Related papers: Phylogenetic toric varieties on graphs

In this paper we construct a spectral sequence computing a modified version of morphic cohomology of a toric variety (even when it is singular) in terms of combinatorial data coming from the fan of the toric variety.

The toric Hilbert scheme parametrizes all algebras isomorphic to a given semigroup algebra as a multigraded vectorspace. All components of the scheme are toric varieties, and among them, there is a fairly well understood coherent component.…

We study the behavior of phylogenetic tree shapes in the tropical geometric interpretation of tree space. Tree shapes are formally referred to as tree topologies; a tree topology can also be thought of as a tree combinatorial type, which is…

We construct and study a class of algebras associated to generalized layered graphs, i.e. directed graphs with a ranking function on their vertices. Each finite directed acyclic graph admits countably many structures of a generalized…

We extend the theory of combinatorial link Floer homology to a class of oriented spatial graphs called transverse spatial graphs. To do this, we define the notion of a grid diagram representing a transverse spatial graph, which we call a…

A graph is a $k$-leaf power of a tree $T$ if its vertices are leaves of $T$ and two vertices are adjacent in $T$ if and only if their distance in $T$ is at most $k$. Then $T$ is a $k$-leaf root of $G$. This notion was introduced by…

In this work, we consider an extension of graphical models to random graphs, trees, and other objects. To do this, many fundamental concepts for multivariate random variables (e.g., marginal variables, Gibbs distribution, Markov properties)…

A hypertoric variety is a quaternionic analogue of a toric variety. Just as the topology of toric varieties is closely related to the combinatorics of polytopes, the topology of hypertoric varieties interacts richly with the combinatorics…

We show that the cyclic and epicyclic categories which play a key role in the encoding of cyclic homology and the lambda operations, are obtained from projective geometry in characteristic one over the infinite semifield F of "max-plus…

Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An…

We classify trivalent vertex-transitive graphs whose edge sets have a partition into a 2-factor composed of two cycles and a 1-factor that is invariant under the action of the automorphism group.

We study certain foliated complex manifolds that behave similarly to complete nonsingular toric varieties. We classify them by combinatorial objects that we call marked fans. We describe the basic cohomology algebras of them in terms of…

We characterize the compatibility of a collection of unrooted phylogenetic trees as a question of determining whether a graph derived from these trees --- the display graph --- has a specific kind of triangulation, which we call legal. Our…

The theory of polyptych lattices is a framework to obtain a family of toric degenerations whose polytopes are related by piecewise-linear transformations. It can be regarded as a generalization of toric degenerations arising from cluster…

We study surjective endomorphisms of projective bundles over toric varieties, achieving three main results. First, we provide a structural theorem describing endomorphisms of projectivized split bundles over arbitrary base varieties, which…

A phylogenetic network is a directed acyclic graph that visualises an evolutionary history containing so-called reticulations such as recombinations, hybridisations or lateral gene transfers. Here we consider the construction of a simplest…

We introduce the notion of a multi-fan. It is a generalization of that of a fan in the theory of toric variety in algebraic geometry. Roughly speaking a toric variety is an algebraic variety with an action of algebraic torus of the same…

We introduce a notion of tropical vector bundle on a tropical toric variety which is a tropical analogue of a torus equivariant vector bundle on a toric variety. Alternatively it can be called a toric matroid bundle. We define equivariant…

Tutte's dichromate T(x,y) is a well known graph invariant. Using the original definition in terms of internal and external activities as our point of departure, we generalize the valuations T(x,1) and T(1,y) to hypergraphs. In the…

To investigate the topological structure of Morse functions on the projective plane we use the Reeb graphs. We describe it properties and prove that it is a complete topological invariant of simple Morse function on $\mathbb{R} P^2$. We…