Related papers: Order-Dependent Dissimilarity Measures on Phylogen…
It is an open question whether there exists a polynomial-time algorithm for computing the rotation distances between pairs of extended ordered binary trees. The problem of computing the rotation distance between an arbitrary pair of trees,…
T-Rex (The Robot for Extracting Leaf Samples) is a gantry-based robotic system developed for autonomous leaf localization, selection, and grasping in greenhouse environments. The system integrates a 6-degree-of-freedom manipulator with a…
The study of species organization and their clustering by genetic or phenotypic similarity is carried out with the tools of phylogenetic trees. An important structural property of phylogenetic trees is the balance, which measures how taxa…
We study restricted computation models related to the Tree Evaluation Problem}. The TEP was introduced in earlier work as a simple candidate for the (*very*) long term goal of separating L and LogDCFL. The input to the problem is a rooted,…
Decision trees are a popular technique in statistical data classification. They recursively partition the feature space into disjoint sub-regions until each sub-region becomes homogeneous with respect to a particular class. The basic…
Metrics for merge trees that are simultaneously stable, informative, and efficiently computable have so far eluded researchers. We show in this work that it is possible to devise such a metric when restricting merge trees to ordered domains…
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…
A proper vertex of a rooted tree with totally ordered vertices is a vertex that is less than all its proper descendants. We count several kinds of labeled rooted trees and forests by the number of proper vertices. Our results are all…
We study randomly growing trees governed by the affine preferential attachment rule. Starting with a seed tree $S$, vertices are attached one by one, each linked by an edge to a random vertex of the current tree, chosen with a probability…
Merge trees are fundamental structures in topological data analysis. Interleaving distance is a widely accepted metric for comparing merge trees, with applications in visualization and scientific computing. While a greedy algorithm exists…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
We consider the problem of computing a Steiner tree of minimum cost under a hop constraint which requires the depth of the tree to be at most $k$. Our main result is an exact algorithm for metrics induced by graphs with bounded treewidth…
In this paper, we consider a tree inference problem motivated by the critical problem in single-cell genomics of reconstructing dynamic cellular processes from sequencing data. In particular, given a population of cells sampled from such a…
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…
Ecological studies have now gone beyond measures of species turnover towards measures of phylogenetic and functional dissimilarity with a main objective: disentangling the processes that drive species distributions from local to broad…
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…
Diversity represents an important aspect of genetic programming, being directly correlated with search performance. When considered at the genotype level, diversity often requires expensive tree distance measures which have a negative…
The phylogenetic tree space introduced by Billera, Holmes, and Vogtmann (BHV tree space) is a CAT(0) continuous space that represents trees with edge weights with an intrinsic geodesic distance measure. The geodesic distance measure unique…
Machine learning algorithms are fundamental components of novel data-informed Artificial Intelligence architecture. In this domain, the imperative role of representative datasets is a cornerstone in shaping the trajectory of artificial…
Given two rooted phylogenetic trees on the same set of taxa X, the Maximum Agreement Forest problem (MAF) asks to find a forest that is, in a certain sense, common to both trees and has a minimum number of components. The Maximum Acyclic…