相关论文: Two metrics for general phylogenetic networks

The Robinson-Foulds (RF) metric is arguably the most widely used measure of phylogenetic tree similarity, despite its well-known shortcomings: For example, moving a single taxon in a tree can result in a tree that has maximum distance to…

A population of complete subgraphs or cliques in a network evolving via duplication-divergence is considered. We find that a number of cliques of each size scales linearly with the size of the network. We also derive a clique population…

We give exact and asymptotic counting results for the number of galled networks and reticulation-visible networks with few reticulation vertices. Our results are obtained with the component graph method, which was introduced by L. Zhang and…

The number of the non-shared edges of two phylogenies is a basic measure of the dissimilarity between the phylogenies. The non-shared edges are also the building block for approximating a more sophisticated metric called the nearest…

Generative networks are opening new avenues in fast event generation for the LHC. We show how generative flow networks can reach percent-level precision for kinematic distributions, how they can be trained jointly with a discriminator, and…

Networks are useful representations for complex systems. Especially, heterogeneous and asymmetrical relations commonly found in complex systems can be converted to weighted directed edges between nodes. The disparity filter (Serrano et al.,…

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…

Metric graphs are meaningful objects for modeling complex structures that arise in many real-world applications, such as road networks, river systems, earthquake faults, blood vessels, and filamentary structures in galaxies. To study metric…

Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…

In a population with haploid reproduction any individual has a single parent in the previous generation. If all genealogical distances among pairs of individuals (generations from the closest common ancestor) are known it is possible to…

Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…

The classical measure of similarity between two polygonal chains in Euclidean space is the Fr\'echet distance, which corresponds to the coordinated motion of two mobile agents along the chains while minimizing their maximum distance. As…

A widely studied model for generating sequences is to ``evolve'' them on a tree according to a symmetric Markov process. We prove that model trees tend to be maximally ``far apart'' in terms of variational distance.

The path-difference metric is one of the oldest distances for the comparison of fully resolved phylogenetic trees, but its statistical properties are still quite unknown. In this paper we compute the mean value of the square of the…

Recent genomic and bioinformatic advances have motivated the development of numerous random network models purporting to describe graphs of biological, technological, and sociological origin. The success of a model has been evaluated by how…

Phylogenetic diversity is a measure for describing how much of an evolutionary tree is spanned by a subset of species. If one applies this to the (unknown) subset of current species that will still be present at some future time, then this…

We introduce a biologically natural, mathematically tractable model of random phylogenetic network to describe evolution in the presence of hybridization. One of the features of this model is that the hybridization rate of the lineages…

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…

In this paper, we present a new metric distance for comparing two large graphs to find similarities and differences between them based on one of the most important graph structural properties, which is Node Adjacency Information, for all…

The Fair Proportion of a species in a phylogenetic tree is a very simple measure that has been used to assess its value relative to the overall phylogenetic diversity represented by the tree. It has recently been proved by Fuchs and Jin to…