Related papers: Topology and inference for multi-type Yule trees
Yule's 1925 paper introducing the branching model that bears his name was a landmark contribution to the biodiversity sciences. In his paper, Yule developed stochastic models to explain the observed distribution of species across genera and…
Consensus methods provide a useful strategy for combining information from a collection of gene trees. An important application of consensus methods is to combine gene trees to estimate a species tree. To investigate the theoretical…
Consider longitudinal networks whose edges turn on and off according to a discrete-time Markov chain with exponential-family transition probabilities. We characterize when their joint distributions are also exponential families with the…
Given an edge-weighted tree $T$ with $n$ leaves, sample the leaves uniformly at random without replacement and let $W_k$, $2 \le k \le n$, be the length of the subtree spanned by the first $k$ leaves. We consider the question, "Can $T$ be…
In population and evolutionary biology, hypotheses about micro-evolutionary and macro-evolutionary processes are commonly tested by comparing the shape indices of empirical evolutionary trees with those predicted by neutral models. A key…
Designing flexible probabilistic models over tree topologies is important for developing efficient phylogenetic inference methods. To do that, previous works often leverage the similarity of tree topologies via hand-engineered heuristic…
In order to conduct a statistical analysis on a given set of phylogenetic gene trees, we often use a distance measure between two trees. In a statistical distance-based method to analyze discordance between gene trees, it is a key to decide…
Phylogenetic trees represent the evolutionary relationships between extant lineages, where extinct or non-sampled lineages are omitted. Extending the work of Stadler and collaborators, this paper focuses on the branch lengths in…
Tree-based protocols are ubiquitous in distributed systems. They are flexible, they perform generally well, and, in static conditions, their analysis is mostly simple. Under churn, however, node joins and failures can have complex global…
We propose a general method to study dependent data in a binary tree, where an individual in one generation gives rise to two different offspring, one of type 0 and one of type 1, in the next generation. For any specific characteristic of…
This paper is concerned with the reliable inference of optimal tree-approximations to the dependency structure of an unknown distribution generating data. The traditional approach to the problem measures the dependency strength between…
In biology, a phylogenetic tree is a tool to represent the evolutionary relationship between species. Unfortunately, the classical Schr\"oder tree model is not adapted to take into account the chronology between the branching nodes. In…
Stochastic models of evolution (Markov random fields on trivalent trees) generally assume that different characters (different runs of the stochastic process) are independent and identically distributed. In this paper we take the first…
We consider a class of branching processes called Markovian binary trees, in which the individuals lifetime and reproduction epochs are modeled using a transient Markovian arrival process (TMAP). We estimate the parameters of the TMAP based…
We consider a multi-type Moran model (in continuous time) with selection and type-dependent mutation. This paper is concerned with the evolution of genealogical information forward in time. For this purpose we define and analytically…
We analyse a simple discrete-time stochastic process for the theoretical modeling of the evolution of protein lengths. At every step of the process a new protein is produced as a modification of one of the proteins already existing and its…
As a representation of relational data over time series, longitudinal networks provide opportunities to study link formation processes. However, networks at scale often exhibits community structure (i.e. clustering), which may confound…
In this work we introduce a variant of the Yule-Simon model for preferential growth by incorporating a finite kernel to model the effects of bounded memory. We characterize the properties of the model combining analytical arguments with…
Phylogenetic data arising on two possibly different tree topologies might be mixed through several biological mechanisms, including incomplete lineage sorting or horizontal gene transfer in the case of different topologies, or simply…
The forest of mutations associated to a multitype branching forest is obtained by merging together all vertices of its clusters and by preserving connections between them. We first show that the forest of mutations of any mulitype branching…