Related papers: Tanglegrams: a reduction tool for mathematical phy…
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…
Latent tree analysis seeks to model the correlations among a set of random variables using a tree of latent variables. It was proposed as an improvement to latent class analysis --- a method widely used in social sciences and medicine to…
Let $\Gamma^{(x_0)}$ be a finite rooted tree, for which $\Gamma$ is the underlying tree and $x_0$ the root. Let $T$ be the Terwilliger algebra of $\Gamma$ with respect to $x_0$. We study the structure of the principal $T$-module. As a…
Finding a common factor of two multivariate polynomials with approximate coefficients is a problem in symbolic-numeric computing. Taking a tropical view on this problem leads to efficient preprocessing techniques, applying polyhedral…
Graded rings provide a natural algebraic framework for encoding symmetry via decompositions into homogeneous components indexed by a group, together with multiplication rules reflecting the group operation. Among graded rings, strongly…
We study isomorphism invariant point processes of $\mathbb{R}^d$ whose groups of symmetries are almost surely trivial. We define a 1-ended, locally finite tree factor on the points of the process, that is, a mapping of the point…
There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…
The purpose of this article is to show how the isotropy subgroup of leaf permutations on binary trees can be used to systematically identify tree-informative invariants relevant to models of phylogenetic evolution. In the quartet case, we…
Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…
In this paper we investigate undirected discrete graphical tree models when all the variables in the system are binary, where leaves represent the observable variables and where all the inner nodes are unobserved. A novel approach based on…
Online educational platforms organize academic questions based on a hierarchical learning taxonomy (subject-chapter-topic). Automatically tagging new questions with existing taxonomy will help organize these questions into different classes…
We apply a recent duality theorem for tangles in abstract separation systems to derive tangle-type duality theorems for width-parameters in graphs and matroids. We further derive a duality theorem for the existence of clusters in large data…
Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…
Plane increasing trees are rooted labeled trees embedded into the plane such that the sequence of labels is increasing on any branch starting at the root. Relaxed binary trees are a subclass of unlabeled directed acyclic graphs. We…
The meander problem is a combinatorial problem which provides a toy model of the compact folding of polymer chains. In this paper we study various questions relating to the enumeration of meander diagrams, using diagrammatical methods. By…
In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…
A tanglegram consists of two rooted binary plane trees with the same number of leaves and a perfect matching between the two leaf sets. Tanglegrams are drawn with the leaves on two parallel lines, the trees on either side of the strip…
Computational inference of dated evolutionary histories relies upon various hypotheses about RNA, DNA, and protein sequence mutation rates. Using mutation rates to infer these dated histories is referred to as molecular clock assumption.…
The inference of new information on the relatedness of species by phylogenetic trees based on DNA data is one of the main challenges of modern biology. But despite all technological advances, DNA sequencing is still a time-consuming and…
Semi-labeled trees are phylogenies whose internal nodes may be labeled by higher-order taxa. Thus, a leaf labeled Mus musculus could nest within a subtree whose root node is labeled Rodentia, which itself could nest within a subtree whose…