Related papers: Determining distances and consensus between mutati…
Nearest neighbor (kNN) methods have been gaining popularity in recent years in light of advances in hardware and efficiency of algorithms. There is a plethora of methods to choose from today, each with their own advantages and…
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…
Phrase structure trees have a hierarchical structure. In many subjects, most notably in Taxonomy such tree structures have been studied using ultrametrics. Here syntactical hierarchical phrase trees are subject to a similar analysis, which…
Historical linguistics aims at inferring the most likely language phylogenetic tree starting from information concerning the evolutionary relatedness of languages. The available information are typically lists of homologous (lexical,…
Given two binary trees on $N$ labeled leaves, the quartet distance between the trees is the number of disagreeing quartets. By permuting the leaves at random, the expected quartets distance between the two trees is…
We introduce a semiparametric approach to neighbor-based classification. We build off the recently proposed Boundary Trees algorithm by Mathy et al.(2015) which enables fast neighbor-based classification, regression and retrieval in large…
Mutation rate variation across loci is well known to cause difficulties, notably identifiability issues, in the reconstruction of evolutionary trees from molecular sequences. Here we introduce a new approach for estimating general…
We study search trees with 2-way comparisons (2WCST's), which involve separate less-than and equal-to tests in their nodes, each test having two possible outcomes, yes and no. These trees have a much subtler structure than standard search…
Random forests and, more generally, (decision\nobreakdash-)tree ensembles are widely used methods for classification and regression. Recent algorithmic advances allow to compute decision trees that are optimal for various measures such as…
The edit distance between two rooted ordered trees with $n$ nodes labeled from an alphabet~$\Sigma$ is the minimum cost of transforming one tree into the other by a sequence of elementary operations consisting of deleting and relabeling…
The class of self-nested trees presents remarkable compression properties because of the systematic repetition of subtrees in their structure. In this paper, we provide a better combinatorial characterization of this specific family of…
Recent theoretical work has demonstrated that Neighbor Joining applied to concatenated DNA sequences is a statistically consistent method of species tree reconstruction. This brief note compares the accuracy of this approach to other…
Model performance is frequently reported only for the overall population under consideration. However, due to heterogeneity, overall performance measures often do not accurately represent model performance within specific subgroups. We…
Existing techniques to reconstruct tree models of progression for accumulative processes, such as cancer, seek to estimate causation by combining correlation and a frequentist notion of temporal priority. In this paper, we define a novel…
A method was developed for Bayesian inference of species phylogeny using the multi-species coalescent model. To improve the mixing properties of the Markov chain Monte Carlo (MCMC) algorithm that traverses the space of species trees, we…
We develop a general statistical framework for the analysis and inference of large tree-structured data, with a focus on developing asymptotic goodness-of-fit tests. We first propose a consistent statistical model for binary trees, from…
A widely used method for determining the similarity of two labeled trees is to compute a maximum agreement subtree of the two trees. Previous work on this similarity measure is only concerned with the comparison of labeled trees of two…
Tree perception is an essential building block toward autonomous forestry operations. Current developments generally consider input data from lidar sensors to solve forest navigation, tree detection and diameter estimation problems. Whereas…
Algorithms to find optimal alignments among strings, or to find a parsimonious summary of a collection of strings, are well studied in a variety of contexts, addressing a wide range of interesting applications. In this paper, we consider…
We introduce a scale-free method for testing the proportionality of branch lengths between two phylogenetic trees that have the same topology and contain the same set of taxa. This method scales both trees to a total length of 1 and sums up…