Geometric characterization of data sets with unique reduced Gröbner bases

DOI10.1007/S11538-019-00624-XMaRDI QIDQ2002131zbMATH OpenOpenAlexWikidataFDO

Authors Qijun He, Elena S. Dimitrova, Brandilyn Stigler, Anyu Zhang

Publication date 11 July 2019

Published in Bulletin of Mathematical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1811.01114

zbMATH Keywords

ideals of pointsalgebraic design of experimentsbiological data sciencestaircases of monomial idealsGröbner bases

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Gröbner bases; other bases for ideals and modules (e.g., Janet and border bases) (13P10)

Abstract: Model selection based on experimental data is an important challenge in biological data science. Particularly when collecting data is expensive or time consuming, as it is often the case with clinical trial and biomolecular experiments, the problem of selecting information-rich data becomes crucial for creating relevant models. We identify geometric properties of input data that result in a unique algebraic model and we show that if the data form a staircase, or a so-called linear shift of a staircase, the ideal of the points has a unique reduced Gro "bner basis and thus corresponds to a unique model. We use linear shifts to partition data into equivalence classes with the same basis. We demonstrate the utility of the results by applying them to a Boolean model of the well-studied lac operon in E. coli.

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Cited in

(3)

• A Unified Approach to Reverse Engineering and Data Selection for Unique Network Identification
• Gröbner bases of convex neural code ideals (research)
• Algebraic model selection and experimental design in biological data science

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