Related papers: An analytical comparison of coalescent-based multi…

A probabilistic reconstruction of genealogies in a polyploid population (from 2x to 4x) is investigated, by considering genetic data analyzed as the probability of allele presence in a given genotype. Based on the likelihood of all possible…

We show that genealogical trees arising from a broad class of non-neutral models of population evolution converge to the Kingman coalescent under a suitable rescaling of time. As well as non-neutral biological evolution, our results apply…

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…

Distances between sequences based on their $k$-mer frequency counts can be used to reconstruct phylogenies without first computing a sequence alignment. Past work has shown that effective use of k-mer methods depends on 1) model-based…

Trait differences between species may be attributable to natural selection. However, quantifying the strength of evidence for selection acting on a particular trait is a difficult task. Here we develop a population-genetic test for…

The sample frequency spectrum of a segregating site is the probability distribution of a sample of alleles from a genetic locus, conditional on observing the sample to have more than one clearly different phenotypes. We present a model for…

We introduce inference trees (ITs), a new class of inference methods that build on ideas from Monte Carlo tree search to perform adaptive sampling in a manner that balances exploration with exploitation, ensures consistency, and alleviates…

Classification of gene trees is an important task both in the analysis of multi-locus phylogenetic data, and assessment of the convergence of Markov Chain Monte Carlo (MCMC) analyses used in Bayesian phylogenetic tree reconstruction. The…

Multiplicative linear logic is a very well studied formal system, and most such studies are concerned with the one-sided sequent calculus. In this paper we look in detail at existing translations between a deep inference system and the…

The paper attempts to validate the effectiveness of tree classifiers to classify tabla strokes especially the ones which are overlapping in nature. It uses decision tree, ID3 and random forest as classifiers. A custom made data sets of 650…

While standard IR models are mainly designed to optimize relevance, real-world search often needs to balance additional objectives such as diversity and fairness. These objectives depend on inter-document interactions and are commonly…

Challenges inherent to high-resolution and high signal-to-noise data as well as model degeneracies can cause systematic biases in analyses of strong lens systems. In the past decade, the number of lens modeling methods has significantly…

Binary rooted trees, both in the ordered and in the un-ordered case, are well studied structures in the field of combinatorics. The aim of this work is to study particular patterns in these classes of trees. We consider completely…

This paper studies high-dimensional regression models with lasso when data is sampled under multi-way clustering. First, we establish convergence rates for the lasso and post-lasso estimators. Second, we propose a novel inference method…

Given overlapping subsets of a set of taxa (e.g. species), and posterior distributions on phylogenetic tree topologies for each of these taxon sets, how can we infer a posterior distribution on phylogenetic tree topologies for the entire…

One regards spaces of trees as stratified spaces, to study distributions of phylogenetic trees. Stratified spaces with may have cycles, however spaces of trees with a fixed number of leafs are contractible. Spaces of trees with three leafs,…

Single-branch object detection methods use shared features for localization and classification, yet the shared features are not fit for the two different tasks simultaneously. Multi-branch object detection methods usually use different…

The goal of these lectures is to review some mathematical aspects of random tree models used in evolutionary biology to model gene trees or species trees. We start with stochastic models of tree shapes (finite trees without edge lengths),…

We show that many topological features of level-1 species networks are identifiable from the distribution of the gene tree quartets under the network multi-species coalescent model. In particular, every cycle of size at least 4 and every…

Loss tomography has received considerable attention in recent years and a number of estimators have been proposed. Unfortunately, almost all of them are devoted to the tree topology despite the general topology is more common in practice.…