Related papers: Distinguishing Level-2 Phylogenetic Networks Using…

Inference of network-like evolutionary relationships between species from genomic data must address the interwoven signals from both gene flow and incomplete lineage sorting. The heavy computational demands of standard approaches to this…

Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level-1 phylogenetic network displaying a given set $\mathcal{T}$ of binary binets or…

Network representations of systems from various scientific and societal domains are neither completely random nor fully regular, but instead appear to contain recurring structural building blocks. These features tend to be shared by…

Rooted phylogenetic networks allow biologists to represent evolutionary relationships between present-day species by revealing ancestral speciation and hybridization events. A convenient and well-studied class of such networks are…

To the best of our knowledge, this paper presents the first large-scale study that tests whether network categories (e.g., social networks vs. web graphs) are distinguishable from one another (using both categories of real-world networks…

One strategy for reconstruction of phylogenetic networks is to solve the phylogenetic network problem, which involves inferring phylogenetic trees first and subsequently computing the smallest phylogenetic network that displays all the…

Identifiability of phylogenetic models is a necessary condition to ensure that the model parameters can be uniquely determined from data. Mixture models are phylogenetic models where the probability distributions in the model are convex…

For a model of molecular evolution to be useful for phylogenetic inference, the topology of evolutionary trees must be identifiable. That is, from a joint distribution the model predicts, it must be possible to recover the tree parameter.…

Semidirected networks have received interest in evolutionary biology as the appropriate generalization of unrooted trees to networks, in which some but not all edges are directed. Yet these networks lack proper theoretical study. We define…

A fundamental problem in the study of phylogenetic networks is to determine whether or not a given phylogenetic network contains a given phylogenetic tree. We develop a quadratic-time algorithm for this problem for binary nearly-stable…

In biodiversity conservation it is often necessary to prioritize the species to conserve. Existing approaches to prioritization, e.g. the Fair Proportion Index and the Shapley Value, are based on phylogenetic trees and rank species…

Many classes of phylogenetic networks have been proposed in the literature. A feature of several of these classes is that if one restricts a network in the class to a subset of its leaves, then the resulting network may no longer lie within…

Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees…

Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…

Latent space models for network data characterize each node through a vector of latent features whose pairwise similarities define the edge probabilities among the pairs of nodes. Although this formulation has led to successful…

Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…

While gradient descent has proven highly successful in learning connection weights for neural networks, the actual structure of these networks is usually determined by hand, or by other optimization algorithms. Here we describe a simple…

Less rigid than phylogenetic trees, phylogenetic networks allow the description of a wider range of evolutionary events. In this note, we explain how to extend the rank invariants from phylogenetic trees to phylogenetic networks evolving…

We describe a method that will reconstruct an unrooted binary phylogenetic level-1 network on n taxa from the set of all quartets containing a certain fixed taxon, in O(n^3) time. We also present a more general method which can handle more…

Network classification aims to group networks (or graphs) into distinct categories based on their structure. We study the connection between classification of a network and of its constituent nodes, and whether nodes from networks in…