Related papers: Phylogenetic toric varieties on graphs

Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…

We define a new topological invariant of line arrangements in the complex projective plane. This invariant is a root of unity defined under some combinatorial restrictions for arrangements endowed with some special torsion character on the…

We describe explicitly the cohomology of the total complex of certain diagrams of invertible sheaves on normal toric varieties. These diagrams, called wheels, arise in the study of toric singularities associated to dimer models. Our main…

Over a smooth projective toric variety we study toric sheaves, that is, reflexive sheaves equivariant with respect to the acting torus, from a polyhedral point of view. One application is the explicit construction of the torus invariant…

We present an algebraic theory of orthogonal polynomials in several variables that includes classical orthogonal polynomials as a special case. Our bottom line is a straightforward connection between apolarity of binary forms and the inner…

We examine connections between the gonality, treewidth, and orientable genus of a graph. Especially, we find that hyperelliptic graphs in the sense of Baker and Norine are planar. We give a notion of a bielliptic graph and show that each of…

A phylogenetic tree is a graphical representation of an evolutionary history of taxa in which the leaves correspond to the taxa and the non-leaves correspond to speciations. One of important problems in phylogenetic analysis is to assemble…

We conjecture a multi-parameter generalization of the toric inequalities of \cite{Czech:2023xed}. We then extend their proof methods for the generalized toric inequalities in two ways. The first extension constructs the graph corresponding…

A connected graph can be associated with two distinct evolution algebras. In the first case, the structural matrix is the adjacency matrix of the graph itself. In the second case, the structural matrix is the transition probabilities matrix…

A classical set of birational invariants of a variety are its spaces of pluricanonical forms and some of their canonically defined subspaces. Each of these vector spaces admits a typical metric structure which is also birationally…

In this article we consider several probabilistic processes defining random grapha. One of these processes appeared recently in connection with a factorization problem in the symmetric group. For each of the probabilistic processes, we…

Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…

To a multi-index filtration (say, on the ring of germs of functions on a germ of a complex analytic variety) one associates several invariants: the Hilbert function, the Poincar\'e series, the generalized Poincar\'e series, and the…

We consider the set of forms of a toric variety over an arbitrary field: those varieties which become isomorphic to a toric variety after base field extension. In contrast to most previous work, we also consider arbitrary isomorphisms…

Jukes-Cantor model is one of the most meaningful statistical models from a biological perspective. We are interested in computing the algebraic degrees for phylogenetic varieties, which we call phylogenetic degrees, associated to the…

General invariants of a geometric mapping of a symmetric affine connection space are obtained in this paper. These invariants are generalizations of the previous obtained basic invariants (see [16]). Moreover, these invariants are related…

The classical Fourier transform is, in essence, a way to take data and extract components (in the form of complex exponentials) which are invariant under cyclic shifts. We consider a case in which the components must instead be invariant…

Using the notion of a valuation into the semifield of piecewise linear functions, we give a classification of torus equivariant flat families of finite type over a toric variety base, by certain piecewise linear maps between fans. As a…

This paper addresses the problem of constructing a cycle-level intersection theory for toric varieties. We show that by making one global choice, we can determine a cycle representative for the intersection of an equivariant Cartier divisor…

We provide a complete classification of normal phylogenetic varieties coming from tripods, and more generally, from trivalent trees. Let $G$ be an abelian group. We prove that the group-based phylogenetic variety $X_{G,\mathcal{T}}$, for…