Searcharxiv⌕ Search
Home/Archive/arXiv

arXiv · 1607.07600

An introduction to computational algebraic statistics

Satoshi Aoki
View original source ↗Read source document ↗Export metadata ↓

Abstract

In this paper, we introduce the fundamental notion of a Markov basis, which is one of the first connections between commutative algebra and statistics. The notion of a Markov basis is first introduced by Diaconis and Sturmfels (1998) for conditional testing problems on contingency tables by Markov chain Monte Carlo methods. In this method, we make use of a connected Markov chain over the given conditional sample space to estimate the P-values numerically for various conditional tests. A Markov basis plays an importance role in this arguments, because it guarantees the connectivity of the chain, which is needed for unbiasedness of the estimate, for arbitrary conditional sample space. As another important point, a Markov basis is characterized as generators of the well-specified toric ideals of polynomial rings. This connection between commutative algebra and statistics is the main result of Diaconis and Sturmfels (1998). After this first paper, a Markov basis is studied intensively by many researchers both in commutative algebra and statistics, which yields an attractive field called computational algebraic statistics. In this paper, we give a review of the Markov chain Monte Carlo methods for contingency tables and Markov bases, with some fundamental examples. We also give some computational examples by algebraic software Macaulay2 and statistical software R. Readers can also find theoretical details of the problems considered in this paper and various results on the structure and examples of Markov bases in Aoki, Hara and Takemura (2012).

Explore related subjects

math.STstat.TH

Keep this discovery

BibTeXRIS

Satoshi Aoki. 2016-07-26. An introduction to computational algebraic statistics. https://arxiv.org/abs/1607.07600

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

A Scale Invariance Property of PCA

The PCA algorithm is sensitive to changes in measurement scale. Measuring one variable of a system in inches rather than centimeters, say, alters both its principal axes and principal eigenvalues. Although this scale dependence is generally complicated, we show here that it nevertheless obeys a strict invariance property: under a continuous scale adjustment, the initial state's $k$-th largest principal component (ordered by eigenvalue) continuously evolves into the final state's $k$-th largest principal component, for each $k$. In this sense, we can say that the modes of PCA are "order-stable" with respect to changes in measurement scale. A special case occurs when scaling along directions that are orthogonal to some modes. Here, apparent eigenvalue crossings can occur. However, we show that we can interpret these apparent crossings as cases where the modes instantaneously swap their orientation, in this way maintaining the required order stability.

math.ST↗
arXiv2026

Small noise asymptotics for linear parabolic SPDEs in two space dimensions with unknown damping factors

We study parametric estimation for second order linear parabolic stochastic partial differential equations in two space dimensions with a small volatility parameter driven by a $Q$-Wiener process with an unknown damping parameter using high frequency spatio-temporal data. We first provide an estimator for the damping parameter of the $Q$-Wiener process utilizing realized quadratic variations based on spatial and temporal increments. We next propose minimum contrast estimators of the diffusive and advective parameters in the SPDE using a contrast function with the proposed estimator of the damping parameter. We then construct a quasi-maximum likelihood estimator of the reaction parameter in the SPDE using the approximate coordinate process derived from the estimators of the diffusive and advective parameters. We also provide simulation results of the proposed estimators.

math.ST↗
arXiv2026

Spike Estimation from Heteroscedastic Noise via Random Splitting

In this paper, we consider a spiked Wigner type matrix with a heteroscedastic and unknown variance profile. It is well known that in the supercritical regime of the BBP transition, strong spikes can create outliers in the spectrum. Unfortunately, in the heteroscedastic case, in general it is not possible to estimate the spike strength from these observed outlier consistently, as the latter is a solution to a Dyson equation with unknown parameters from the variance profile. In this paper, inspired by the work on sparse matrix completion \citep{BordenaveCosteNadakuditi2023}, we introduce an asymmetrized model by randomly splitting the spiked matrix into two parts, which transforms the noisy Wigner type matrix into a non Hermitian random matrix, while preserving the Hermitian spikes at the cost of a dilution. We establish a BBP type transition for the asymmetrized model, from which we can estimate the strength of the spikes precisely, even without knowing the variance profile of the noise part. We then further apply our approach to study the correlation between two correlated spiked models, where the spike/signal parts of the two models are correlated, and the noise parts are independent but may both be heteroscedastic. By applying our asymmetrization approach to the two models separately and also jointly, we are able to obtain a precise estimate of the correlation between the signal parts of the two models.

math.ST↗