Related papers: Order-Dependent Dissimilarity Measures on Phylogen…
Given a rooted tree and a ranking of its leaves, what is the minimum number of inversions of the leaves that can be attained by ordering the tree? This variation of the problem of counting inversions in arrays originated in mathematical…
This article presents a general framework for the transport of probability measures towards minimum divergence generative modeling and sampling using ordinary differential equations (ODEs) and Reproducing Kernel Hilbert Spaces (RKHSs),…
We present a new approximation algorithm for the treewidth problem which finds an upper bound on the treewidth and constructs a corresponding tree decomposition as well. Our algorithm is a faster variation of Reed's classical algorithm. For…
Random forest (RF) stands out as a highly favored machine learning approach for classification problems. The effectiveness of RF hinges on two key factors: the accuracy of individual trees and the diversity among them. In this study, we…
We propose a novel technique, termed compact shape trees, for computing correspondences of single-boundary 2-D shapes in O(n2) time. Together with zero or more features defined at each of n sample points on the shape's boundary, the compact…
We study treewidth sparsifiers. Informally, given a graph $G$ of treewidth $k$, a treewidth sparsifier $H$ is a minor of $G$, whose treewidth is close to $k$, $|V(H)|$ is small, and the maximum vertex degree in $H$ is bounded. Treewidth…
Planning for the protection of species often involves difficult choices about which species to prioritize, given constrained resources. One way of prioritizing species is to consider their "evolutionary distinctiveness", i.e. their relative…
Here we present a new fixed parameter tractable algorithm to compute the hybridization number r of two rooted, not necessarily binary phylogenetic trees on taxon set X in time (6^r.r!).poly(n)$, where n=|X|. The novelty of this approach is…
Ranked tree-child networks are a recently introduced class of rooted phylogenetic networks in which the evolutionary events represented by the network are ordered so as to respect the flow of time. This class includes the well-studied…
We construct a tree-based dependence structure for the representation of binomial, Poisson and Gaussian random vectors having a given covariance matrix, using sums of independent random variables. This construction allows us to characterize…
This paper proposes a design of hierarchical fuzzy inference tree (HFIT). An HFIT produces an optimum treelike structure, i.e., a natural hierarchical structure that accommodates simplicity by combining several low-dimensional fuzzy…
Estimating a joint Highest Posterior Density credible set for a multivariate posterior density is challenging as dimension gets larger. Credible intervals for univariate marginals are usually presented for ease of computation and…
We present TreeFrog, a massively parallel halo merger tree builder that is capable comparing different halo catalogues and producing halo merger trees. The code is written in c++11, use the MPI and OpenMP API's for parallelisation, and…
The ancestral maximum-likelihood and phylogeography problems are two fundamental problems involving evolutionary studies. The ancestral maximum-likelihood problem involves identifying a rooted tree alongside internal node sequences that…
Our current understanding of the taxonomic and phylogenetic diversity of cellular organisms, especially the bacteria and archaea, is mostly based upon studies of sequences of the small- subunit rRNAs (ssu-rRNAs). To address the limitation…
A k-dissimilarity D on a finite set X, |X| >= k, is a map from the set of size k subsets of X to the real numbers. Such maps naturally arise from edge-weighted trees T with leaf-set X: Given a subset Y of X of size k, D(Y) is defined to be…
Distance-based phylogenetic algorithms attempt to solve the NP-hard least squares phylogeny problem by mapping an arbitrary dissimilarity map representing biological data to a tree metric. The set of all dissimilarity maps is a Euclidean…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
The notion of $\mathcal{H}$-treewidth, where $\mathcal{H}$ is a hereditary graph class, was recently introduced as a generalization of the treewidth of an undirected graph. Roughly speaking, a graph of $\mathcal{H}$-treewidth at most $k$…
In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…