arXiv subjects

Jane Ivy Coons

Publications and source records attributed to Jane Ivy Coons.

18 recordsLinked to original sources

arXiv2026

Markov and lattice bases for Forman-Ricci curvature of graphs

Discrete Forman-Ricci curvature is a quantity associated to each edge of a graph that describes its local geometry. It has proven to be a useful tool in network analysis in a variety of applications. Recent work by Roost et al.\ (2024) proposed the use of Markov bases to sample from the space of graphs with prescribed vertex degrees and curvatures. In the present work, we further develop the algebraic and combinatorial theory of these Markov bases. We show that the degree of an indispensable Markov move grows at least quadratically in the maximum degree of the graph. In light of this result, a compact description of all Markov basis elements seems unattainable at present. Instead, we find a lattice basis for this problem using only degree three Markov moves, which allows us to employ recently-developed reinforcement learning methods for finding Markov moves that can be applied to a specific graph.

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arXiv2026

Algebraic statistics of Hüsler-Reiss graphical models in multivariate extremes

The field of extreme value statistics is concerned with modeling and predicting rare events. In a Hüsler-Reiss graphical model, a graph represents extremal conditional independence (CI) relations between random variables. These models are exponential families parameterized by a graph Laplacian and are considered the analogue of multivariate Gaussian models in the extremal setting. We study these models from the perspective of algebraic geometry. Translating the CI relations into polynomial constraints in the parameters, we define extremal CI ideals and find a determinantal representation of their generators. In terms of parametric inference, we study the extremal maximum likelihood degree as the number of solutions to a conditionally negative definite matrix completion problem. We also define and analyze the extremal maximum likelihood threshold for Hüsler-Reiss graphical models, which provides a certificate for the existence of a surrogate MLE in terms of the dimensionality of the point configuration that realizes the underlying summary statistic as a Euclidean distance matrix. We highlight throughout many interesting similarities but also differences with respect to Gaussian graphical models.

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arXiv2026

Identifiability in Graphical Discrete Lyapunov Models

In this paper, we study discrete Lyapunov models, which consist of steady-state distributions of first-order vector autoregressive models. The parameter matrix of such a model encodes a directed graph whose vertices correspond to the components of the random vector. This combinatorial framework naturally allows for cycles in the graph structure. We focus on the fundamental problem of identifying the entries of the parameter matrix. In contrast to the classical setting, we assume non-Gaussian error terms, which allows us to use the higher-order cumulants of the model. In this setup, we show generic identifiability for directed acyclic graphs with self-loops at each vertex and show how to express the parameters as a rational function of the cumulants. Furthermore, we establish local identifiability for all directed graphs containing self loops at each vertex and no isolated vertices. Finally, we provide first results on the defining equations of the models, showing model equivalence for certain graphs and paving the way towards structure learning.

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arXiv2025

Maximum Likelihood Degrees of Brownian Motion Tree Models: Star Trees and Root Invariance

A Brownian motion tree (BMT) model is a Gaussian model whose associated set of covariance matrices is linearly constrained according to common ancestry in a phylogenetic tree. We study the complexity of inferring the maximum likelihood (ML) estimator for a BMT model by computing its ML-degree. Our main result is that the ML-degree of the BMT model on a star tree with $n + 1$ leaves is $2^{n+1}-2n-3$, which was previously conjectured by Améndola and Zwiernik. We also prove that the ML-degree of a BMT model is independent of the choice of the root. The proofs rely on the toric geometry of concentration matrices in a BMT model. Toward this end, we produce a combinatorial formula for the determinant of the concentration matrix of a BMT model, which generalizes the Cayley-Prüfer theorem to complete graphs with weights given by a tree.

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arXiv2024

Mixtures of Discrete Decomposable Graphical Models

We study mixtures of decomposable graphical models, focusing on their ideals and dimensions. For mixtures of clique stars, we characterize the ideals in terms of ideals of mixtures of independence models. We also give a recursive formula for their ML degrees. Finally, we prove that second secant varieties of all other decomposable graphical models have the expected dimension.

