Related papers: Exchangeable and Sampling Consistent Distributions…
On a finite graph, there is a natural family of Boltzmann probability measures on cycle-rooted spanning forests, parametrized by weights on cycles. For a certain subclass of those weights, we construct Gibbs measures in infinite volume, as…
Phylogenetics begins with reconstructing biological family trees from genetic data. Since Nature is not limited to tree-like histories, we use networks to organize our data, and have discovered new polytopes, metric spaces, and simplicial…
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…
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…
The evolutionary relationships between species are typically represented in the biological literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate processes, such as the formation of hybrid species or…
A tree-based network $N$ on $X$ is called universal if every phylogenetic tree on $X$ is a base tree for $N$. Recently, binary universal tree-based networks have attracted great attention in the literature and their existence has been…
The dynamical phenomena of complex networks are very difficult to predict from local information due to the rich microstructures and corresponding complex dynamics. On the other hands, it is a horrible job to compute some stochastic…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
A phylogenetic tree is an acyclic graph with distinctly labeled leaves, whose internal edges have a positive weight. Given a set of n leaves, the collection of all phylogenetic trees with this leaf set can be assembled into a metric cube…
For a pair consisting of a gene tree and a species tree, the ancestral configurations at an internal node of the species tree are the distinct sets of gene lineages that can be present at that node. Ancestral configurations appear in…
Gene trees are evolutionary trees representing the ancestry of genes sampled from multiple populations. Species trees represent populations of individuals -- each with many genes -- splitting into new populations or species. The coalescent…
The Sackin and Colless indices are two widely-used metrics for measuring the balance of trees and for testing evolutionary models in phylogenetics. This short paper contributes two results about the Sackin and Colless indices of trees. One…
The selection of the most suitable evolutionary model to analyze the given molecular data is usually left to biologist's choice. In his famous book, J Felsenstein suggested that certain linear equations satisfied by the expected…
Exchangeability is a central notion in statistics and probability theory. The assumption that an infinite sequence of data points is exchangeable is at the core of Bayesian statistics. However, finite exchangeability as a statistical…
Phylogenetic networks are rooted, labelled directed acyclic graphs which are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any…
We compare three basic kinds of discrete mathematical models used to portray phylogenetic relationships among species and higher taxa: phylogenetic trees, Hennig trees and Nelson cladograms. All three models are trees, as that term is…
Billey et al. [arXiv:1507.04976] have recently discovered a surprisingly simple formula for the number $a_n(\sigma)$ of leaf-labelled rooted non-embedded binary trees (also known as phylogenetic trees) with $n\geq 1$ leaves, fixed (for the…
Phylogenetic networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…
Most computational models of dependency syntax consist of distributions over spanning trees. However, the majority of dependency treebanks require that every valid dependency tree has a single edge coming out of the ROOT node, a constraint…
We address an open question of Francis and Steel about phylogenetic networks and trees. They give a polynomial time algorithm to decide if a phylogenetic network, N, is tree-based and pose the problem: given a fixed tree T and network N, is…