相关论文: A consistency lemma in statistical phylogenetics

Justification theory is an abstract unifying formalism that captures semantics of various non-monotonic logics. One intriguing problem that has received significant attention is the consistency problem: under which conditions are…

Biologists have long sought a way to explain how statistical properties of genetic sequences emerged and are maintained through evolution. On the one hand, non-random structures at different scales indicate a complex genome organisation. On…

Evolutionary events such as incomplete lineage sorting and lateral gene transfer constitute major problems for inferring species trees from gene trees, as they can sometimes lead to gene trees which conflict with the underlying species…

The last decade has shed some light on theoretical properties such as their consistency for regression tasks. In the current paper, we propose a new class of very simple learners based on so-called naive trees. These naive trees partition…

A consensus tree is a phylogenetic tree that synthesizes a given collection of phylogenetic trees, all of which share the same leaf labels but may have different topologies, typically obtained through bootstrapping. Our research focuses on…

A classical result, fundamental to evolutionary biology, states that an edge-weighted tree $T$ with leaf set $X$, positive edge weights, and no vertices of degree 2 can be uniquely reconstructed from the set of leaf-to-leaf distances…

Compatibility of phylogenetic trees is the most important concept underlying widely-used methods for assessing the agreement of different phylogenetic trees with overlapping taxa and combining them into common supertrees to reveal the tree…

Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…

It is common in phylogenetics to have some, perhaps partial, information about the overall evolutionary tree of a group of organisms and wish to find an evolutionary tree of a specific gene for those organisms. There may not be enough…

For a pair consisting of a gene tree and a species tree, the ancestral configurations at an internal node of the species tree are the distinct sets of gene lineages that can be present at that node. Ancestral configurations appear in…

In this paper the bootstrap conditions that follow from the general postulates of effective scattering theory (EST) are checked in the strange sector. We construct the system of tree level bootstrap constraints for the renormalization…

We study the bootstrap for the maxima of the sums of independent random variables, a problem of high relevance to many applications in modern statistics. Since the consistency of bootstrap was justified by Gaussian approximation in…

Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…

Modern biological techniques enable very dense genetic sampling of unfolding evolutionary histories, and thus frequently sample some genotypes multiple times. This motivates strategies to incorporate genotype abundance information in…

Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…

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…

The classical Technical Lemma for congruences is not difficult to prove but it is very efficient in its applications. We present here a Technical Lemma for congruences on \emph{finite lattices}. This is not difficult to prove either but it…

Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…

A phylogenetic tree is a way to organize a finite set of species, individuals or other sources of related data. The species for which we have existing DNA data make up the set of leaves of the tree. The balanced minimal evolution method of…

Connected acyclic graphs (trees) are data objects that hierarchically organize categories. Collections of trees arise in a diverse variety of fields, including evolutionary biology, public health, machine learning, social sciences and…