arXiv subjects

Dimitra Kosta

Publications and source records attributed to Dimitra Kosta.

16 recordsLinked to original sources

arXiv2026

Distance Reduction in Bouquet Decompositions and Toric Ideals of Graphs

The distance-reduction property for a generating set, i.e., a Markov basis, of a toric ideal is a condition that ensures tight connectivity of its fibres. In this paper, we study the distance-reduction property for toric ideals of graphs and move on to explore the relationship between the distance-reduction property and the bouquet structure of homogeneous toric ideals, which includes the class of toric ideals of graphs. For toric ideals of graphs which are complete intersection, we show that the minimal Markov bases are distance-reducing if and only if they distance-reduce the circuits of the ideal. We then consider how the distance-reduction properties interact with the bouquet structure of the toric ideal. Bouquets are a combinatorial structure that capture the essential combinatorial information of the toric ideal. Under the condition of homogeneity, we show that, for toric ideals with the same bouquet structure and signature, the distance-reduction properties are preserved. For homogeneous toric ideals whose bouquet matrix is a monomial curve in $\mathbb{A}^3$, we give necessary and sufficient conditions for when the minimal Markov bases are distance-reducing.

math.AC↗

arXiv2025

Singular Learning Theory for Factor Analysis

Watanabe's singular learning theory provides a framework for asymptotic analysis of Bayesian model selection for statistical models with singularities, where traditional statistical regularity assumptions fail. Learning coefficients, also known as real log canonical thresholds, play a central role in singular learning, as they govern the asymptotic behavior of Bayesian marginal likelihood integrals in settings where the Laplace approximations used for regular statistical models are not applicable. Learning coefficients are algebraic invariants that quantify the geometric complexity of a model and reveal how the singular structure impacts the model's generalization properties. In this paper, we apply algebraic methods to study the learning coefficients of factor analysis models, which are widely used latent variable models for continuously distributed data. Our main result provides exact formulas for learning coefficients of factor analysis models. Moreover, we study the singularity types of specific factor analysis models in detail.

math.ST↗

arXiv2025

On the dimension of the strongly robust complex for configurations in general position

Strongly robust toric ideals are the toric ideals for which the set of indispensable binomials is the Graver basis. The strongly robust simplicial complex $\Delta _T$ of a simple toric ideal $I_T$ determines the strongly robust property for all toric ideals that have $I_T$ as their bouquet ideal. We prove that $\text{dim} \Delta_T<\text{rank}(T)$ for configurations in general position, partially answering a question posed by Sullivant.

math.AC↗

arXiv2024

Classification of real hyperplane singularities by real log canonical thresholds

The log canonical threshold (lct) is a fundamental invariant in birational geometry, essential for understanding the complexity of singularities in algebraic varieties. Its real counterpart, the real log canonical threshold (rlct), also known as the learning coefficient, has become increasingly relevant in statistics and machine learning, where it plays a critical role in model selection and error estimation for singular statistical models. In this paper, we investigate the rlct and its multiplicity for real (not necessarily reduced) hyperplane arrangements. We derive explicit combinatorial formulas for these invariants, generalizing earlier results that were limited to specific examples. Moreover, we provide a general algebraic theory for real log canonical thresholds, and present a SageMath implementation for efficiently computing the rlct and its multiplicity in the case or real hyperplane arrangements. Applications to examples are given, illustrating how the formulas can also be used to analyze the asymptotic behavior of high-dimensional volume integrals.

math.AG↗

arXiv2024

Distance Reducing Markov Bases

The distance reducing property for Markov bases is an important property that provides a bound on the mixing time of the associated Markov chain. The goal of this project is to understand properties of distance-reducing Markov bases. We explore the distance reducing property for monomial curves and give a complete characterisation of distance reduction in the case of complete intersection monomial curves. Our characterisation carefully uses the notion of gluings for numerical semigroups. We also characterise the distance reducing property for non-complete intersection monomial curves in small dimensions. We also explore the distance irreducible elements: the moves that appear in all distance reducing Markov bases.

math.AC↗

arXiv2023

The strongly robust simplicial complex of monomial curves

To every simple toric ideal $I_T$ one can associate the strongly robust simplicial complex $\Delta _T$, which determines the strongly robust property for all ideals that have $I_T$ as their bouquet ideal. We show that for the simple toric ideals of monomial curves in $\mathbb{A}^{s}$, the strongly robust simplicial complex $\Delta _T$ is either $\{\emptyset \}$ or contains exactly one 0-dimensional face. In the case of monomial curves in $\mathbb{A}^{3}$, the strongly robust simplicial complex $\Delta _T$ contains one 0-dimensional face if and only if the toric ideal $I_T$ is a complete intersection ideal with exactly two Betti degrees. Finally, we provide a construction to produce infinitely many strongly robust ideals with bouquet ideal the ideal of a monomial curve and show that they are all produced this way.

math.AC↗

arXiv2022

On the strongly robustness property of toric ideals

To every toric ideal one can associate an oriented matroid structure, consisting of a graph and another toric ideal, called bouquet ideal. The connected components of this graph are called bouquets. Bouquets are of three types; free, mixed and non mixed. We prove that the cardinality of the following sets - the set of indispensable elements, minimal Markov bases, the Universal Markov basis and the Universal Gröbner basis of a toric ideal - depends only on the type of the bouquets and the bouquet ideal. These results enable us to introduce the strongly robustness simplicial complex and show that it determines the strongly robustness property. For codimension 2 toric ideals, we study the strongly robustness simplicial complex and prove that robustness implies strongly robustness.

