Related papers: On the complexity of computing MP distance between…
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…
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…
Selective inference is considered for testing trees and edges in phylogenetic tree selection from molecular sequences. This improves the previously proposed approximately unbiased test by adjusting the selection bias when testing many trees…
Phylogenetic Diversity (PD) is a prominent quantitative measure of the biodiversity of a collection of present-day species (taxa). This measure is based on the evolutionary distance among the species in the collection. Loosely speaking, if…
Kondo et al. (DS 2014) proposed methods for computing distances between unordered rooted trees by transforming an instance of the distance computing problem into an instance of the integer programming problem. They showed that the tree edit…
We present approximation algorithms for the following NP-hard optimization problems related to bottleneck spanning trees in metric spaces. 1. The disjoint bottleneck spanning tree problem: Given $n$ pairs of points in a metric space, find…
We establish a log-supermodularity property for probability distributions on binary patterns observed at the tips of a tree that are generated under any 2--state Markov process. We illustrate the applicability of this result in…
We develop a new family of linear programs, that yield upper bounds on the rate of binary linear codes of a given distance. Our bounds apply {\em only to linear codes.} Delsarte's LP is the weakest member of this family and our LP yields…
The Maximum Agreement Forest (Maf) problem is a well-studied problem in evolutionary biology, which asks for a largest common subforest of a given collection of phylogenetic trees with identical leaf label-set. However, the previous work…
In a population with haploid reproduction any individual has a single parent in the previous generation. If all genealogical distances among pairs of individuals (generations from the closest common ancestor) are known it is possible to…
The Gromov-Hausdorff (GH) distance is a natural way to measure distance between two metric spaces. We prove that it is $\mathrm{NP}$-hard to approximate the Gromov-Hausdorff distance better than a factor of $3$ for geodesic metrics on a…
We discuss the computational complexity of approximating maximum a posteriori inference in sum-product networks. We first show NP-hardness in trees of height two by a reduction from maximum independent set; this implies non-approximability…
Understanding the mutational history of tumor cells is a critical endeavor in unraveling the mechanisms underlying cancer. Since the modeling of tumor cell evolution employs labeled trees, researchers are motivated to develop different…
A merge tree is a fundamental topological structure used to capture the sub-level set (and similarly, super-level set) topology in scalar data analysis. The interleaving distance is a theoretically sound, stable metric for comparing merge…
We develop combinatorial methods for computing the rotation distance between binary trees, i.e., equivalently, the flip distance between triangulations of a polygon. As an application, we prove that, for each n, there exist size n trees at…
The exact computation of the matching distance for multi-parameter persistence modules is an active area of research in computational topology. Achieving an easily obtainable exact computation of this distance would permit multi-parameter…
In phylogenetic analysis, for non-molecular data, particularly morphology, parsimony optimization is the most commonly employed approach. In the past and present application of the parsimony principle, extra step numbers have been added…
Multi-view learning is a learning task in which data is described by several concurrent representations. Its main challenge is most often to exploit the complementarities between these representations to help solve a…
In the longest plane spanning tree problem, we are given a finite planar point set $\mathcal{P}$, and our task is to find a plane (i.e., noncrossing) spanning tree for $\mathcal{P}$ with maximum total Euclidean edge length. Despite more…
Adapting a definition given by Bjerkevik and Lesnick for multiparameter persistence modules, we introduce an $\ell^p$-type extension of the interleaving distance on merge trees. We show that our distance is a metric, and that it…