Related papers: Reconstructing Ultrametric Trees from Noisy Experi…
We consider the task of learning Ising models when the signs of different random variables are flipped independently with possibly unequal, unknown probabilities. In this paper, we focus on the problem of robust estimation of…
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…
A Yule tree is the result of a branching process with constant birth and death rates. Such a process serves as an instructive null model of many empirical systems, for instance, the evolution of species leading to a phylogenetic tree.…
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
We provide high-probability sample complexity guarantees for exact structure recovery and accurate predictive learning using noise-corrupted samples from an acyclic (tree-shaped) graphical model. The hidden variables follow a…
We introduce a simple algorithm for reconstructing phylogenies from multiple gene trees in the presence of incomplete lineage sorting, that is, when the topology of the gene trees may differ from that of the species tree. We show that our…
We observe $n$ sequences at each of $m$ sites, and assume that they have evolved from an ancestral sequence that forms the root of a binary tree of known topology and branch lengths, but the sequence states at internal nodes are unknown.…
Tree representations of (sets of) symmetric binary relations, or equivalently edge-colored undirected graphs, are of central interest, e.g.\ in phylogenomics. In this context symbolic ultrametrics play a crucial role. Symbolic ultrametrics…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
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…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. Here we explore the practical impact of kernelization (i.e. data reduction) on the NP-hard problem of computing the TBR distance between two unrooted binary…
The study of Markov processes and broadcasting on trees has deep connections to a variety of areas including statistical physics, graphical models, phylogenetic reconstruction, Markov Chain Monte Carlo, and community detection in random…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
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…
In order to conduct a statistical analysis on a given set of phylogenetic gene trees, we often use a distance measure between two trees. In a statistical distance-based method to analyze discordance between gene trees, it is a key to decide…
Several real-world and abstract structures and systems are characterized by marked hierarchy to the point of being expressed as trees. Because the study of these entities often involves sampling (or discovering) the tree nodes in a specific…
Rooted phylogenetic networks are often constructed by combining trees, clusters, triplets or characters into a single network that in some well-defined sense simultaneously represents them all. We review these four models and investigate…
In this paper, we investigate adaptive nonlinear regression and introduce tree based piecewise linear regression algorithms that are highly efficient and provide significantly improved performance with guaranteed upper bounds in an…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
Phylogenomics, even more so than traditional phylogenetics, needs to represent the uncertainty in evolutionary trees due to systematic error. Here we illustrate the analysis of genome-scale alignments of yeast, using robust measures of the…