Markov basis and Gröbner basis of Segre-Veronese configuration for testing independence in group-wise selections

DOI10.1007/S10463-008-0171-7MaRDI QIDQ904091zbMATH OpenOpenAlexFDO

Authors Satoshi Aoki, Takayuki Hibi, Hidefumi Ohsugi, Akimichi Takemura

Publication date 15 January 2016

Published in Annals of the Institute of Statistical Mathematics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/0704.1074

zbMATH Keywords

Markov chain Monte Carlocontingency tableexact testshaplotypeHardy-Weinberg modeldiplotypeNational Center Test (Japan)structural zero

Mathematics Subject Classification ID

Computational methods for problems pertaining to statistics (62-08) Applications of statistics to biology and medical sciences; meta analysis (62P10) Contingency tables (62H17) Gröbner bases; other bases for ideals and modules (e.g., Janet and border bases) (13P10)

Abstract: We consider testing independence in group-wise selections with some restrictions on combinations of choices. We present models for frequency data of selections for which it is easy to perform conditional tests by Markov chain Monte Carlo (MCMC) methods. When the restrictions on the combinations can be described in terms of a Segre-Veronese configuration, an explicit form of a Gr"obner basis consisting of moves of degree two is readily available for performing a Markov chain. We illustrate our setting with the National Center Test for university entrance examinations in Japan. We also apply our method to testing independence hypotheses involving genotypes at more than one locus or haplotypes of alleles on the same chromosome.

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Cited in

(5)

• A Gröbner basis characterization for chordal comparability graphs
• Gröbner bases of nested configurations
• Markov-chain Monte Carlo methods for the Box-Behnken designs and centrally symmetric configurations
• Lexicographic and reverse lexicographic quadratic Gröbner bases of cut ideals
• Conditional inference given partial information in contingency tables using Markov bases

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