math.AC↗

arXiv2022

Embeddability of centrosymmetric matrices capturing the double-helix structure in natural and synthetic DNA

In this paper, we discuss the embedding problem for centrosymmetric matrices, which are higher order generalizations of the matrices occurring in Strand Symmetric Models. These models capture the substitution symmetries arising from the double helix structure of the DNA. Deciding whether a transition matrix is embeddable or not enables us to know if the observed substitution probabilities are consistent with a homogeneous continuous time substitution model, such as the Kimura models, the Jukes-Cantor model or the general time-reversible model. On the other hand, the generalization to higher order matrices is motivated by the setting of synthetic biology, which works with different sizes of genetic alphabets.

q-bio.PE↗

arXiv2021

The Model-Specific Markov Embedding Problem for Symmetric Group-Based Models

We study model embeddability, which is a variation of the famous embedding problem in probability theory, when apart from the requirement that the Markov matrix is the matrix exponential of a rate matrix, we additionally ask that the rate matrix follows the model structure. We provide a characterisation of model embeddable Markov matrices corresponding to symmetric group-based phylogenetic models. In particular, we provide necessary and sufficient conditions in terms of the eigenvalues of symmetric group-based matrices. To showcase our main result on model embeddability, we provide an application to hachimoji models, which are eight-state models for synthetic DNA. Moreover, our main result on model embeddability enables us to compute the volume of the set of model embeddable Markov matrices relative to the volume of other relevant sets of Markov matrices within the model.

q-bio.PE↗

arXiv2019

Maximum Likelihood Estimation of Toric Fano Varieties

We study the maximum likelihood estimation problem for several classes of toric Fano models. We start by exploring the maximum likelihood degree for all $2$-dimensional Gorenstein toric Fano varieties. We show that the ML degree is equal to the degree of the surface in every case except for the quintic del Pezzo surface with two ordinary double points and provide explicit expressions that allow one to compute the maximum likelihood estimate in closed form whenever the ML degree is less than 5. We then explore the reasons for the ML degree drop using $A$-discriminants and intersection theory. Finally, we show that toric Fano varieties associated to 3-valent phylogenetic trees have ML degree one and provide a formula for the maximum likelihood estimate. We prove it as a corollary to a more general result about the multiplicativity of ML degrees of codimension zero toric fiber products, and it also follows from a connection to a recent result about staged trees.

math.ST↗

arXiv2018

Unboundedness of Markov complexity of monomial curves in ${\mathbb A}^n$ for $n\geq 4$

Computing the complexity of Markov bases is an extremely challenging problem; no formula is known in general and there are very few classes of toric ideals for which the Markov complexity has been computed. A monomial curve $C$ in $\mathbb{A}^3$ has Markov complexity $m(C)$ two or three. Two if the monomial curve is complete intersection and three otherwise. Our main result shows that there is no $d\in \mathbb{N}$ such that $m(C)\leq d$ for all monomial curves $C$ in $\mathbb{A}^4$. The same result is true even if we restrict to complete intersections. We extend this result to all monomial curves in $\mathbb{A}^n, n\geq 4$.

math.AC↗

arXiv2017

A note on Maximum Likelihood Estimation for cubic and quartic canonical toric del Pezzo Surfaces

This article focuses on the study of toric algebraic statistical models which correspond to toric Del Pezzo surfaces with Du Val singularities. A closed-form for the Maximum Likelihood Estimate of algebraic statistical models which correspond to cubic and quartic toric Del Pezzo surfaces with Du Val singular points is given. Also, we calculate the ML degrees of some toric Del Pezzo surfaces of degree less than or equal to six, which equals the degree of the surface in all the case but one, namely the quintic with two points of type $\mathbb{A}_1$.

math.ST↗

arXiv2017

Geometry of symmetric group-based models

Phylogenetic models have polynomial parametrization maps. For symmetric group-based models, Matsen studied the polynomial inequalities that characterize the joint probabilities in the image of these parametrizations. We employ this description for maximum likelihood estimation via numerical algebraic geometry. In particular, we explore an example where the maximum likelihood estimate does not exist, which would be difficult to discover without using algebraic methods. We also study the embedding problem for symmetric group-based models, i.e. we identify which mutation matrices are matrix exponentials of rate matrices that are invariant under a group action.

q-bio.PE↗

arXiv2012

Computing $α$-invariants of singular del Pezzo surfaces

We prove new local inequality for divisors on surfaces and utilize it to compute $α$-invariants of singular del Pezzo surfaces, which implies that del Pezzo surfaces of degree one whose singular points are of type $\mathbb{A}_{1}$, $\mathbb{A}_{2}$, $\mathbb{A}_{3}$, $\mathbb{A}_{4}$, $\mathbb{A}_{5}$ or $\mathbb{A}_{6}$ are Kähler-Einstein.

math.AG↗

arXiv2009

Del Pezzo surfaces with Du Val singularities

In this paper we study the problem of existence of orbifold Kaehler-Einstein metrics on del Pezzo surfaces of degree 1 with Du Val singular points. Moreover we compute global log canonical thresholds of del Pezzo surfaces of degree 1 with Du Val singularities and of del Pezzo surfaces of Picard rank 1 with Du Val singularities.

math.AG↗

arXiv2008

Factoriality of complete intersection threefolds

Let X be a complete intersection of two hypersurfaces F_n and F_k in the projective space P^5 of degree n and k respectively with n >= k, such that the singularities of X are nodal and F_k is smooth. We prove that if the threefold X has at most (n+k-2)(n-1)-1 singular points, then it is factorial.

math.AG↗