相关论文: Identifying species network features from gene tre…

A general scheme for detecting and analyzing topological patterns in large complex networks is presented. In this scheme the network in question is compared with its properly randomized version that preserves some of its low-level…

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…

We study the distribution of cycles of length h in large networks (of size N>>1) and find it to be an excellent ergodic estimator, even in the extreme inhomogeneous case of scale-free networks. The distribution is sharply peaked around a…

Networks are ubiquitous in biology and computational approaches have been largely investigated for their inference. In particular, supervised machine learning methods can be used to complete a partially known network by integrating various…

A rooted acyclic digraph N with labelled leaves displays a tree T when there exists a way to select a unique parent of each hybrid vertex resulting in the tree T. Let Tr(N) denote the set of all trees displayed by the network N. In general,…

This paper introduces a convex optimization framework for identifying switched network systems, in which both the node dynamics and the underlying graph topology switch between a finite number of configurations. Building on our recent…

The investigation of social networks is often hindered by their size as such networks often consist of at least thousands of vertices and edges. Hence, it is of major interest to derive compact structures that represent important…

Internet mapping projects generally consist in sampling the network from a limited set of sources by using traceroute probes. This methodology, akin to the merging of spanning trees from the different sources to a set of destinations, leads…

Many real-world networks display a natural bipartite structure. It is necessary and important to study the bipartite networks by using the bipartite structure of the data. Here we propose a modification of the clustering coefficient given…

Network science has presented community detection as a valuable tool for revealing functional modules in complex systems rooted in the wiring architectures of complex networks. The varying procedures of community detection can produce,…

In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…

A network can be analyzed at different topological scales, ranging from single nodes to motifs, communities, up to the complete structure. We propose a novel intermediate-level topological analysis that considers non-overlapping subgraphs…

We consider in this paper the problem of discovering, via a traceroute algorithm, the topology of a network, whose graph is spanned by an infinite branching process. A subset of nodes is selected according to some criterion. As a measure of…

Percolation theory can be used to describe the structural properties of complex networks using the generating function formulation. This mapping assumes that the network is locally tree-like and does not contain short-range loops between…

We study the evolution of the network properties of a populated network embedded in a genotype space characterised by either a low or a high number of potential links, with particular emphasis on the connectivity and clustering. Evolution…

Mutation rate variation across loci is well known to cause difficulties, notably identifiability issues, in the reconstruction of evolutionary trees from molecular sequences. Here we introduce a new approach for estimating general…

This paper deals with dynamical networks for which the relations between node signals are described by proper transfer functions and external signals can influence each of the node signals. We are interested in graph-theoretic conditions…

In this paper we present a sufficient condition that guarantees identifiability of linear network dynamic systems exhibiting continuous-time weighted consensus protocols with acyclic structure. Each edge of the underlying network graph…

Subgraphs and cycles are often used to characterize the local properties of complex networks. Here we show that the subgraph structure of real networks is highly time dependent: as the network grows, the density of some subgraphs remains…

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…