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Emilie Dufresne

Publications and source records attributed to Emilie Dufresne.

18 recordsLinked to original sources
arXiv2026

Shuffling the Deck: Invariant Theory and the Graph Reconstruction Conjecture

The graph reconstruction conjecture asserts that every simple graph on at least three vertices is uniquely determined by its deck of vertex-deleted subgraphs. In this expository article we survey the conjecture and present an invariant-theoretic approach to studying it. The aim is to be able to show that polynomials that distinguish between decks also distinguish between original graphs, thus translating a graph-theoretic problem into an algebraic one.

math.CO↗
arXiv2025

Nondimensionalization is more science than art

When faced with a mathematical model, often the first step is to reduce the complexity of the model by turning variables and parameters into dimensionless quantities. This process is often performed by hand, relying on a skill practiced over many years, and attempted for small models. Nondimensionalization is often considered an art, as there is no formal method accessible to applied scientists. Here we show how to systematically perform nondimensionalization for arbitrarily sized models described by rational first order ordinary differential equations. We translate and extend an existing approach for computing rational invariants of the maximal scaling symmetry, which combines ideas from differential algebra, invariant theory and linear algebra, to the setting arising in biological models. The modeler inputs the system of equations and our implemented algorithm outputs the nondimensional quantities for the corresponding nondimensionalized model. We extend the algorithm to include initial conditions, and the modeler's choice of invariants, thereby including a larger class of nondimensionalizations. We further prove that any dimensionally consistent change of variables preserves the dimension of the maximal scaling symmetry. We showcase the framework on various models, including the classical Michaelis-Menten equations, which serves as a benchmark for asking and answering specific modeling questions.

q-bio.QM↗
arXiv2021

Algebra, Geometry and Topology of ERK Kinetics

The MEK/ERK signalling pathway is involved in cell division, cell specialisation, survival and cell death. Here we study a polynomial dynamical system describing the dynamics of MEK/ERK proposed by Yeung et al. with their experimental setup, data and known biological information. The experimental dataset is a time-course of ERK measurements in different phosphorylation states following activation of either wild-type MEK or MEK mutations associated with cancer or developmental defects. We demonstrate how methods from computational algebraic geometry, differential algebra, Bayesian statistics and computational algebraic topology can inform the model reduction, identification and parameter inference of MEK variants, respectively. Throughout, we show how this algebraic viewpoint offers a rigorous and systematic analysis of such models.

q-bio.QM↗
arXiv2021

Rees algebras of sparse determinantal ideals

We determine the defining equations of the Rees algebra and of the special fiber ring of the ideal of maximal minors of a $2\times n$ sparse matrix. We prove that their initial algebras are ladder determinantal rings. This allows us to show that the Rees algebra and the special fiber ring are Cohen-Macaulay domains, they are Koszul, they have rational singularities in characteristic zero and are F-rational in positive characteristic.

math.AC↗
arXiv2018

On Some Configurations of Oppositely Charged Trapped Vortices in the Plane

Our aim in the present work is to identify all the possible standing wave configurations involving few vortices of different charges in an atomic Bose-Einstein condensate (BEC). In this effort, we deploy the use of a computational algebra approach in order to identify stationary multi-vortex states with up to 6 vortices. The use of invariants and symmetries enables deducing a set of equations in elementary symmetric polynomials, which can then be fully solved via computational algebra packages within Maple. We retrieve a number of previously identified configurations, including collinear ones and polygonal (e.g. quadrupolar and hexagonal) ones. However, importantly, we also retrieve a configuration with 4 positive charges and 2 negative ones which is unprecedented, to the best of our knowledge, in BEC studies. We corroborate these predictions via numerical computations in the fully two-dimensional PDE system of the Gross-Pitaevskii type which characterizes the BEC at the mean-field level.

nlin.PS↗
arXiv2018

Sampling real algebraic varieties for topological data analysis

Topological data analysis (TDA) provides a growing body of tools for computing geometric and topological information about spaces from a finite sample of points. We present a new adaptive algorithm for finding provably dense samples of points on real algebraic varieties given a set of defining polynomials. The algorithm utilizes methods from numerical algebraic geometry to give formal guarantees about the density of the sampling and it also employs geometric heuristics to reduce the size of the sample. As TDA methods consume significant computational resources that scale poorly in the number of sample points, our sampling minimization makes applying TDA methods more feasible. We provide a software package that implements the algorithm and also demonstrate the implementation with several examples.

math.AT↗
arXiv2018

Mapping toric varieties into low dimensional spaces

A smooth $d$-dimensional projective variety $X$ can always be embedded into $2d+1$-dimensional space. In contrast, a singular variety may require an arbitrary large ambient space. If we relax our requirement and ask only that the map is injective, then any $d$-dimensional projective variety can be mapped injectively to $2d+1$-dimensional projective space. A natural question then arises: what is the minimal $m$ such that a projective variety can be mapped injectively to $m$-dimensional projective space? In this paper we investigate this question for normal toric varieties, with our most complete results being for Segre-Veronese varieties.

math.AC↗
arXiv2018

The geometry of sloppiness

The use of mathematical models in the sciences often involves the estimation of unknown parameter values from data. Sloppiness provides information about the uncertainty of this task. In this paper, we develop a precise mathematical foundation for sloppiness and define rigorously its key concepts, such as `model manifold', in relation to concepts of structural identifiability. We redefine sloppiness conceptually as a comparison between the premetric on parameter space induced by measurement noise and a reference metric. This opens up the possibility of alternative quantification of sloppiness, beyond the standard use of the Fisher Information Matrix, which assumes that parameter space is equipped with the usual Euclidean metric and the measurement error is infinitesimal. Applications include parametric statistical models, explicit time dependent models, and ordinary differential equation models.

