Related papers: Distorted metrics on trees and phylogenetic forest…
There are multiple factors which can cause the phylogenetic inference process to produce two or more conflicting hypotheses of the evolutionary history of a set X of biological entities. That is: phylogenetic trees with the same set of leaf…
A \emph{metric tree embedding} of expected \emph{stretch~$\alpha \geq 1$} maps a weighted $n$-node graph $G = (V, E, \omega)$ to a weighted tree $T = (V_T, E_T, \omega_T)$ with $V \subseteq V_T$ such that, for all $v,w \in V$,…
Motivated by applications to low-rank matrix completion, we give a combinatorial characterization of the independent sets in the algebraic matroid associated to the collection of $m\times n$ rank-2 matrices and $n\times n$ skew-symmetric…
Divergence time estimation requires the reconciliation of two major sources of data. These are fossil and/or biogeographic evidence that give estimates of the absolute age of nodes (ancestors) and molecular estimates that give us estimates…
The mutational heterogeneity of tumours can be described with a tree representing the evolutionary history of the tumour. With noisy sequencing data there may be uncertainty in the inferred tree structure, while we may also wish to study…
We consider noisy binary channels on regular trees and introduce periodic enhancements consisting of locally self-correcting the signal in blocks without break of the symmetry of the model. We focus on the realistic class of within-descent…
Rotation distance between trees measures the number of simple operations it takes to transform one tree into another. There are no known polynomial-time algorithms for computing rotation distance. In the case of ordered rooted trees, we…
Consider a Markov chain on the space of rooted real binary trees that randomly removes leaves and reinserts them on a random edge and suitably rescales the lengths of edges. This chain was introduced by David Aldous who conjectured a…
It follows from a classical result of Jordan that every tree with maximum degree at most $r$ containing a vertex set labeled by $[n]$, has a single-edge cut which separates two subsets $A,B \subset [n]$ for which $\min\{|A|,|B|\} \ge…
Modelling the substitution of nucleotides along a phylogenetic tree is usually done by a hidden Markov process. This allows to define a distribution of characters at the leaves of the trees and one might be able to obtain polynomial…
Several classification methods assume that the underlying distributions follow tree-structured graphical models. Indeed, trees capture statistical dependencies between pairs of variables, which may be crucial to attain low classification…
In 1996, Bodlaender showed the celebrated result that an optimal tree decomposition of a graph of bounded treewidth can be found in linear time. The algorithm is based on an algorithm of Bodlaender and Kloks that computes an optimal tree…
Ultametrics are an important class of distances used in applications such as phylogenetics, clustering and classification theory. Ultrametrics are essentially distances that can be represented by an edge-weighted rooted tree so that all of…
Hybridization networks are representations of evolutionary histories that allow for the inclusion of reticulate events like recombinations, hybridizations, or lateral gene transfers. The recent growth in the number of hybridization network…
Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…
Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…
We consider a natural variant of the well-known Feedback Vertex Set problem, namely the problem of deleting a small subset of vertices or edges to a full binary tree. This version of the problem is motivated by real-world scenarios that are…
Let T be a (not necessarily positive) weighted tree with n leaves numbered by the set {1,...,n}. Define the k-weights of the tree D_{i_1,....,i_k}(T) as the sum of the lengths of the edges of the minimal subtree connecting i_1,....,i_k. We…
Phylogenetic (i.e. leaf-labeled) trees play a fundamental role in evolutionary research. A typical problem is to reconstruct such trees from data like DNA alignments (whose columns are often referred to as characters), and a simple…
Given a connected undirected graph G = [V; E] where |E| =2(|V| -1), we present two algorithms to check if G can be decomposed into two edge disjoint spanning trees, and provide such a decomposition when it exists. Unlike previous algorithms…