相关论文: Clustering Systems of Phylogenetic Networks

This paper considers networks where relationships between nodes are represented by directed dissimilarities. The goal is to study methods that, based on the dissimilarity structure, output hierarchical clusters, i.e., a family of nested…

Synchronization is of central importance in power distribution, telecommunication, neuronal, and biological networks. Many networks are observed to produce patterns of synchronized clusters, but it has been difficult to predict these…

A classic problem in computational biology is constructing a phylogenetic tree given a set of distances between n species. In most cases, a tree structure is too constraining. We consider a circular split network, a generalization of a tree…

Clustering methods based on deep neural networks have proven promising for clustering real-world data because of their high representational power. In this paper, we propose a systematic taxonomy of clustering methods that utilize deep…

Cycles, which can be found in many different kinds of networks, make the problems more intractable, especially when dealing with dynamical processes on networks. On the contrary, tree networks in which no cycle exists, are simplifications…

Transport networks are crucial to the functioning of natural and technological systems. Nature features transport networks that are adaptive over a vast range of parameters, thus providing an impressive level of robustness in supply.…

In continuation of prior work, we investigate ties between a network's connectivity and ensemble dynamics. This relationship is notoriously difficult to approach mathematically in natural, complex networks. In our work, we aim to understand…

Network science provides an indispensable theoretical framework for studying the structure and function of real complex systems. Different network models are often used for finding the rules that govern their evolution, whereby the correct…

This paper characterizes hierarchical clustering methods that abide by two previously introduced axioms -- thus, denominated admissible methods -- and proposes tractable algorithms for their implementation. We leverage the fact that, for…

Coupled cell systems model interacting dynamical units and provide a natural framework for studying synchrony phenomena arising from collective behavior. Graph symmetries often induce such patterns, but certain networks exhibit additional…

Motivated by the analysis of social networks, we study a model of random networks that has both a given degree distribution and a tunable clustering coefficient. We consider two types of growth processes on these graphs: diffusion and…

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…

Phylogenetic networks are used in biology to represent evolutionary histories. The class of orchard phylogenetic networks was recently introduced for their computational benefits, without any biological justification. Here, we show that…

Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which…

Stream graphs are a very useful mode of representation for temporal network data, whose richness offers a wide range of possible approaches. The various methods aimed at generalising the classical approaches applied to static networks are…

A complex network is a condensed representation of the relational topological framework of a complex system. A main reason for the existence of such networks is the transmission of items through the entities of these complex systems. Here,…

Unrooted phylogenetic networks are graphs used to represent evolutionary relationships. Accurately reconstructing such networks is of great relevance for evolutionary biology. It has recently been conjectured that all phylogenetic networks…

The behaviour and functioning of a variety of complex physical and biological systems depend on the spatial organisation of their constituent units, and on the presence and formation of clusters of functionally similar or related…

Tree-child networks, one of the prominent network classes in phylogenetics, have been introduced for the purpose of modeling reticulate evolution. Recently, the first author together with Gittenberger and Mansouri (2019) showed that the…

Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks…