Related papers: Phylogenetic toric varieties on graphs

This contribution proposes a new approach towards developing a class of probabilistic methods for classifying attributed graphs. The key concept is random attributed graph, which is defined as an attributed graph whose nodes and edges are…

Graph polynomials encode fundamental combinatorial invariants of graphs. Their computation is investigated using tree and path decomposition frameworks, with formal definitions of treewidth, k-trees, and pathwidth establishing the…

This paper reexamines univariate reduction from a toric geometric point of view. We begin by constructing a binomial variant of the $u$-resultant and then retailor the generalized characteristic polynomial to fully exploit sparsity in the…

We introduce a collection of convex polytopes associated to a torus-equivariant vector bundle on a smooth complete toric variety. We show that the lattice points in these polytopes correspond to generators for the space of global sections…

We show that the counting of rational curves on a complete toric variety that are in general position to the toric prime divisors coincides with the counting of certain tropical curves. The proof is algebraic-geometric and relies on…

Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…

We propose a definition of the rotation number for transverse graph diagrams, extending the classical notion of the rotation number for plane curves. Using this, we introduce a normalized multi-variable Alexander polynomial for framed,…

Multi-fan is an analogous notion of fan. As a fan is associated to a toric variety a multi-fan is associated to a torus orbifold. Orbifold elliptic class and orbifold elliptic genus are defined for a triple of a multi-fan, a set of…

In this paper we will prove that there exists a covariant functor from the category of schemes to the category of graphs. This functor provides a combination between algebraic varieties and combinatorial graphs so that the invariants…

We describe explicitly all multisets of weights whose defining projective toric varieties are self-dual. In addition, we describe a remarkable and unexpected combinatorial behaviour of the defining ideals of these varieties. The toric ideal…

The genus 0, fixed-domain log Gromov-Witten invariants of a smooth, projective toric variety X enumerate maps from a general pointed rational curve to a smooth, projective toric variety passing through the maximal number of general points…

We introduce graph potentials, which are Laurent polynomials associated to (colored) trivalent graphs. We show that the birational type of the graph potential only depends on the homotopy type of the colored graph, and use this to define a…

The paper introduces a generalization for known probabilistic models such as log-linear and graphical models, called here multiplicative models. These models, that express probabilities via product of parameters are shown to capture…

One can associate to a bipartite graph a so-called edge ring whose spectrum is an affine normal toric variety. We characterize the faces of the (edge) cone associated to this toric variety in terms of some independent sets of the bipartite…

Toric ideals to hierarchical models are invariant under the action of a product of symmetric groups. Taking the number of factors, say m, into account, we introduce and study invariant filtrations and their equivariant Hilbert series. We…

We define an algebraic setup of homology for hypergraphs, which defaults to simplicial homology in the case of graphs, and study its basic properties. As part of our study we define algebraic spanning trees of hypergraphs, along with…

The variation graph toolkit (VG) represents genetic variation as a graph. Each path in the graph is a potential haplotype, though most paths are unlikely recombinations of true haplotypes. We augment the VG model with haplotype information…

A clover is a framed trivalent graph with some additional structure, embedded in a 3-manifold. We define surgery on clovers, generalizing surgery on Y-graphs used earlier by the second author to define a new theory of finite-type invariants…

This is an outline of work in progress concerning an algebro-geometric form of the Strominger-Yau-Zaslow conjecture. We introduce a limited type of degeneration of Calabi-Yau manifolds, which we call toric degenerations. For these, the…

We study the algebraic dynamics of endomorphisms of projective varieties. First, we characterize their iterated images, i.e. the intersection of the images of their iterates. Next, we explore the Stein factorizations of the iterates,…