Related papers: Phylogenetic trees and Euclidean embeddings
An evolutionary tree is a cascade of bifurcations starting from a single common root, generating a growing set of daughter species as time goes by. Species here is a general denomination for biological species, spoken languages or any other…
The reconstruction of transmission trees for epidemics from genetic data has been the subject of some recent interest. It has been demonstrated that the transmission tree structure can be investigated by augmenting internal nodes of a…
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…
Nested (or reconciled) phylogenetic trees model co-evolutionary systems in which one evolutionary history is embedded within another. We introduce a geometric framework for such systems by defining $\sigma$-space, a moduli space of fully…
Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…
In this article we study the treewidth of the \emph{display graph}, an auxiliary graph structure obtained from the fusion of phylogenetic (i.e., evolutionary) trees at their leaves. Earlier work has shown that the treewidth of the display…
Phylogenetic trees illustrate the evolutionary history of genes and species. In most cases, although genes evolve along with the species they belong to, a species tree and gene tree are not identical, because of evolutionary events at the…
Modelling the substitution of nucleotides along a phylogenetic tree is usually done by a hidden Markov process. This allows to define a distribution of characters at the leaves of the trees and one might be able to obtain polynomial…
The Euclidean scattering transform was introduced nearly a decade ago to improve the mathematical understanding of the success of convolutional neural networks (ConvNets) in image data analysis and other tasks. Inspired by recent interest…
In this paper, we lay the groundwork on the comparison of phylogenetic networks based on edge contractions and expansions as edit operations, as originally proposed by Robinson and Foulds to compare trees. We prove that these operations…
Analyzing changes in network evolution is central to statistical network inference, as underscored by recent challenges of predicting and distinguishing pandemic-induced transformations in organizational and communication networks. We…
The investigation of dynamical processes on networks has been one focus for the study of contagion processes. It has been demonstrated that contagions can be used to obtain information about the embedding of nodes in a Euclidean space.…
Analyzing data collected from multiple sources to estimate common and heterogeneous structures through a hierarchical model is a central task in Bayesian inference, and to this end, Bayesian factor models are one of the most widely used…
Suppose N is a phylogenetic network indicating a complicated relationship among individuals and taxa. Often of interest is a much simpler network, for example, a species tree T, that summarizes the most fundamental relationships. The…
We introduce new methods for phylogenetic tree quartet construction by using machine learning to optimize the power of phylogenetic invariants. Phylogenetic invariants are polynomials in the joint probabilities which vanish under a model of…
The conception of multi-alphabetical genetics is represented. Matrix forms of the representation of the multi-level system of molecular-genetic alphabets have revealed algebraic properties of this system. These properties are connected with…
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…
Since the advent of modern bioinformatics, the challenging, multifaceted problem of reconstructing phylogenetic history from biological sequences has hatched perennial statistical and algorithmic innovation. Studies of the phylogenetic…
Phylogenetic reconciliation seeks to explain host-symbiont co-evolution by mapping parasite trees onto host trees through events such as cospeciation, duplication, host switching, and loss. Finding an optimal reconciliation that ensures…
The parameters of many classes of birth-death processes cannot be inferred uniquely from phylogenetic trees: infinitely many parameter combinations yield the same distribution of phylogenetic trees. Here, we show that parameter…