Related papers: Phylogenetic network models as graphical models

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…

Normal networks are an important class of phylogenetic networks that have compelling mathematical properties which align with intuition about inference from genetic data. While tools enabling widespread use of phylogenetic networks in the…

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…

The goal of the work is to implement molecular phylogenetic calculations using the Grid paradigm by means of the MrBayes software using Directed Acyclic Graphs (DAG) jobs. In this method, a set of jobs depends on the input or the output of…

Our goal is to infer the topology of a network when (i) we can send probes between sources and receivers at the edge of the network and (ii) intermediate nodes can perform simple network coding operations, i.e., additions. Our key intuition…

Models of random phylogenetic networks have been used since the inception of the field, but the introduction and rigorous study of mathematically tractable models is a much more recent topic that has gained momentum in the last 5 years.…

We develop a general methodological framework for probabilistic inference in discrete- and continuous-time stochastic processes evolving on directed acyclic graphs (DAGs). The process is observed only at the leaf nodes, and the challenge is…

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…

We consider the problem of uniformly generating a spanning tree, of a connected undirected graph. This process is useful to compute statistics, namely for phylogenetic trees. We describe a Markov chain for producing these trees. For cycle…

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.…

Structural learning of directed acyclic graphs (DAGs) or Bayesian networks has been studied extensively under the assumption that data are independent. We propose a new Gaussian DAG model for dependent data which assumes the observations…

Dynamic networks consist of interconnected dynamical systems. The subsystems can be viewed as transformations of input signals into output signals, where signals flow from one system into another through interconnections. The signal flows…

Learning a faithful directed acyclic graph (DAG) from samples of a joint distribution is a challenging combinatorial problem, owing to the intractable search space superexponential in the number of graph nodes. A recent breakthrough…

Large scale real-world network data such as social and information networks are ubiquitous. The study of such social and information networks seeks to find patterns and explain their emergence through tractable models. In most networks, and…

We propose a new statistical model suitable for machine learning of systems with long distance correlations such as natural languages. The model is based on directed acyclic graph decorated by multi-linear tensor maps in the vertices and…

Directed acyclic graphs (DAGs) are commonly used to represent causal relationships among random variables in graphical models. Applications of these models arise in the study of physical, as well as biological systems, where directed edges…

Tree-child networks are a recently-described class of directed acyclic graphs that have risen to prominence in phylogenetics (the study of evolutionary trees and networks). Although these networks have a number of attractive mathematical…

An important problem in evolutionary biology is to reconstruct the evolutionary history of a set $X$ of species. This history is often represented as a phylogenetic network, that is, a connected graph with leaves labelled by elements in $X$…

We propose a method to identify nonlinear acyclic networks in continuous time when the dynamics are located on the edges and all the nodes are excited. We show that it is necessary and sufficient to measure all the sinks to identify any…

This paper presents the current state of the art on attack and defense modeling approaches that are based on directed acyclic graphs (DAGs). DAGs allow for a hierarchical decomposition of complex scenarios into simple, easily understandable…