Related papers: How much can evolved characters tell us about the …
Predictive constructions are a powerful way of characterizing the probability law of stochastic processes with certain forms of invariance, such as exchangeability or Markov exchangeability. When de Finetti-like representation theorems are…
We introduce a Markov model for the evolution of a gene family along a phylogeny. The model includes parameters for the rates of horizontal gene transfer, gene duplication, and gene loss, in addition to branch lengths in the phylogeny. The…
Reconstructing evolutionary trees from molecular sequence data is a fundamental problem in computational biology. Stochastic models of sequence evolution are closely related to spin systems that have been extensively studied in statistical…
Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is…
Horizontal gene transfer inference approaches are usually based on gene sequences: parametric methods search for patterns that deviate from a particular genomic signature, while phylogenetic methods use sequences to reconstruct the gene and…
Markov models are extensively used in the analysis of molecular evolution. A recent line of research suggests that pairs of proteins with functional and physical interactions co-evolve with each other. Here, by analyzing hundreds of…
We propose a new statistical model for computational linguistics. Rather than trying to estimate directly the probability distribution of a random sentence of the language, we define a Markov chain on finite sets of sentences with many…
Phylogenetic (i.e. leaf-labeled) trees play a fundamental role in evolutionary research. A typical problem is to reconstruct such trees from data like DNA alignments (whose columns are often referred to as characters), and a simple…
We consider a simple discrete-time Markov chain with values in $[0,\infty)^{Z^d}$. The Markov chain describes various interesting examples such as oriented percolation, directed polymers in random environment, time discretizations of binary…
Recombination is a powerful evolutionary process that shapes the genetic diversity observed in the populations of many species. Reconstructing genealogies in the presence of recombination from sequencing data is a very challenging problem,…
Comparative and evolutive ecologists are interested in the distribution of quantitative traits among related species. The classical framework for these distributions consists of a random process running along the branches of a phylogenetic…
We consider the branch-length estimation problem on a bifurcating tree: a character evolves along the edges of a binary tree according to a two-state symmetric Markov process, and we seek to recover the edge transition probabilities from…
Generating function equation has been derived for the probability distribution of the number of nodes with $k \ge 0$ outgoing lines in randomly evolving special trees. The stochastic properties of end-nodes (k=0) have been analyzed, and it…
Recent evidence suggests that nongenetic (epigenetic) mechanisms play an important role at all stages of cancer evolution. In many cancers, these mechanisms have been observed to induce dynamic switching between two or more cell states,…
Studying characters plays a vital role in computationally representing and interpreting narratives. Unlike previous work, which has focused on inferring character roles, we focus on the problem of modeling their relationships. Rather than…
Random forests are decision tree ensembles that can be used to solve a variety of machine learning problems. However, as the number of trees and their individual size can be large, their decision making process is often incomprehensible. In…
The parameters of many classes of birth-death processes cannot be inferred uniquely from phylogenetic trees: infinitely many parameter combinations yield the same distribution of phylogenetic trees. Here, we show that parameter…
Phylogenetic trees play a key role in the reconstruction of evolutionary relationships. Typically, they are derived from aligned sequence data (like DNA, RNA, or proteins) by using optimization criteria like, e.g., maximum parsimony (MP).…
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…
We consider Markov jump processes describing structured populations with interactions via density dependance. We propose a Markov construction with a distinguished individual which allows to describe the random tree and random sample at a…