Related papers: Non-bifurcating phylogenetic tree inference via th…

In this paper, we propose DeepTree, a novel method for modeling trees based on learning developmental rules for branching structures instead of manually defining them. We call our deep neural model situated latent because its behavior is…

The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large-scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their…

Phylogenetic networks are a generalization of phylogenetic trees allowing for the representation of non-treelike evolutionary events such as hybridization. Typically, such networks have been analyzed based on their `level', i.e. based on…

The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…

Regression trees and their ensemble methods are popular methods for nonparametric regression: they combine strong predictive performance with interpretable estimators. To improve their utility for locally smooth response surfaces, we study…

Attempting to recognize a tree inside a phylogenetic network is a fundamental undertaking in evolutionary analysis. In the last few years, therefore, tree-based phylogenetic networks, which are defined by a spanning tree called a…

Historical linguistics aims at inferring the most likely language phylogenetic tree starting from information concerning the evolutionary relatedness of languages. The available information are typically lists of homologous (lexical,…

Decision trees are a crucial class of models offering robust predictive performance and inherent interpretability across various domains, including healthcare, finance, and logistics. However, current tree induction methods often face…

Decision trees are widely used for their low computational cost, good predictive performance, and ability to assess the importance of features. Though often used in practice for feature selection, the theoretical guarantees of these methods…

Evolutionary models used for describing molecular sequence variation suppose that at a non-recombining genomic segment, sequences share ancestry that can be represented as a genealogy--a rooted, binary, timed tree, with tips corresponding…

When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…

This work illustrates potentials for recognition within {\em ad hoc} sensor networks if their nodes possess individual inter-related biologically inspired genetic codes. The work takes ideas from natural immune systems protecting organisms…

Sparse linear models are one of several core tools for interpretable machine learning, a field of emerging importance as predictive models permeate decision-making in many domains. Unfortunately, sparse linear models are far less flexible…

We perform a reverse engineering from the ``extended Spellman data'', consisting of 6178 mRNA levels measured by microarrays at 73 instances in four time series during the cell cycle of the yeast Saccharomyces cerevisae. By assuming a…

Understanding the patterns and processes of diversification of life in the planet is a key challenge of science. The Tree of Life represents such diversification processes through the evolutionary relationships among the different taxa, and…

The log-det distance between two aligned DNA sequences was introduced as a tool for statistically consistent inference of a gene tree under simple non-mixture models of sequence evolution. Here we prove that the log-det distance, coupled…

Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…

Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of…

The displayed tree phylogenetic network model is shown to sit as a natural submodel of the graphical model associated to a directed acyclic graph (DAG). This representation allows to derive a number of results about the displayed tree…

Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following…