while still capturing the essential features of the data. We propose a fast and general method for matrix factorization which is based on decomposition by parts that can reduce the dimension of expression data from thousands of genes to several factors. Unlike classification and regression, matrix decomposition requires no response variable and thus falls into category of unsupervised learning methods. We demonstrate the effectiveness of this approach to the supervised classification of gene expression data.

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Paper citation in several formats:
Nikulin V.; J. McLachlan G. and (2010). ON THE GRADIENT-BASED ALGORITHM FOR MATRIX FACTORIZATION APPLIED TO DIMENSIONALITY REDUCTION.In Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010) ISBN 978-989-674-019-1, pages 147-152. DOI: 10.5220/0002736601470152

@conference{bioinformatics10,
author={Vladimir Nikulin and Geoffrey {J. McLachlan}},
title={ON THE GRADIENT-BASED ALGORITHM FOR MATRIX FACTORIZATION APPLIED TO DIMENSIONALITY REDUCTION},
booktitle={Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010)},
year={2010},
pages={147-152},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0002736601470152},
isbn={978-989-674-019-1},
}

TY - CONF

JO - Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010)
TI - ON THE GRADIENT-BASED ALGORITHM FOR MATRIX FACTORIZATION APPLIED TO DIMENSIONALITY REDUCTION
SN - 978-989-674-019-1
AU - Nikulin, V.
AU - J. McLachlan, G.
PY - 2010
SP - 147
EP - 152
DO - 10.5220/0002736601470152

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