Related papers: Markovian log-supermodularity, and its application…

We consider hidden Markov models indexed by a binary tree where the hidden state space is a general metric space. We study the maximum likelihood estimator (MLE) of the model parameters based only on the observed variables. In both…

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…

Self-similar Markov trees constitute a remarkable family of random compact real trees carrying a decoration function that is positive on the skeleton. As the terminology suggests, they are self-similar objects that further satisfy a Markov…

We studied how to obtain a distribution for the number of ancestors in species of sexual reproduction. Present models concentrate on the estimation of distributions repetitions of ancestors in genealogical trees. It has been shown that is…

The purpose of this paper is to make a comprehensive connection between the basic results and properties derived from the two kinds of topologies (namely the $(\epsilon,\lambda)-$topology introduced by the author and the stronger locally…

Phylogenetic mixture models, in which the sites in sequences undergo different substitution processes along the same or different trees, allow the description of heterogeneous evolutionary processes. As data sets consisting of longer…

Using terminologies of information geometry, we derive upper and lower bounds of the tail probability of the sample mean. Employing these bounds, we obtain upper and lower bounds of the minimum error probability of the 2nd kind of error…

We consider a branching model in discrete time where each individual has a trait in some general state space. Both the reproduction law and the trait inherited by the offsprings may depend on the trait of the mother and the environment. We…

Multitype branching processes (MTBP) model branching structures, where the nodes of the resulting tree are objects of different types. One field of application of such models in biology is in studies of cell proliferation. A sampling scheme…

We obtain explicit bounds on the moments of character sums, refining estimates of Montgomery and Vaughan. As an application we obtain results on the distribution of the maximal magnitude of character sums normalized by the square root of…

We give a closed form of the discrete-time evolution of a recombination transformation in population genetics. This decomposition allows to define a Markov chain in a natural way. We describe the geometric decay rate to the limit…

We derive a Poisson random field model for population site polymorphisms differences within and between two species that share a relatively recent common ancestor. The model can be either equilibrium or time inhomogeneous. We first consider…

Focusing on the discrete probabilistic setting we generalize the combinatorial definition of cumulants to L-cumulants. This generalization keeps all the desired properties of the classical cumulants like semi-invariance and vanishing for…

We consider a broadcasting problem on a tree where a binary digit (e.g., a spin or a nucleotide's purine/pyrimidine type) is propagated from the root to the leaves through symmetric noisy channels on the edges that randomly flip the state…

It is proposed that the co-expression of statistically significant motifs among the sequences of a proteome is a phylogenetic trait. From the co-expression matrix of such motifs in a group of prokaryotic proteomes a suitable definition of a…

In the principles-and-parameters framework, the structural features of languages depend on parameters that may be toggled on or off, with a single parameter often dictating the status of multiple features. The implied covariance between…

The Moran model with recombination is considered, which describes the evolution of the genetic composition of a population under recombination and resampling. There are $n$ sites (or loci), a finite number of letters (or alleles) at every…

We are interested in the evolving genealogy of a birth and death process with trait structure and ecological interactions. Traits are hereditarily transmitted from a parent to its offspring unless a mutation occurs. The dynamics may depend…

These lecture notes introduce the statistical analysis of continuous-time generative models built from Markov dynamics. We begin with the stochastic-calculus foundations of score-based diffusion models, including time reversal, score…

A theory of systems with long-range correlations based on the consideration of binary N-step Markov chains is developed. In our model, the conditional probability that the i-th symbol in the chain equals zero (or unity) is a linear function…