math.MG↗
arXiv2017

Determinantal Generalizations of Instrumental Variables

Linear structural equation models relate the components of a random vector using linear interdependencies and Gaussian noise. Each such model can be naturally associated with a mixed graph whose vertices correspond to the components of the random vector. The graph contains directed edges that represent the linear relationships between components, and bidirected edges that encode unobserved confounding. We study the problem of generic identifiability, that is, whether a generic choice of linear and confounding effects can be uniquely recovered from the joint covariance matrix of the observed random vector. An existing combinatorial criterion for establishing generic identifiability is the half-trek criterion (HTC), which uses the existence of trek systems in the mixed graph to iteratively discover generically invertible linear equation systems in polynomial time. By focusing on edges one at a time, we establish new sufficient and necessary conditions for generic identifiability of edge effects extending those of the HTC. In particular, we show how edge coefficients can be recovered as quotients of subdeterminants of the covariance matrix, which constitutes a determinantal generalization of formulas obtained when using instrumental variables for identification.

math.ST↗
arXiv2014

Separating Invariants and Local Cohomology

The study of separating invariants is a recent trend in invariant theory. For a finite group acting linearly on a vector space, a separating set is a set of invariants whose elements separate the orbits of G. In some ways, separating sets often exhibit better behavior than generating sets for the ring of invariants. We investigate the least possible cardinality of a separating set for a given G-action. Our main result is a lower bound that generalizes the classical result of Serre that if the ring of invariants is polynomial then the group action must be generated by pseudoreflections. We find these bounds to be sharp in a wide range of examples.

math.AC↗
arXiv2014

Invariants and Separating Morphisms for Algebraic Group Actions

The first part of this paper is a refinement of Winkelmann's work on invariant rings and quotients of algebraic groups actions on affine varieties, where we take a more geometric point of view. We show that the (algebraic) quotient $X/\!/\!G$ given by the possibly not finitely generated ring of invariants is "almost" an algebraic variety, and that the quotient morphism $π\colon X \to X/\!/\! G$ has a number of nice properties. One of the main difficulties comes from the fact that the quotient morphism is not necessarily surjective. These general results are then refined for actions of the additive group $\mathbb{G}_a$, where we can say much more. We get a rather explicit description of the so-called plinth variety and of the separating variety, which measures how much orbits are separated by invariants. The most complete results are obtained for representations. We also give a complete and detailed analysis of Roberts' famous example of a an action of $\mathbb{G}_a$ on 7-dimensional affine space with a non-finitely generated ring of invariants.

math.AC↗
arXiv2012

Finite separating sets and quasi-affine quotients

Nagata's famous counterexample to Hilbert's fourteenth problem shows that the ring of invariants of an algebraic group action on an affine algebraic variety is not always finitely generated. In some sense, however, invariant rings are not far from affine. Indeed, invariant rings are always quasi-affine, and there always exist finite separating sets. In this paper, we give a new method for finding a quasi-affine variety on which the ring of regular functions is equal to a given invariant ring, and we give a criterion to recognize separating algebras. The method and criterion are used on some known examples and in a new construction.

math.AC↗
arXiv2012

The separating variety for the basic representations of the additive group

For a group $G$ acting on an affine variety $X$, the separating variety is the closed subvariety of $X\times X$ encoding which points of $X$ are separated by invariants. We concentrate on the indecomposable rational linear representations $V_n$ of dimension $n+1$ of the additive group of a field of characteristic zero, and decompose the separating variety into the union of irreducible components. We show that if $n$ is odd, divisible by four, or equal to two, the closure of the graph of the action, which has dimension $n+2$, is the only component of the separating variety. In the remaining cases, there is a second irreducible component of dimension $n+1$. We conclude that in these cases, there are no polynomial separating algebras.

math.AC↗
arXiv2010

On the finite generation of additive group invariants in positive characteristic

Roberts, Freudenburg, and Daigle and Freudenburg have given the smallest counterexamples to Hilbert's fourteenth problem as rings of invariants of algebraic groups. Each is of an action of the additive group on a finite dimensional vector space over a field of characteristic zero, and thus, each is the kernel of a locally nilpotent derivation. In positive characteristic, additive group actions correspond to locally finite iterative higher derivations. We set up characteristic-free analogs of the three examples, and show that, contrary to characteristic zero, in every positive charateristic, the invariants are finitely generated.

math.AC↗
arXiv2009

The Cohen-Macaulay property of separating invariants of finite groups

In the case of finite groups, a separating algebra is a subalgebra of the ring of invariants which separates the orbits. Although separating algebras are often better behaved than the ring of invariants, we show that many of the criteria which imply that the ring of invariants is non Cohen-Macaulay actually imply that no graded separating algebra is Cohen-Macaulay. For example, we show that, over a field of positive characteristic p, given sufficiently many copies of a faithful modular representation, no graded separating algebra is Cohen-Macaulay. Furthermore, we show that, for a p-group, the existence of a Cohen-Macaulay graded separating algebra implies the group is generated by bireflections. Furthermore, we show that, for a $p$-group, the existence of a Cohen-Macaulay graded separating algebra implies the group is generated by bireflections. Additionally, we give an example which shows that Cohen-Macaulay separating algebras can occur when the ring of invariants is not Cohen-Macaulay.

math.AC↗
arXiv2008

Separating algebras and finite reflection groups

A separating algebra is, roughly speaking, a subalgebra of the ring of invariants whose elements distinguish between any two orbits that can be distinguished using invariants. In this paper, we introduce a geometric notion of separating algebra. This allows us to prove that only groups generated by reflections may have polynomial separating algebras, and only groups generated by bireflections may have complete intersection separating algebras.

math.AC↗