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arXiv2024

Geometry of rational quasi-independence models as toric fiber products

We investigate the geometry of a family of log-linear statistical models called quasi-independence models. The toric fiber product is useful for understanding the geometry of parameter inference in these models because the maximum likelihood degree is multiplicative under the TFP. We define the coordinate toric fiber product, or cTFP, and give necessary and sufficient conditions under which a quasi-independence model is a cTFP of lower-order models. We show that the vanishing ideal of every 2-way quasi-independence model with ML-degree 1 can be realized as an iterated toric fiber product of linear ideals. We also classify which Lawrence lifts of 2-way quasi-independence models are cTFPs and give a necessary condition under which a $k$-way model has ML-degree 1 using its facial submodels.

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arXiv2023

Parametric and nonparametric symmetries in graphical models for extremes

Colored graphical models provide a parsimonious approach to modeling high-dimensional data by exploiting symmetries in the model parameters. In this work, we introduce the notion of coloring for extremal graphical models on multivariate Pareto distributions, a natural class of limiting distributions for threshold exceedances. Thanks to a stability property of the multivariate Pareto distributions, colored extremal tree models can be defined fully nonparametrically. For more general graphs, the parametric family of Hüsler--Reiss distributions allows for two alternative approaches to colored graphical models. We study both model classes and introduce statistical methodology for parameter estimation. It turns out that for Hüsler--Reiss tree models the different definitions of colored graphical models coincide. In addition, we show a general parametric description of extremal conditional independence statements for Hüsler--Reiss distributions. Finally, we demonstrate that our methodology outperforms existing approaches on a real data set.

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arXiv2023

Mixed volumes of networks with binomial steady-states

The steady-state degree of a chemical reaction network is the number of complex steady-states for generic rate constants and initial conditions. One way to bound the steady-state degree is through the mixed volume of the steady-state system or an equivalent system. In this work, we show that for partionable binomial networks, whose resulting steady-state systems are given by a set of binomials and a set of linear (not necessarily binomial) conservation equations, computing the mixed volume is equivalent to finding the volume of a single mixed cell that is the translate of a parallelotope. We then turn our attention to identifying cycles with binomial steady-state ideals. To this end, we give a coloring condition on directed cycles that guarantees the network has a binomial steady-state ideal. We highlight both of these theorems using a class of networks referred to as species-overlapping networks and give a formula for the mixed volume of these networks.

math.CO↗

arXiv2023

Identifiability of the Rooted Tree Parameter under the Cavender-Farris-Neyman Model with a Molecular Clock

Identifiability of the discrete tree parameter is a key property for phylogenetic models since it is necessary for statistically consistent estimation of the tree from sequence data. Algebraic methods have proven to be very effective at showing that tree and network parameters of phylogenetic models are identifiable, especially when the underlying models are group-based. However, since group-based models are time-reversible, only the unrooted tree topology is identifiable and the location of the root is not. In this note we show that the rooted tree parameter of the Cavender-Farris-Neyman Model with a Molecular Clock is generically identifiable by using the invariants of the model which were characterized by Coons and Sullivant.

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arXiv2022

Rational partition models under iterative proportional scaling

In this work we investigate partition models, the subset of log-linear models for which one can perform the iterative proportional scaling (IPS) algorithm to numerically compute the maximum likelihood estimate (MLE). Partition models include families of models such as hierarchical models and balanced, stratified staged trees. We define a sufficient condition, called the Generalized Running Intersection Property (GRIP), on the matrix representation of a partition model under which IPS algorithm produces the exact MLE in one cycle. Additionally we connect the GRIP to the toric fiber product and to previous results for hierarchical models and balanced, stratified staged trees. This leads to a characterization of balanced, stratified staged trees in terms of the GRIP.

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arXiv2022

Symmetrically colored Gaussian graphical models with toric vanishing ideal

A colored Gaussian graphical model is a linear concentration model in which equalities among the concentrations are specified by a coloring of an underlying graph. The model is called RCOP if this coloring is given by the edge and vertex orbits of a subgroup of the automorphism group of the graph. We show that RCOP Gaussian graphical models on block graphs are toric in the space of covariance matrices and we describe Markov bases for them. To this end, we learn more about the combinatorial structure of these models and their connection with Jordan algebras.

