Related papers: Markov embedding of ranked unlabelled evolutionary…
Modelling the substitution of nucleotides along a phylogenetic tree is usually done by a hidden Markov process. This allows to define a distribution of characters at the leaves of the trees and one might be able to obtain polynomial…
Topological phylogenetic trees can be assigned edge weights in several natural ways, highlighting different aspects of the tree. Here the rooted triple and quartet metrizations are introduced, and applied to formulate novel fast methods of…
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),…
Efforts to reconstruct phylogenetic trees and understand evolutionary processes depend fundamentally on stochastic models of speciation and mutation. The simplest continuous-time model for speciation in phylogenetic trees is the Yule…
Null models of binary phylogenetic trees are useful for testing hypotheses on real world phylogenies. In this paper we consider phylogenies as binary trees without edge lengths together with a sampling measure and encode them as algebraic…
We introduce a random recursive tree model with two communities, called balanced community modulated random recursive tree, or BCMRT in short. In this setting, pairs of nodes of different type appear sequentially. Each node of the pair…
Full Bayesian computational inference for model determination in undirected graphical models is currently restricted to decomposable graphs, except for problems of very small scale. In this paper we develop new, more efficient methodology…
We present new MCMC algorithms for computing the posterior distributions and expectations of the unknown variables in undirected graphical models with regular structure. For demonstration purposes, we focus on Markov Random Fields (MRFs).…
We study (plane) tree-valued Markov chains $(T_n,n \geq 1)$ with uniform backward dynamics and show that they can be obtained by sampling from a real tree. As non--plane trees, every such Markov chain is represented by a weighted real tree.…
This work considers the problem of learning the structure of multivariate linear tree models, which include a variety of directed tree graphical models with continuous, discrete, and mixed latent variables such as linear-Gaussian models,…
Stochastic optimization methods such as mirror descent have wide applications due to low computational cost. Those methods have been well studied under assumption of the independent and identical distribution, and usually achieve sublinear…
Tree-based networks are a class of phylogenetic networks that attempt to formally capture what is meant by "tree-like" evolution. A given non-tree-based phylogenetic network, however, might appear to be very close to being tree-based, or…
A dynamical picture of phylogenetic evolution is given in terms of Markov models on a state space, comprising joint probability distributions for character types of taxonomic classes. Phylogenetic branching is a process which augments the…
Computational inference of dated evolutionary histories relies upon various hypotheses about RNA, DNA, and protein sequence mutation rates. Using mutation rates to infer these dated histories is referred to as molecular clock assumption.…
We consider novel phylogenetic models with rate matrices that arise via the embedding of a progenitor model on a small number of character states, into a target model on a larger number of character states. Adapting representation-theoretic…
The goal of branch length estimation in phylogenetic inference is to estimate the divergence time between a set of sequences based on compositional differences between them. A number of software is currently available facilitating branch…
Merge trees are a type of topological descriptors that record the connectivity among the sublevel sets of scalar fields. They are among the most widely used topological tools in visualization. In this paper, we are interested in sketching a…
Balancing treatment allocation for influential covariates is critical in clinical trials. This has become increasingly important as more and more biomarkers are found to be associated with different diseases in translational research…
A metric phylogenetic tree relating a collection of taxa induces weighted rooted triples and weighted quartets for all subsets of three and four taxa, respectively. New intertaxon distances are defined that can be calculated from these…
We consider the probability that a spanning tree chosen uniformly at random from a graph can be partitioned into a fixed number $k$ of trees of equal size by removing $k-1$ edges. In that case, the spanning tree is called {\em splittable}.…