相关论文: On phylogenetic trees - a geometer's view

We investigate Gorenstein toric Fano varieties by combinatorial methods using the notion of a reflexive polytope which appeared in connection to mirror symmetry. The paper contains generalisations of tools and previously known results for…

We propose a new space of phylogenetic trees which we call wald space. The motivation is to develop a space suitable for statistical analysis of phylogenies, but with a geometry based on more biologically principled assumptions than…

Q-factorial Gorenstein toric Fano varieties X of dimension d with Picard number rho(X) correspond to simplicial reflexive d-polytopes with rho(X)+d vertices. Casagrande showed that any simplicial reflexive d-polytope has at most 3d…

Phylogenetic trees are binary nonplanar trees with labelled leaves, and plane oriented recursive trees are planar trees with an increasing labelling. Both families are enumerated by double factorials. A bijection is constructed, using the…

Phylogenetic invariants are certain polynomials in the joint probability distribution of a Markov model on a phylogenetic tree. Such polynomials are of theoretical interest in the field of algebraic statistics and they are also of practical…

It has been shown by Hacking and Prokhorov that if the projective surface X with quotient singularities and self-intersection number 9 has a smoothing to the projective plane, then X is the general fiber of a Q-Gorenstein deformation of the…

A phylogenetic tree is an acyclic graph with distinctly labeled leaves, whose internal edges have a positive weight. Given a set of n leaves, the collection of all phylogenetic trees with this leaf set can be assembled into a metric cube…

Tilting bundles $\mathcal{T}$ on a weighted projective line $\mathbb{X}$ have been intensively studied by representation theorists since they give rise to a derived equivalence between $\mathbb{X}$ and the finite dimensional algebra End…

A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…

We describe how simple machine learning methods successfully predict geometric properties from Hilbert series (HS). Regressors predict embedding weights in projective space to ${\sim}1$ mean absolute error, whilst classifiers predict…

Given a weighted flag variety $w\Sigma(\mu,u)$ corresponding to chosen fixed parameters $\mu$ and $u$, we present an algorithm to compute lists of all possible projectively Gorenstein $n$-folds, having canonical weight $k$ and isolated…

Firstly, we see that the bases of the miniversal deformations of isolated $\mathbb{Q}$-Gorenstein toric singularities are quite restricted. In particular, we classify the analytic germs of embedding dimension $\leq 2$ which are the bases of…

We study the Gorenstein property for phylogenetic group-based models. We prove that for the groups $\mathbb Z_3$ and $\mathbb Z_2\times \mathbb Z_2$ and trivalent trees the associated polytopes are always Gorenstein extending the results of…

A phylogenetic tree is a tree with a fixed set of leaves that has no vertices of degree two. In this paper, we axiomatically define four other discrete structures on the set of leaves. We prove that each of these structures is an equivalent…

This is the unabridged web version of the paper that will be published on the American Journal of Mathematics. In this paper, we study the birational geometry of certain examples of mildly singular quartic 3-folds. A quartic 3-fold is an…

We classify Fano threefolds with only Gorenstein terminal singularities and Picard number greater than 1 satisfying an additional assumption that the $G$-invariant part of the Weil divisor class group is of rank 1 with respect to an action…

Null models of binary phylogenetic trees are useful for testing hypotheses on real world phylogenies. In this paper we consider phylogenies as binary trees without edge lengths together with a sampling measure and encode them as algebraic…

Phylogenetic trees summarize evolutionary relationships. The Billera-Holmes-Vogtmann (BHV) space for comparing phylogenetic trees has many elegant mathematical properties, but it does not encompass trees with differing leaf sets. To…

The goal of this work is to study geometric properties of geometrically irreducible subschemes on degenerations of Fano varieties (more generally, of separably rationally connected varieties). It is known that these geometrically…

Explicit birational geometry of 3-folds represents a second phase of Mori theory, going beyond the foundational work of the 1980s. This paper is a tutorial and colloquial introduction to the explicit classification of Fano 3-folds (Q-Fano…