Related papers: A Beta-splitting model for evolutionary trees
A model of genomic sequence evolution on a species tree should include not only a sequence substitution process, but also a coalescent process, since different sites may evolve on different gene trees due to incomplete lineage sorting.…
The time process of transport on randomly evolving trees is investigated. By introducing the notions of living and dead nodes a model of random tree evolution is constructed which describes the spreading in time of objects corresponding to…
We apply the theory of markov random fields on trees to derive a phase transition in the number of samples needed in order to reconstruct phylogenies. We consider the Cavender-Farris-Neyman model of evolution on trees, where all the inner…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
Following Poupard's study of strictly ordered binary trees with respect to two parameters, namely, "end of minimal chain" and "parent of maximum leaf" a true Tree Calculus is being developed to solve a partial difference equation system and…
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…
The tree-based ensembles are known for their outstanding performance in classification and regression problems characterized by feature vectors represented by mixed-type variables from various ranges and domains. However, considering…
Phylogenetic networks provide a more general description of evolutionary relationships than rooted phylogenetic trees. One way to produce a phylogenetic network is to randomly place $k$ arcs between the edges of a rooted binary phylogenetic…
Phylogenetic comparative methods explore the relationships between quantitative traits adjusting for shared evolutionary history. This adjustment often occurs through a Brownian diffusion process along the branches of the phylogeny that…
As a flexible nonparametric learning tool, the random forests algorithm has been widely applied to various real applications with appealing empirical performance, even in the presence of high-dimensional feature space. Unveiling the…
We consider a neutral dynamical model of biological diversity, where individuals live and reproduce independently. They have i.i.d. lifetime durations (which are not necessarily exponentially distributed) and give birth (singly) at constant…
Bayesian Additive Regression Trees [BART, Chipman et al., 2010] have gained significant popularity due to their remarkable predictive performance and ability to quantify uncertainty. However, standard decision tree models rely on recursive…
In a supercritical branching particle system, the trimmed tree consists of those particles which have descendants at all times. We develop this concept in the superprocess setting. For a class of continuous superprocesses with Feller…
We consider the set of random Bienaym\'e-Galton-Watson trees with a bounded number of offspring and bounded number of generations as a statistical mechanics model: a random tree is a rooted subtree of the maximal tree; the spin at a given…
Binary trait data record the presence or absence of distinguishing traits in individuals. We treat the problem of estimating ancestral trees with time depth from binary trait data. Simple analysis of such data is problematic. Each homology…
Decision trees built with data remain in widespread use for nonparametric prediction. Predicting probability distributions is preferred over point predictions when uncertainty plays a prominent role in analysis and decision-making. We study…
Bayesian model-based spatial clustering methods are widely used for their flexibility in estimating latent clusters with an unknown number of clusters while accounting for spatial proximity. Many existing methods are designed for clustering…
A major task of evolutionary biology is the reconstruction of phylogenetic trees from molecular data. The evolutionary model is given by a Markov chain on a tree. Given samples from the leaves of the Markov chain, the goal is to reconstruct…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
Some, but not all processes of the form $M_t=\exp(-\xi_t)$ for a pure-jump subordinator $\xi$ with Laplace exponent $\Phi$ arise as residual mass processes of particle 1 (tagged particle) in Bertoin's partition-valued exchangeable…