Related papers: Phylogenetic Algebraic Geometry
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…
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…
We define and investigate a geometric object, called an associative geometry, corresponding to an associative algebra (and, more generally, to an associative pair). Associative geometries combine aspects of Lie groups and of generalized…
We define and investigate a geometric object, called an associative geometry, corresponding to an associative algebra (and, more generally, to an associative pair). Associative geometries combine aspects of Lie groups and of generalized…
This is an introduction to geometric algebra, an alternative to traditional vector algebra that expands on it in two ways: 1. In addition to scalars and vectors, it defines new objects representing subspaces of any dimension. 2. It defines…
This is the first paper in a series of eight where in the first three we develop a systematic approach to the geometric algebras of multivectors and extensors, followed by five papers where those algebraic concepts are used in a novel…
The geometry of algebraic curves over finite fields is a rich area of research. In previous work, the authors investigated a particular aspect of the geometry over finite fields of the classical unit circle, namely how the number of…
Evolution algebras are a special class of non-associative algebras exhibiting connections with different fields of Mathematics. Hilbert evolution algebras generalize the concept through a framework of Hilbert spaces. This allows to deal…
A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…
We observe algebraic derivations on an affine domain B defined over an algebraically closed field of characteristic 0, which are called locally finite derivations in commutative and non-commutative contexts in other references. We observe…
Variational analysis presents a unified theory encompassing in particular both smoothness and convexity. In a Euclidean space, convex sets and smooth manifolds both have straightforward local geometry. However, in the most basic hybrid case…
We study the algebraic varieties defined by the conditional independence statements of Bayesian Networks. A complete algebraic classification is given for Bayesian Networks on at most five random variables. Hidden variables are related to…
We find a new class of the Fuchsian equations, which have an algebraic geometric solutions with the parameter belonging to a hyperelliptic curve. Methods of calculating the algebraic genus of the curve, and its branching points, are…
Recently, much attention has been given to understanding recombination events along a chromosome in a variety of field. For instance, many population genetics problems are limited by the inaccuracy of inferred evolutionary histories of…
Here we briefly describe some topics along the lines of projective spaces and related geometric constructions connected to linear algebra, which provide fundamental examples in classical geometry and analysis.
The mitosis process of an eukaryotic cell can be represented by the structure constants of an evolution algebra. Any isotopism of the latter corresponds to a mutation of genotypes of the former. This paper uses Computational Algebraic…
One considers geometry with the intransitive equaivalence relation. Such a geometry is a physical geometry, i.e. it is described completely by the world function, which is a half of the squared distance function. The physical geometry…
Classes of algebraic structures that are defined by equational laws are called varieties or equational classes. A variety is finitely generated if it is defined by the laws that hold in some fixed finite algebra. We show that every…
The goal of these lectures is to review some mathematical aspects of random tree models used in evolutionary biology to model gene trees or species trees. We start with stochastic models of tree shapes (finite trees without edge lengths),…
Recent years have seen a surprising connection between the physics of scattering amplitudes and a class of mathematical objects--the positive Grassmannian, positive loop Grassmannians, tree and loop Amplituhedra--which have been loosely…