Related papers: Evolutionary distances in the twilight zone -- a r…

In this paper, we propose a new time-aware dissimilarity measure that takes into account the temporal dimension. Observations that are close in the description space, but distant in time are considered as dissimilar. We also propose a…

Estimating the effective sample size (ESS) is fundamental in Bayesian phylogenetic inference to properly account for autocorrelation in MCMC samples. While methods for continuous parameters are well established, the discrete and…

Statistically consistent estimation of phylogenetic trees or gene trees is possible if pairwise sequence dissimilarities can be converted to a set of distances that are proportional to the true evolutionary distances. Susko et al. (2004)…

The algebraic properties of flattenings and subflattenings provide direct methods for identifying edges in the true phylogeny -- and by extension the complete tree -- using pattern counts from a sequence alignment. The relatively small…

We introduce a new distance-based phylogeny reconstruction technique which provably achieves, at sufficiently short branch lengths, a polylogarithmic sequence-length requirement -- improving significantly over previous polynomial bounds for…

Evolutionary modeling applications are the best way to provide full information to support in-depth understanding of evaluation of organisms. These applications mainly depend on identifying the evolutionary history of existing organisms and…

We consider the problem of distance estimation under the TKF91 model of sequence evolution by insertions, deletions and substitutions on a phylogeny. In an asymptotic regime where the expected sequence lengths tend to infinity, we show that…

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…

Canonical distances such as Euclidean distance often fail to capture the appropriate relationships between items, subsequently leading to subpar inference and prediction. Many algorithms have been proposed for automated learning of suitable…

Each gene has its own evolutionary history which can substantially differ from the evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer and recombination…

Metric learning has the aim to improve classification accuracy by learning a distance measure which brings data points from the same class closer together and pushes data points from different classes further apart. Recent research has…

A metric phylogenetic tree relating a collection of taxa induces weighted rooted triples and weighted quartets for all subsets of three and four taxa, respectively. New intertaxon distances are defined that can be calculated from these…

A fundamental notion of distance between train and test distributions from the field of domain adaptation is discrepancy distance. While in general hard to compute, here we provide the first set of provably efficient algorithms for testing…

Phylogenetic trees and networks are graphs used to model evolutionary relationships, with trees representing strictly branching histories and networks allowing for events in which lineages merge, called reticulation events. While the…

Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…

Motivation: Word-based or `alignment-free' methods for phylogeny reconstruction are much faster than traditional approaches, but they are generally less accurate. Most of these methods calculate pairwise distances for a set of input…

In many interesting cases the reconstruction of a correct phylogeny is blurred by high mutation rates and/or horizontal transfer events. As a consequence a divergence arises between the true evolutionary distances and the differences…

Evolutionary mechanism in a self-organized system cause some functional changes that force to adapt new conformation of the interaction pattern between the components of that system. Measuring the structural differences one can retrace the…

Semidirected networks have received interest in evolutionary biology as the appropriate generalization of unrooted trees to networks, in which some but not all edges are directed. Yet these networks lack proper theoretical study. We define…

We derive tractable criteria for the consistency of Bayesian tree reconstruction procedures, which constitute a central class of algorithms for inferring common ancestry among DNA sequence samples in phylogenetics. Our results encompass…