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The power of any kind of network approach lies in the ability to simplify a complex system so that one can better understand its function as a whole. Sometimes it is beneficial, however, to include more information than in a simple graph of…
Many modern networks are \emph{reconfigurable}, in the sense that the topology of the network can be changed by the nodes in the network. For example, peer-to-peer, wireless and ad-hoc networks are reconfigurable. More generally, many…
Networks have in recent years emerged as an invaluable tool for describing and quantifying complex systems in many branches of science. Recent studies suggest that networks often exhibit hierarchical organization, where vertices divide into…
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…
Different network models have been suggested for the topology underlying complex interactions in natural systems. These models are aimed at replicating specific statistical features encountered in real-world networks. However, it is rarely…
Interaction networks, consisting of agents linked by their interactions, are ubiquitous across many disciplines of modern science. Many methods of analysis of interaction networks have been proposed, mainly concentrating on node degree…
Fake news gains has gained significant momentum, strongly motivating the need for fake news research. Many fake news detection approaches have thus been proposed, where most of them heavily rely on news content. However, network-based clues…
Many methods have been proposed to detect communities, not only in plain, but also in attributed, directed or even dynamic complex networks. From the modeling point of view, to be of some utility, the community structure must be…
The next step in the understanding of the genome organization, after the determination of complete sequences, involves proteomics. The proteome includes the whole set of protein-protein interactions, and two recent independent studies have…
Identifying emerging influential or popular node/item in future on network is a current interest of the researchers. Most of previous works focus on identifying leaders in time evolving networks on the basis of network structure or node's…
Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
Real networks often grow through the sequential addition of new nodes that connect to older ones in the graph. However, many real systems evolve through the branching of fundamental units, whether those be scientific fields, countries, or…
With the rise of social networks, information on the internet is no longer solely organized by web pages. Rather, content is generated and shared among users and organized around their social relations on social networks. This presents new…
Most network data are collected from partially observable networks with both missing nodes and missing edges, for example, due to limited resources and privacy settings specified by users on social media. Thus, it stands to reason that…
Latent variable models for network data extract a summary of the relational structure underlying an observed network. The simplest possible models subdivide nodes of the network into clusters; the probability of a link between any two nodes…
Finding efficient algorithms to explore large networks with the aim of recovering information about their structure is an open problem. Here, we investigate this challenge by proposing a model in which random walkers with previously…
In this paper, we consider the problem of exploring structural regularities of networks by dividing the nodes of a network into groups such that the members of each group have similar patterns of connections to other groups. Specifically,…
We introduce a minimal model for the evolution of functional protein-interaction networks using a sequence-based mutational algorithm, and apply the model to study neutral drift in networks that yield oscillatory dynamics. Starting with a…
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 $X$…