相关论文: Clustering Systems of Phylogenetic Networks

In evolutionary biology, networks are becoming increasingly used to represent evolutionary histories for species that have undergone non-treelike or reticulate evolution. Such networks are essentially directed acyclic graphs with a leaf set…

Phylogenetic networks provide a way to describe and visualize evolutionary histories that have undergone so-called reticulate evolutionary events such as recombination, hybridization or horizontal gene transfer. The level k of a network…

Summary: Both theory and empirical evidence indicate that phylogenies (trees) of different genes (loci) do not display precisely matched topologies. This phylogenetic incongruence is attributed to the reticulated evolutionary history of…

Roughly speaking, clustering evolving networks aims at detecting structurally dense subgroups in networks that evolve over time. This implies that the subgroups we seek for also evolve, which results in many additional tasks compared to…

In phylogenetics, tree-based networks are used to model and visualize the evolutionary history of species where reticulate events such as horizontal gene transfer have occurred. Formally, a tree-based network $N$ consists of a phylogenetic…

The rich and varied ways that genetic material can be passed between species has motivated extensive research into the theory of phylogenetic networks. Features that align with biological processes, or with desirable mathematical…

The paper tackles the problem of clustering multiple networks, directed or not, that do not share the same set of vertices, into groups of networks with similar topology. A statistical model-based approach based on a finite mixture of…

Cluster algebras have recently become an important player in mathematics and physics. In this work, we investigate them through the lens of modern data science, specifically with techniques from network science and machine learning. Network…

A directed phylogenetic network is tree-child if every non-leaf vertex has a child that is not a reticulation. As a class of directed phylogenetic networks, tree-child networks are very useful from a computational perspective. For example,…

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…

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…

Nowadays there is a multitude of measures designed to capture different aspects of network structure. To be able to say if the structure of certain network is expected or not, one needs a reference model (null model). One frequently used…

We give a Hasse-diagram characterization of when a clustering system $\mathcal C$ on a finite taxa set $X$ is the hardwired clustering system $C_N$ of a rooted level-$k$ network. For each non-trivial block $B$ of $H=\mathcal H[\mathcal C]$,…

Phylogenetic networks are an important way to represent evolutionary histories that involve reticulations such as hybridization or horizontal gene transfer, yet fundamental questions such as how many networks there are that satisfy certain…

We study the behavior of the clustering coefficient in tagged networks. The rich variety of tags associated with the nodes in the studied systems provide additional information about the entities represented by the nodes which can be…

Complex networks of real-world systems are believed to be controlled by common phenomena, producing structures far from regular or random. Clustering, community structure and assortative mixing by degree are perhaps among most prominent…

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…

Clustering is typically measured by the ratio of triangles to all triples, open or closed. Generating clustered networks, and how clustering affects dynamics on networks, is reasonably well understood for certain classes of networks…

We develop a network in which the natural numbers are the vertices. We use the decomposition of natural numbers by prime numbers to establish the connections. We perform data collapse and show that the degree distribution of these networks…

Clusters appear in nature in a diversity of contexts, involving distances as long as the cosmological ones, and down to atoms and molecules and the very small nuclear size. They also appear in several other scenarios, in particular in…