Related papers: The Cavender-Farris-Neyman Model with a Molecular …
We consider the phylogenetic tree model in which every node of the tree is observed and binary and the transitions are given by the same matrix on each edge of the tree. We are able to compute the Grobner basis and Markov basis of the toric…
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…
Statistical models of evolution are algebraic varieties in the space of joint probability distributions on the leaf colorations of a phylogenetic tree. The phylogenetic invariants of a model are the polynomials which vanish on the variety.…
Algebraic techniques in phylogenetics have historically been successful at proving identifiability results and have also led to novel reconstruction algorithms. In this paper, we study the ideal of phylogenetic invariants of the…
We address the problem of studying the toric ideals of phylogenetic invariants for a general group-based model on an arbitrary claw tree. We focus on the group $\mathbb Z_2$ and choose a natural recursive approach that extends to other…
Phylogenetic networks can model more complicated evolutionary phenomena that trees fail to capture such as horizontal gene transfer and hybridization. The same Markov models that are used to model evolution on trees can also be extended to…
We consider arrangements of tropical hyperplanes where the apices of the hyperplanes are taken to infinity in certain directions. Such an arrangement defines a decomposition of Euclidean space where a cell is determined by its `type' data,…
Phylogenetic invariants are equations that vanish on algebraic varieties associated with Markov processes that model molecular substitutions on phylogenetic trees. For practical applications, it is essential to understand these equations…
The motivic nearby fiber is an invariant obtained from degenerating a complex variety over a disc. It specializes to the Euler characteristic of the original variety but also contains information on the variation of Hodge structure…
A lattice model of critical dense polymers is solved exactly for arbitrary system size on the torus. More generally, an infinite family of lattice loop models is studied on the torus and related to the corresponding Fortuin-Kasteleyn random…
Each partition $\lambda = (\lambda_1, \lambda_2, ..., \lambda_n)$ determines a so-called Ferrers tableau or, equivalently, a Ferrers bipartite graph. Its edge ideal, dubbed Ferrers ideal, is a squarefree monomial ideal that is generated by…
Motivated by the construction of Newton--Okounkov bodies and toric degenerations via cluster algebras in [GHKK18, FO25], we consider a family of Newton--Okounkov polytopes of a complex smooth Fano variety $X$ related by a composition of…
We introduce an efficient way, called Newton algorithm, to study arbitrary ideals in C[[x,y]], using a finite succession of Newton polygons. We codify most of the data of the algorithm in a useful combinatorial object, the Newton tree. For…
In this work we present a formula for the Euler characteristic of the Milnor fiber of non-degenerate functions $f: X \to \mathbb{C}$ with isolated critical set relative to a stratification, where $X$ is a $2$-generic symmetric determinantal…
The Hamiltonian of the $N$-state clock model is written in terms of a coupled Temperley-Lieb (TL) algebra defined by $N-1$ types of TL generators. This generalizes a previous result for $N=3$ obtained by J. F. Fjelstad and T. M\r{a}nsson…
We find a relation between mixed volumes of several polytopes and the convex hull of their union, deducing it from the following fact: the mixed volume of a collection of polytopes only depends on the product of their support functions…
Characteristic imsets are 0-1 vectors which correspond to Markov equivalence classes of directed acyclic graphs. The study of their convex hull, named the characteristic imset polytope, has led to new and interesting geometric perspectives…
Q-Gorenstein toric contact manifolds provide an interesting class of examples of contact manifolds with torsion first Chern class. They are completely determined by certain rational convex polytopes, called toric diagrams, and arise both as…
We consider a large class of monomial maps respecting an action of the infinite symmetric group, and prove that the toric ideals arising as their kernels are finitely generated up to symmetry. Our class includes many important examples…
We analyze the algebraic structure of the Connes fusion tensor product (CFTP) in the case of bi-finite Hilbert modules over a von Neumann algebra M. It turns out that all complications in its definition disappear if one uses the closely…