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Collapse Lineage Tree (CLTree) is a software tool that annotates, roots, and evaluates phylogenetic trees by using lineages. A recursive algorithm was designed to annotate the branches by the common taxonomic lineage of its descendants in a…
The election is a classical problem in distributed algorithmic. It aims to design and to analyze a distributed algorithm choosing a node in a graph, here, in a tree. In this paper, a class of randomized algorithms for the election is…
The ability to adequately model risks is crucial for insurance companies. The method of "Copula-based hierarchical risk aggregation" by Arbenz et al. offers a flexible way in doing so and has attracted much attention recently. We briefly…
We identify the complexity of the classification problem for automorphisms of a given countable regularly branching tree up to conjugacy. We consider both the rooted and unrooted cases. Additionally, we calculate the complexity of the…
We study a model of growing planar tree graphs where in each time step we separate the tree into two components by splitting a vertex and then connect the two pieces by inserting a new link between the daughter vertices. This model…
This paper introduces a new combinatorial framework for modeling the growth of binary trees through a discrete evolution process that incorporates a growing rule and an extinction rule. Building upon the theory of increasingly labeled…
We study the influence of the seed in random trees grown according to the uniform attachment model, also known as uniform random recursive trees. We show that different seeds lead to different distributions of limiting trees from a total…
We consider species tree estimation under a standard stochastic model of gene tree evolution that incorporates incomplete lineage sorting (as modeled by a coalescent process) and gene duplication and loss (as modeled by a branching…
Selective inference is considered for testing trees and edges in phylogenetic tree selection from molecular sequences. This improves the previously proposed approximately unbiased test by adjusting the selection bias when testing many trees…
Transformation-based learning has been successfully employed to solve many natural language processing problems. It has many positive features, but one drawback is that it does not provide estimates of class membership probabilities. In…
The node-averaged complexity of a problem captures the number of rounds nodes of a graph have to spend on average to solve the problem in the LOCAL model. A challenging line of research with regards to this new complexity measure is to…
A probabilistic framework is introduced that represents stylized banking networks and aims to predict the size of contagion events. In contrast to previous work on random financial networks, which assumes independent connections between…
We give a simple characterisation of the distribution of the independence number, and equivalently the matching number, of a random tree on $n$ labelled vertices chosen uniformly among the $n^{n-2}$ such trees: Roll an $n$-sided die…
We investigated testing the likelihood of a phylogenetic tree by comparison to its subtree pruning and regrafting (SPR) neighbors, with or without re-optimizing branch lengths. This is inspired by aspects of Bayesian significance tests, and…
In this paper we investigate the use of staged tree models for discrete longitudinal data. Staged trees are a type of probabilistic graphical model for finite sample space processes. They are a natural fit for longitudinal data because a…
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…
Inference of evolutionary trees and rates from biological sequences is commonly performed using continuous-time Markov models of character change. The Markov process evolves along an unknown tree while observations arise only from the tips…
Credible intervals and credible sets, such as highest posterior density (HPD) intervals, form an integral statistical tool in Bayesian phylogenetics, both for phylogenetic analyses and for development. Readily available for continuous…
A fringe subtree of a rooted tree is a subtree consisting of one of the nodes and all its descendants. In this paper, we are specifically interested in the number of non-isomorphic trees that appear in the collection of all fringe subtrees…
Understanding the effects of the choice of the tree on the joint distribution of a tree-structured Markov random field (MRF) is crucial for fully exploiting the intelligibility of such probabilistic graphical models. Tools must be developed…