Related papers: Counting Phylogenetic Networks with Few Reticulati…
We recover Gessel's determinantal formula for the generating function of permutations with no ascending subsequence of length m+1. The starting point of our proof is the recursive construction of these permutations by insertion of the…
Recently much attention has been paid to deep generative models, since they have been used to great success for variational inference, generation of complex data types, and more. In most all of these settings, the goal has been to find a…
Frequencies of $k$-mers in sequences are sometimes used as a basis for inferring phylogenetic trees without first obtaining a multiple sequence alignment. We show that a standard approach of using the squared-Euclidean distance between…
Recently much attention has been devoted to the construction of phylogenetic networks which generalize phylogenetic trees in order to accommodate complex evolutionary processes. Here we present an efficient, practical algorithm for…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
We define the (random) $k$-cut number of a rooted graph to model the difficulty of the destruction of a resilient network. The process is as the cut model of Meir and Moon except now a node must be cut $k$ times before it is destroyed. The…
We consider the problem of uniformly generating a spanning tree, of a connected undirected graph. This process is useful to compute statistics, namely for phylogenetic trees. We describe a Markov chain for producing these trees. For cycle…
In this work we introduce and study various generalizations of the notion of increasingly labelled trees, where the label of a child node is always larger than the label of its parent node, to multilabelled tree families, where the nodes in…
The class of ranked tree-child networks, tree-child networks arising from an evolution process with a fixed embedding into the plane, has recently been introduced by Bienvenu, Lambert, and Steel. These authors derived counting results for…
A central theme in phylogenetics is the reconstruction and analysis of evolutionary trees from a given set of data. To determine the optimal search methods for reconstructing trees, it is crucial to understand the size and structure of the…
Phylogenetic networks are used to represent evolutionary scenarios in biology and linguistics. To find the most probable scenario, it may be necessary to compare candidate networks, to distinguish different networks, and to see when one…
Using the theoretical basis developed by Yao and Zeilberger, we consider certain graph families whose structure results in a rational generating function for sequences related to spanning tree enumeration. Said families are Powers of Cycles…
We study the asymptotic distribution of integers sharing the same rooted-tree structure that encodes their complete prime factorization tower. For each tree we derive an explicit density formula depending only on a pair $(m,k)$, the density…
An inverted semistandard Young tableau is a row-standard tableau along with a collection of inversion pairs that quantify how far the tableau is from being column semistandard. Such a tableau with precisely $k$ inversion pairs is said to be…
We introduce a simple algorithm for reconstructing phylogenies from multiple gene trees in the presence of incomplete lineage sorting, that is, when the topology of the gene trees may differ from that of the species tree. We show that our…
Phylogenetic networks are a special type of graph which generalize phylogenetic trees and that are used to model non-treelike evolutionary processes such as recombination and hybridization. In this paper, we consider {\em unrooted}…
Networks are a powerful abstraction with applicability to a variety of scientific fields. Models explaining their morphology and growth processes permit a wide range of phenomena to be more systematically analysed and understood. At the…
In this paper, we derive non-asymptotic achievability and converse bounds on the random number generation with/without side-information. Our bounds are efficiently computable in the sense that the computational complexity does not depend on…
We focus on counting the number of labeled graphs on $n$ vertices and treewidth at most $k$ (or equivalently, the number of labeled partial $k$-trees), which we denote by $T_{n,k}$. So far, only the particular cases $T_{n,1}$ and $T_{n,2}$…
The evolutionary relationships between species are typically represented in the biological literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate processes, such as the formation of hybrid species or…