Related papers: Fitting Tree Metrics with Minimum Disagreements
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…
We consider the numerical taxonomy problem of fitting a positive distance function ${D:{S\choose 2}\rightarrow \mathbb R_{>0}}$ by a tree metric. We want a tree $T$ with positive edge weights and including $S$ among the vertices so that…
We study the problem of how well a tree metric is able to preserve the sum of pairwise distances of an arbitrary metric. This problem is closely related to low-stretch metric embeddings and is interesting by its own flavor from the line of…
We study the Ultrametric Violation Distance problem introduced by Cohen-Addad, Fan, Lee, and Mesmay [FOCS, 2022]. Given pairwise distances $x\in \mathbb{R}_{>0}^{\binom{[n]}{2}}$ as input, the goal is to modify the minimum number of…
Given a distance matrix consisting of pairwise distances between species, a distance-based phylogenetic reconstruction method returns a tree metric or equidistant tree metric (ultrametric) that best fits the data. We investigate…
Optimal transport provides a metric which quantifies the dissimilarity between probability measures. For measures supported in discrete metric spaces, finding the optimal transport distance has cubic time complexity in the size of the…
Given $x \in (\mathbb{R}_{\geq 0})^{\binom{[n]}{2}}$ recording pairwise distances, the METRIC VIOLATION DISTANCE (MVD) problem asks to compute the $\ell_0$ distance between $x$ and the metric cone; i.e., modify the minimum number of entries…
Building trees to represent or to fit distances is a critical component of phylogenetic analysis, metric embeddings, approximation algorithms, geometric graph neural nets, and the analysis of hierarchical data. Much of the previous…
In this work we study the interleaving distance between merge trees from a combinatorial point of view. We use a particular type of matching between trees to obtain a novel formulation of the distance. With such formulation, we tackle the…
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,…
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…
The (unweighted) tree edit distance problem for $n$ node trees asks to compute a measure of dissimilarity between two rooted trees with node labels. The current best algorithm from more than a decade ago runs in $O(n ^ 3)$ time [Demaine,…
Ancestral mixture model, proposed by Chen and Lindsay (2006), is an important model to build a hierarchical tree from high dimensional binary sequences. Mixture trees created from ancestral mixture models involve in the inferred…
Since 1997 there has been a steady stream of advances for the maximum disjoint paths problem. Achieving tractable results has usually required focusing on relaxations such as: (i) to allow some bounded edge congestion in solutions, (ii) to…
Finding an optimal assignment between two sets of objects is a fundamental problem arising in many applications, including the matching of `bag-of-words' representations in natural language processing and computer vision. Solving the…
We present a simple 4-approximation algorithm for computing a maximum agreement forest of multiple unrooted binary trees. This algorithm applies LP rounding to an extension of a recent ILP formulation of the maximum agreement forest problem…
This paper addresses the basic question of how well can a tree approximate distances of a metric space or a graph. Given a graph, the problem of constructing a spanning tree in a graph which strongly preserves distances in the graph is a…
Finding a minimum spanning tree (MST) for $n$ points in an arbitrary metric space is a fundamental primitive for hierarchical clustering and many other ML tasks, but this takes $\Omega(n^2)$ time to even approximate. We introduce a…
This paper addresses the problem of finding a representation of a subtree distance, which is an extension of the tree metric. We show that a minimal representation is uniquely determined by a given subtree distance, and give a linear time…
The tree metric theorem provides a combinatorial four point condition that characterizes dissimilarity maps derived from pairwise compatible split systems. A similar (but weaker) four point condition characterizes dissimilarity maps derived…