相关论文: A consistency lemma in statistical phylogenetics

Phylogenomics heavily relies on well-curated sequence data sets that consist, for each gene, exclusively of 1:1-orthologous. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe…

The occurrence and the distribution of patterns of trees associated to natural numbers are investigated. Bounds from above and below are proven for certain natural quantities.

Turing progressions arise by iteratedly adding consistency statements to a base theory. Different notions of consistency give rise to different Turing progressions. In this paper we present a logic that generates exactly all relations that…

The spread of infectious disease in a human community or the proliferation of fake news on social media can be modeled as a randomly growing tree-shaped graph. The history of the random growth process is often unobserved but contains…

This paper investigates the (in)-consistency of various bootstrap methods for making inference on a change-point in time in the Cox model with right censored survival data. A criterion is established for the consistency of any bootstrap…

This work develops formal statistical inference procedures for machine learning ensemble methods. Ensemble methods based on bootstrapping, such as bagging and random forests, have improved the predictive accuracy of individual trees, but…

It is shown that a natural notion of congruence permutability for quasivarieties already implies ``being a variety''. The result follows immediately from [3] and the sole aim of this note is to state it explicitly, together with a…

We propose an evolutionary mechanism of phyllotaxis, regular arrangement of leaves on a plant stem. It is shown that the phyllotactic pattern with the Fibonacci sequence has a selective advantage, for it involves the least number of…

Good large sample performance is typically a minimum requirement of any model selection criterion. This article focuses on the consistency property of the Bayes factor, a commonly used model comparison tool, which has experienced a recent…

A classical problem in phylogenetic tree analysis is to decide whether there is a phylogenetic tree $T$ that contains all information of a given collection $\cP$ of phylogenetic trees. If the answer is "yes" we say that $\cP$ is compatible…

Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…

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 study the efficiency of genus statistics in differentiating between different models of structure formation. Simple models which reproduce the salient features of the structure seeded by topological defects are examined. We consider…

An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…

In this note we demonstrate that a number of case-heavy combinatorial proofs in the mathematical phylogenetics literature can be proven more compactly using computational support. We use these techniques to also prove several new…

The standard approach to estimate species trees is to align a selected set of genes, concatenate the alignments and then estimate a consensus tree. However, individual genes contain differing levels of evolutionary information, either…

Bootstrap for nonlinear statistics like U-statistics of dependent data has been studied by several authors. This is typically done by producing a bootstrap version of the sample and plugging it into the statistic. We suggest an alternative…

The purpose of this paper is twofold. First, the definition of new statistical convergence with Fibonacci sequence is given and some fundamental properties of statistical convergence are examined. Second, approximation theory worked as a…

We consider the problem of estimating the evolutionary history of a set of species (phylogeny or species tree) from several genes. It is known that the evolutionary history of individual genes (gene trees) might be topologically distinct…

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…