Related papers: A rearrangement distance for fully-labelled trees
Measuring tree morphology for phenotyping is an essential but labor-intensive activity in horticulture. Researchers often rely on manual measurements which may not be accurate for example when measuring tree volume. Recent approaches on…
The problem of Distance Edge Labeling is a variant of Distance Vertex Labeling (also known as $L_{2,1}$ labeling) that has been studied for more than twenty years and has many applications, such as frequency assignment. The Distance Edge…
Tree comparison metrics have proven to be an invaluable aide in the reconstruction and analysis of phylogenetic (evolutionary) trees. The path-length distance between trees is a particularly attractive measure as it reflects differences in…
One of the main challenges in Computational Biology is to find the evolutionary distance between two organisms. In the field of comparative genomics, one way to estimate such distance is to find a minimum cost sequence of rearrangements…
{\em Reoptimization} is a setting in which we are given an (near) optimal solution of a problem instance and a local modification that slightly changes the instance. The main goal is that of finding an (near) optimal solution of the…
In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…
Here we show that deciding whether two rooted binary phylogenetic trees on the same set of taxa permit a cherry-picking sequence, a special type of elimination order on the taxa, is NP-complete. This improves on an earlier result which…
Motivation: Word-based or `alignment-free' methods for phylogeny reconstruction are much faster than traditional approaches, but they are generally less accurate. Most of these methods calculate pairwise distances for a set of input…
We study the asymptotic number of certain monotonically labeled increasing trees arising from a generalized evolution process. The main difference between the presented model and the classical model of binary increasing trees is that the…
A variety of algorithms have been proposed for reconstructing trees that show the evolutionary relationships between species by comparing differences in genetic data across present-day taxa. If the leaf-to-leaf distances in a tree can be…
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…
In the absence of horizontal gene transfer it is possible to reconstruct the history of gene families from empirically determined orthology relations, which are equivalent to event-labeled gene trees. Knowledge of the event labels…
We present a new probabilistic proof of Otter's asymptotic formula for the number of unlabelled trees with a given number of vertices. We additionally prove a new approximation result, showing that the total variation distance between…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
We derive the exact partition function for a discrete model of random trees embedded in a one-dimensional space. These trees have vertices labeled by integers representing their position in the target space, with the SOS constraint that…
Finding tumour genetic markers is essential to biomedicine due to their relevance for cancer detection and therapy development. In this paper, we explore a recently released dataset of chromosome rearrangements in 2,586 cancer patients,…
Multi-label classification is a type of supervised learning where an instance may belong to multiple labels simultaneously. Predicting each label independently has been criticized for not exploiting any correlation between labels. In this…
Fitting distances to tree metrics and ultrametrics are two widely used methods in hierarchical clustering, primarily explored within the context of numerical taxonomy. Given a positive distance function…
In this paper we consider the problem of connected edge searching of weighted trees. It is shown that there exists a polynomial-time algorithm for finding optimal connected search strategy for bounded degree trees with arbitrary weights on…
Several real-world and abstract structures and systems are characterized by marked hierarchy to the point of being expressed as trees. Because the study of these entities often involves sampling (or discovering) the tree nodes in a specific…