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arXiv2021

Reciprocal Maximum Likelihood Degrees of Brownian Motion Tree Models

We give an explicit formula for the reciprocal maximum likelihood degree of Brownian motion tree models. To achieve this, we connect them to certain toric (or log-linear) models, and express the Brownian motion tree model of an arbitrary tree as a toric fiber product of star tree models.

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arXiv2020

Quasi-independence models with rational maximum likelihood estimator

We classify the two-way independence quasi-independence models (or independence models with structural zeros) that have rational maximum likelihood estimators, or MLEs. We give a necessary and sufficient condition on the bipartite graph associated to the model for the MLE to be rational. In this case, we give an explicit formula for the MLE in terms of combinatorial features of this graph. We also use the Horn uniformization to show that for general log-linear models $\mathcal{M}$ with rational MLE, any model obtained by restricting to a face of the cone of sufficient statistics of $\mathcal{M}$ also has rational MLE.

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arXiv2020

Generalized Cut Polytopes for Binary Hierarchical Models

Marginal polytopes are important geometric objects that arise in statistics as the polytopes underlying hierarchical log-linear models. These polytopes can be used to answer geometric questions about these models, such as determining the existence of maximum likelihood estimates or the normality of the associated semigroup. Cut polytopes of graphs have been useful in analyzing binary marginal polytopes in the case where the simplicial complex underlying the hierarchical model is a graph. We introduce a generalized cut polytope that is isomorphic to the binary marginal polytope of an arbitrary simplicial complex via a generalized covariance map. This polytope is full dimensional in its ambient space and has a natural switching operation among its facets that can be used to deduce symmetries between the facets of the correlation and binary marginal polytopes. We find complete H-representations of the generalized cut polytope for some important families of simplicial complexes. We also compute the volume of these polytopes in some instances.

math.CO↗

arXiv2020

Maximum likelihood degree of the two-dimensional linear Gaussian covariance model

In algebraic statistics, the maximum likelihood degree of a statistical model is the number of complex critical points of its log-likelihood function. A priori knowledge of this number is useful for applying techniques of numerical algebraic geometry to the maximum likelihood estimation problem. We compute the maximum likelihood degree of a generic two-dimensional subspace of the space of $n\times n$ Gaussian covariance matrices. We use the intersection theory of plane curves to show that this number is $2n-3$.

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arXiv2020

The Cavender-Farris-Neyman Model with a Molecular Clock

We give a combinatorial description of the toric ideal of invariants of the Cavender-Farris-Neyman model with a molecular clock (CFN-MC) on a rooted binary phylogenetic tree and prove results about the polytope associated to this toric ideal. Key results about the polyhedral structure include that the number of vertices of this polytope is a Fibonacci number, the facets of the polytope can be described using the combinatorial "cluster" structure of the underlying rooted tree, and the volume is equal to an Euler zig-zag number. The toric ideal of invariants of the CFN-MC model has a quadratic Groebner basis with squarefree initial terms. Finally, we show that the Ehrhart polynomial of these polytopes, and therefore the Hilbert series of the ideals, depends only on the number of leaves of the underlying binary tree, and not on the topology of the tree itself. These results are analogous to classic results for the Cavender-Farris-Neyman model without a molecular clock. However, new techniques are required because the molecular clock assumption destroys the toric fiber product structure that governs group-based models without the molecular clock.

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arXiv2020

The $h^*$-polynomial of the order polytope of the zig-zag poset

We describe a family of shellings for the canonical triangulation of the order polytope of the zig-zag poset. This gives a new combinatorial interpretation for the coefficients in the numerator of the Ehrhart series of this order polytopein terms of the swap statistic on alternating permutations.

math.CO↗

arXiv2014

Combinatorics of k-Interval Cospeciation for Cophylogeny

We show that the cophylogenetic distance, k-interval cospeciation, is distinct from other metrics and accounts for global congruence between locally incongruent trees. The growth of the neighborhood of trees which satisfy the largest possible k-interval cospeciation with a given tree indicates that k-interval cospeciation is useful for analyzing simulated data.

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