Related papers: A basic limitation on inferring phylogenies by pai…
We introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree. The algorithm returns a forest which is…
We study the problem of learning a latent tree graphical model where samples are available only from a subset of variables. We propose two consistent and computationally efficient algorithms for learning minimal latent trees, that is, trees…
Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…
In a recent paper on 'Estimating Species Trees from Unrooted Gene Trees' Liu and Yu observe that the distance matrix on the underlying taxon set, which is built up from expected internode distances on gene trees under the multispecies…
Phylogenetic comparative methods are well established tools for using inter-species variation to analyse phenotypic evolution and adaptation. They are generally hampered, however, by predominantly univariate approaches and failure to…
Determining the interaction partners among protein/domain families poses hard computational problems, in particular in the presence of paralogous proteins. Available approaches aim to identify interaction partners among protein/domain…
Topological phylogenetic trees can be assigned edge weights in several natural ways, highlighting different aspects of the tree. Here the rooted triple and quartet metrizations are introduced, and applied to formulate novel fast methods of…
In 2007, Eickmeyer et al. showed that the tree topologies outputted by the Neighbor-Joining (NJ) algorithm and the balanced minimum evolution (BME) method for phylogenetic reconstruction are each determined by a polyhedral subdivision of…
We address phylogenetic reconstruction when the data is generated from a mixture distribution. Such topics have gained considerable attention in the biological community with the clear evidence of heterogeneity of mutation rates. In our…
In this paper, we present a flexible and probabilistic framework for tracking topological features in time-varying scalar fields using merge trees and partial optimal transport. Merge trees are topological descriptors that record the…
Identifiability is a crucial property for a statistical model since distributions in the model uniquely determine the parameters that produce them. In phylogenetics, the identifiability of the tree parameter is of particular interest since…
A common assumption in multiple scientific applications is that the distribution of observed data can be modeled by a latent tree graphical model. An important example is phylogenetics, where the tree models the evolutionary lineages of a…
Statistical models for families of evolutionary related proteins have recently gained interest: in particular pairwise Potts models, as those inferred by the Direct-Coupling Analysis, have been able to extract information about the…
We consider machine learning in a comparison-based setting where we are given a set of points in a metric space, but we have no access to the actual distances between the points. Instead, we can only ask an oracle whether the distance…
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…
This paper introduces constNJ, the first algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees which…
Binary trees are fundamental objects in models of evolutionary biology and population genetics. Here, we discuss some of their combinatorial and structural properties as they depend on the tree class considered. Furthermore, the process by…
Inference of evolutionary trees and rates from biological sequences is commonly performed using continuous-time Markov models of character change. The Markov process evolves along an unknown tree while observations arise only from the tips…
The Robinson-Foulds (RF) metric is arguably the most widely used measure of phylogenetic tree similarity, despite its well-known shortcomings: For example, moving a single taxon in a tree can result in a tree that has maximum distance to…
Edit distances between merge trees of scalar fields have many applications in scientific visualization, such as ensemble analysis, feature tracking or symmetry detection. In this paper, we propose branch mappings, a novel approach to the…