相关论文: Species tree inference by the STAR method, and gen…

Based on decision trees, many fields have arguably made tremendous progress in recent years. In simple words, decision trees use the strategy of "divide-and-conquer" to divide the complex problem on the dependency between input features and…

The segmentation of individual trees from forest point clouds is a crucial task for downstream analyses such as carbon sequestration estimation. Recently, deep-learning-based methods have been proposed which show the potential of learning…

Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…

Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their…

With the availability of multi-object spectrometers and the designing \& running of some large scale sky surveys, we are obtaining massive spectra. Therefore, it becomes more and more important to deal with the massive spectral data…

We consider general Gaussian latent tree models in which the observed variables are not restricted to be leaves of the tree. Extending related recent work, we give a full semi-algebraic description of the set of covariance matrices of any…

Coalescent histories are combinatorial structures that describe for a given gene tree and species tree the possible lists of branches of the species tree on which the gene tree coalescences take place. Properties of the number of coalescent…

We review recent progress in the understanding of the role of multiple- and simultaneous multiple merger coalescents as models for the genealogy in idealised and real populations with exceptional reproductive behaviour. In particular, we…

Genetic data are often used to infer demographic history and changes or detect genes under selection. Inferential methods are commonly based on models making various strong assumptions: demography and population structures are supposed…

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…

In a phylogenetic tree, we often don't have information about the time a speciation event (inner node) occured. Under a neutral model for speciation, I develop fast algorithms for calculating the probability that an inner node i is the k-th…

By measuring or calculating coalescence times for several models of coalescence or evolution, with and without selection, we show that the ratios of these coalescence times become universal in the large size limit and we identify a few…

We define a new family of generalized Stirling permutations that can be interpreted in terms of ordered trees and forests. We prove that the number of generalized Stirling permutations with a fixed number of ascents is given by a natural…

Estimation of epidemiological and population parameters from molecular sequence data has become central to the understanding of infectious disease dynamics. Various models have been proposed to infer details of the dynamics that describe…

We introduce a new Bayesian model for hierarchical clustering based on a prior over trees called Kingman's coalescent. We develop novel greedy and sequential Monte Carlo inferences which operate in a bottom-up agglomerative fashion. We show…

We present a generalization of the Yule model for macroevolution in which, for the appearance of genera, we consider point processes with the order statistics property, while for the growth of species we use nonlinear time-fractional pure…

We study a model of a population with individuals sampled from different species. The Yule-$\Lambda$ nested coalescent describes the genealogy of the sample when each species merges with another randomly chosen species with a constant rate…

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…

In this paper, we characterize the structure and topological indices of a class of random spider trees (RSTs) such as degree-based Gini index, degree-based Hoover index, generalized Zagreb index and other indices associated with these. We…

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…