Related papers: Reduction rules for the maximum parsimony distance…
Gromov-Hausdorff (GH) distance is a natural way to measure the distortion between two metric spaces. However, there has been only limited algorithmic development to compute or approximate this distance. We focus on computing the…
Given a compact $E \subset \mathbb{R}^n$ and $s > 0$, the maximum distance problem seeks a compact and connected subset of $\mathbb{R}^n$ of smallest one dimensional Hausdorff measure whose $s$-neighborhood covers $E$. For $E\subset…
Metrics on rooted phylogenetic trees are integral to a number of areas of phylogenetic analysis. Cluster-similarity metrics have recently been introduced in order to limit skew in the distribution of distances, and to ensure that trees in…
A multilabeled tree (or MUL-tree) is a rooted tree in which every leaf is labelled by an element from some set, but in which more than one leaf may be labelled by the same element of that set. In phylogenetics, such trees are used in…
The threshold-$k$ metric dimension ($\mathrm{Tmd}_k$) of a graph is the minimum number of sensors -- a subset of the vertex set -- needed to uniquely identify any vertex in the graph, solely based on its distances from the sensors, when the…
We augment a tree $T$ with a shortcut $pq$ to minimize the largest distance between any two points along the resulting augmented tree $T+pq$. We study this problem in a continuous and geometric setting where $T$ is a geometric tree in the…
In this paper, we investigate a conjecture by von Haeseler concerning the Maximum Parsimony method for phylogenetic estimation, which was published by the Newton Institute in Cambridge on a list of open phylogenetic problems in 2007. This…
In this work, we present an $\Omega\left(\min\{\log \Delta, \sqrt{\log n}\}\right)$ lower bound for Maximal Matching (MM) in $\Delta$-ary trees against randomized algorithms. By a folklore reduction, the same lower bound applies to Maximal…
UPGMA is a heuristic method identifying the least squares equidistant phylogenetic tree given empirical distance data among $n$ taxa. We study this classic algorithm using the geometry of the space of all equidistant trees with $n$ leaves,…
Phylogenetic trees and networks are leaf-labelled graphs used to model evolution. Display graphs are created by identifying common leaf labels in two or more phylogenetic trees or networks. The treewidth of such graphs is bounded as a…
Labeling schemes seek to assign a short label to each node in a network, so that a function on two nodes can be computed by examining their labels alone. For the particular case of trees, optimal bounds (up to low order terms) were recently…
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…
The goal of this paper is to study the similarity between sequences using a distance between the \emph{context} trees associated to the sequences. These trees are defined in the framework of \emph{Sparse Probabilistic Suffix Trees} (SPST),…
Maximum distance separable (MDS) are constructed to required specifications. The codes are explicitly given over finite fields with efficient encoding and decoding algorithms. Series of such codes over finite fields with ratio of distance…
We define, analyze, and give efficient algorithms for two kinds of distance measures for rooted and unrooted phylogenies. For rooted trees, our measures are based on the topologies the input trees induce on triplets; that is, on…
Inference is typically intractable in high-treewidth undirected graphical models, making maximum likelihood learning a challenge. One way to overcome this is to restrict parameters to a tractable set, most typically the set of…
We investigate the complexity of finding a transformation from a given spanning tree in a graph to another given spanning tree in the same graph via a sequence of edge flips. The exchange property of the matroid bases immediately yields…
In this article, we propose tree edit distance with variables, which is an extension of the tree edit distance to handle trees with variables and has a potential application to measuring the similarity between mathematical formulas,…
Finding the most parsimonious tree inside a phylogenetic network with respect to a given character is an NP-hard combinatorial optimization problem that for many network topologies is essentially inapproximable. In contrast, if the network…
Maximum likelihood is one of the most widely used techniques to infer evolutionary histories. Although it is thought to be intractable, a proof of its hardness has been lacking. Here, we give a short proof that computing the maximum…