Related papers: Computing phylogenetic invariants for time-reversi…
In this paper we study group-based Markov models of evolution and their mixtures. In the algebreo-geometric setting, group-based phylogenetic tree models correspond to toric varieties, while their mixtures correspond to secant and join…
Twisted period integrals are ubiquitous in theoretical physics and mathematics, where they inhabit a finite-dimensional vector space governed by an inner product known as the intersection number. In this work, we uncover the associated…
Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of…
The variety of bicommutative algebras consists of all nonassociative algebras satisfying the polynomial identities of right- and left-commutativity $(x_1x_2)x_3=(x_1x_3)x_2$ and $x_1(x_2x_3)=x_2(x_1x_3)$. Let $F_d$ be the free $d$-generated…
The discovery of topological insulators has reformed modern materials science, promising to be a platform for tabletop relativistic physics, electronic transport without scattering, and stable quantum computation. Topological invariants are…
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…
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…
For a system of partial differential equations admitting point, contact, or higher symmetries, the framework of invariant reduction systematically computes how invariant geometric structures, such as conservation laws, presymplectic…
We present a symbolic algorithmic approach that allows to compute invariant manifolds and corresponding reduced systems for differential equations modeling biological networks which comprise chemical reaction networks for cellular…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
Quantum invariants in low dimensional topology offer a wide variety of valuable invariants of knots and 3-manifolds, presented by explicit formulas that are readily computable. Their computational complexity has been actively studied and is…
We observe $n$ sequences at each of $m$ sites, and assume that they have evolved from an ancestral sequence that forms the root of a binary tree of known topology and branch lengths, but the sequence states at internal nodes are unknown.…
Phylogenetic trees provide a fundamental representation of evolutionary relationships, yet the combinatorial explosion of possible tree topologies renders inference computationally challenging. Classical approaches to characterizing tree…
More than ever, today we are left with the abundance of molecular data outpaced by the advancements of the phylogenomic methods. Especially in the case of presence of many genes over a set of species under the phylogeny question, more…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
Traditionally, covariant scalar field theory models are either super renormalizable, strictly renormalizable, or nonrenormalizable. The goal of `Mixed Models' is to make sense of sums of these distinct examples, e.g.,…
We propose a novel method for the inference of phylogenetic trees that utilises point configurations on hyperbolic space as its optimisation landscape. Each taxon corresponds to a point of the point configuration, while the evolutionary…
We derive a Poisson random field model for population site polymorphisms differences within and between two species that share a relatively recent common ancestor. The model can be either equilibrium or time inhomogeneous. We first consider…
We define a new balance index for rooted phylogenetic trees based on the symmetry of the evolutive history of every set of 4 leaves. This index makes sense for multifurcating trees and it can be computed in time linear in the number of…
The displayed tree phylogenetic network model is shown to sit as a natural submodel of the graphical model associated to a directed acyclic graph (DAG). This representation allows to derive a number of results about the displayed tree…