Related papers: Computing all minimal Markov bases in Macaulay2
We present Binomials, a package for the computer algebra system Macaulay2, which specializes well known algorithms to binomial ideals. These come up frequently in algebraic statistics and commutative algebra, and it is shown that…
Symbolic powers are a classical commutative algebra topic that relates to primary decomposition, consisting, in some circumstances, of the functions that vanish up to a certain order on a given variety. However, these are notoriously…
We introduce the MatrixSchubert package for the computer algebra system Macaulay2. This package has tools to construct and study matrix Schubert varieties and alternating sign matrix (ASM) varieties. The package also introduces tools for…
A toric ideal is called robust if its universal Gr\"obner basis is a minimal set of generators, and is called generalized robust if its universal Gr\"obner basis equals its universal Markov basis (the union of all its minimal sets of…
This paper is concerned with the topological invariant of a graph given by the maximum degree of a Markov basis element for the corresponding graph model for binary contingency tables. We describe a degree four Markov basis for the model…
We introduce the package "GraphicalModelsMLE" for computing the maximum likelihood estimates (MLEs) of a Gaussian graphical model in the computer algebra system Macaulay2. This package allows the computation of MLEs for the class of…
We introduce the Macaulay2 package $\mathtt{LinearTruncations}$ for finding and studying the truncations of a multigraded module over a standard multigraded ring that have linear resolutions.
Using discrete Morse theory, Batzies and Welker introduced Morse resolutions of monomial ideals. In this note, we present the {\it Macaulay2} package {\tt MorseResolutions} for working with two important classes of Morse resolutions:…
In this Macaulay2 \cite{M2} package we define an object called {\it linear code}. We implement functions that compute basic parameters and objects associated with a linear code, such as generator and parity check matrices, the dual code,…
We study Markov bases of decomposable graphical models consisting of primitive moves (i.e., square-free moves of degree two) by determining the structure of fibers of sample size two. We show that the number of elements of fibers of sample…
This paper describes the RationalMaps package for Macaulay2. This package provides functionality for computing several aspects of rational maps such as whether a map is birational, or a closed embedding.
Let $X$ be a complete simplicial toric variety over a finite field with a split torus $T_X$. For any matrix $Q$, we are interested in the subgroup $Y_Q$ of $T_X$ parameterized by the columns of $Q$. We give an algorithm for obtaining a…
Given a collection of line bundles on a complete toric variety, the Macaulay2 package QuiversToricVarieties contains functions to construct its quiver of sections and check whether the collection is strong exceptional. It contains a…
A graph-theoretic method, simpler than existing ones, is used to characterize the minimal set of monomial generators for the integral closure of any algebra of polynomials generated by quadratic monomials. The toric ideal of relations…
We consider conditional exact tests of factor effects in designed experiments for discrete response variables. Similarly to the analysis of contingency tables, Markov chain Monte Carlo methods can be used for performing exact tests,…
{\tt AbstractSimplicialComplexes.m2} is a computer algebra package written for the computer algebra system {\tt Macaulay2} \cite{M2}. It provides new infrastructure to work with abstract simplicial complexes and related homological…
Two correspondences have been provided that associate any linear code over a finite field with a binomial ideal. In this paper, algorithms for computing their Graver bases and universal Gr\"obner bases are given. To this end, a connection…
This note describes a Macaulay2 package for handling divisors. Group operations for divisors are included. There are methods for converting divisors to reflexive or invertible sheaves. Additionally, there are methods for checking whether…
The package Binomials contains implementations of specialized algorithms for binomial ideals, including primary decomposition into binomial ideals. The current implementation works in characteristic zero. Primary decomposition is restricted…
We introduce the Macaulay2 package GradedLieAlgebras for doing computations in graded Lie algebras presented by generators and relations.