Related papers: Order-Dependent Dissimilarity Measures on Phylogen…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…
The Robinson-Foulds (RF) distance is by far the most widely used measure of dissimilarity between trees. Although the distribution of these distances has been investigated for twenty years, an algorithm that is explicitly polynomial time…
Three-way dissimilarities are a generalization of (two-way) dissimilarities which can be used to indicate the lack of homogeneity or resemblance between any three objects. Such maps have applications in cluster analysis, and have been used…
A Multinomial Processing Tree (MPT) is a directed tree with a probability associated with each arc. Here we consider an additional parameter associated with each arc, a measure such as the time required to select the arc. MPTs are often…
An ordered labeled tree is a tree in which the nodes are labeled and the left-to-right order among siblings is relevant. The edit distance between two ordered labeled trees is the minimum cost of changing one tree into the other through a…
Consider a rooted tree $T$ with leaf-set $[n]$, and with all non-leaf vertices having out-degree $2$, at least. A rooted tree $\mathcal T$ with leaf-set $S\subset [n]$ is induced by $S$ in $T$ if $\mathcal T$ is the lowest common ancestor…
The \emph{Tree Augmentation Problem (TAP)} is given a tree $T=(V,E_T)$ and additional set of {\em links} $E$ on $V\times V$, find $F \subseteq E$ such that $T \cup F$ is $2$-edge-connected, and $|F|$ is minimum. The problem is APX-hard…
Semidirected networks have received interest in evolutionary biology as the appropriate generalization of unrooted trees to networks, in which some but not all edges are directed. Yet these networks lack proper theoretical study. We define…
Phylogenomics, even more so than traditional phylogenetics, needs to represent the uncertainty in evolutionary trees due to systematic error. Here we illustrate the analysis of genome-scale alignments of yeast, using robust measures of the…
We study the growth of a time-ordered rooted tree by probabilistic attachment of new vertices to leaves. We construct a likelihood function of the leaves based on the connectivity of the tree. We take such connectivity to be induced by the…
Given a set $X$ of species, a phylogenetic tree is an unrooted binary tree whose leaves are bijectively labelled by $X$. Such trees can be used to show the way species evolve over time. One way of understanding how topologically different…
Phylogenetic trees are used to model evolution: leaves are labelled to represent contemporary species ("taxa") and interior vertices represent extinct ancestors. Informally, convex characters are measurements on the contemporary species in…
Phylogenetics is a fundamental component of evolutionary analysis frameworks in biology and linguistics. Recently, the advent of large-scale genomics and the SARS-CoV-2 pandemic has highlighted the necessity for phylogenetic software to…
When we apply comparative phylogenetic analyses to genome data, it is a well-known problem and challenge that some of given species (or taxa) often have missing genes. In such a case, we have to impute a missing part of a gene tree from a…
Oblique decision trees combine the transparency of trees with the power of multivariate decision boundaries, but learning high-quality oblique splits is NP-hard, and practical methods still rely on slow search or theory-free heuristics. We…
This paper is concerned with the approximation of tensors using tree-based tensor formats, which are tensor networks whose graphs are dimension partition trees. We consider Hilbert tensor spaces of multivariate functions defined on a…
An arborescence, which is a directed analogue of a spanning tree in an undirected graph, is one of the most fundamental combinatorial objects in a digraph. In this paper, we study arborescences in digraphs from the viewpoint of…
We describe a kernel of size 9k-8 for the NP-hard problem of computing the Tree Bisection and Reconnect (TBR) distance k between two unrooted binary phylogenetic trees. We achieve this by extending the existing portfolio of reduction rules…
The effect of training data size on machine learning methods has been well investigated over the past two decades. The predictive performance of tree based machine learning methods, in general, improves with a decreasing rate as the size of…
We consider the Restricted Inverse Optimal Value Problem (RIOVSP) on trees under weighted bottleneck Hamming distance, denoted as (RIOVSPT$_{BH}$). The problem aims to minimize the total cost under weighted bottle-neck Hamming distance such…