Related papers: Species tree inference by the STAR method, and gen…

Latent tree models are graphical models defined on trees, in which only a subset of variables is observed. They were first discussed by Judea Pearl as tree-decomposable distributions to generalise star-decomposable distributions such as the…

In population genetics, there is often interest in inferring selection coefficients. This task becomes more challenging if multiple linked selected loci are considered simultaneously. For such a situation, we propose a novel generalized…

In this paper, we present a density estimation framework based on tree tensor-network states. The proposed method consists of determining the tree topology with Chow-Liu algorithm, and obtaining a linear system of equations that defines the…

Galactic archaeology relies on accurate stellar parameters to reconstruct the galaxy's history, including information on stellar ages. While the precision of data has improved significantly in recent years, stellar models used for age…

Multitype branching processes with immigration in one type are used to model the dynamics of stage-structured plant populations. Parametric inference is first carried out when count data of all types are observed. Statistical…

We introduce a Poissonization method to study the coalescent structure of uniform samples from branching processes. This method relies on the simple observation that a uniform sample of size $k$ taken from a random set with positive…

We prove a new formula for the generating function of multitype Cayley trees counted according to their degree distribution. Using this formula we recover and extend several enumerative results about trees. In particular, we extend some…

We investigate star-galaxy classification for astronomical surveys in the context of four methods enabling the interpretation of black-box machine learning systems. The first is outputting and exploring the decision boundaries as given by…

Fixed tree topologies are widely used in phylodynamic analyses to reduce computational burden, yet the consequences of this assumption remain insufficiently understood. Here, we systematically assess the impact of various fixed-topology…

With the coming data deluge from synoptic surveys, there is a growing need for frameworks that can quickly and automatically produce calibrated classification probabilities for newly-observed variables based on a small number of time-series…

Given a set of species whose evolution is represented by a species tree, a gene family is a group of genes having evolved from a single ancestral gene. A gene family evolves along the branches of a species tree through various mechanisms,…

Widely used models in genetics include the Wright-Fisher diffusion and its moment dual, Kingman's coalescent. Each has a multilocus extension but under neither extension is the sampling distribution available in closed-form, and their…

The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been…

A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree based networks. Reticulation-visible networks and child-sibling networks are all…

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…

We propose a fully Bayesian approach for causal inference with multivariate categorical data based on staged tree models, a class of probabilistic graphical models capable of representing asymmetric and context-specific dependencies. To…

A method for creating a forest of model trees to fit samples of a function defined on images is described in several steps: down-sampling the images, determining a tree's hyperplanes, applying convolutions to the hyperplanes to handle small…

Since chemical abundances are inherited between generations of stars, we use them to trace the evolutionary history of our Galaxy. We present a robust methodology for creating a phylogenetic tree, a biological tool used for centuries to…

Ultrametric matrices are a class of covariance matrices that arise in latent tree models. As a parameter space in a statistical model, the set of ultrametric matrices is neither convex nor a smooth manifold. Focus in the literature has…

Galled trees are studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into tree-child, galled and reticulation-visible network classes by relaxing a structural condition imposed on…