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Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…

This paper presents a statistically sound method for using likelihood to assess potential models of network evolution. The method is tested on data from five real networks. Data from the internet autonomous system network, from two photo…

The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been…

The ability to compare complex systems can provide new insight into the fundamental nature of the processes captured in ways that are otherwise inaccessible to observation. Here, we introduce the $n$-tangle method to directly compare two…

Recent approaches to drape garments quickly over arbitrary human bodies leverage self-supervision to eliminate the need for large training sets. However, they are designed to train one network per clothing item, which severely limits their…

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 $X$…

Recently, so-called treebased phylogenetic networks have gained considerable interest in the literature, where a treebased network is a network that can be constructed from a phylogenetic tree, called the base tree, by adding additional…

Termites form complex dynamical trail networks from simple individual rules when exploring their environment. To help identify those simple rules, we reconstructed trail networks from time-lapse images of roaming termites. We quantified the…

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.…

Phylogenetic networks are rooted directed acyclic graphs that represent evolutionary relationships between species whose past includes reticulation events such as hybridisation and horizontal gene transfer. To search the space of…

One of the biggest needs in network science research is access to large realistic datasets. As data analytics methods permeate a range of diverse disciplines---e.g., computational epidemiology, sustainability, social media analytics,…

The study of networks has grown into a substantial interdisciplinary endeavour that encompasses myriad disciplines in the natural, social, and information sciences. Here we introduce a framework for constructing taxonomies of networks based…

The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…

The evolutionary relationships between species are typically represented in the biological literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate processes, such as the formation of hybrid species or…

Phylogenetic trees and networks are graphs used to model evolutionary relationships, with trees representing strictly branching histories and networks allowing for events in which lineages merge, called reticulation events. While the…

Background: The reconstruction of the phylogenetic tree topology of four taxa is, still nowadays, one of the main challenges in phylogenetics. Its difficulties lie in considering not too restrictive evolutionary models, and correctly…

Genetic and comparative genomic studies indicate that extant genomes are more properly considered to be a fusion product of random mutations over generations and genomic material transfers between individuals of different lineages. This has…

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…

Network intrusion detection systems play a vital role in protecting networks by detecting malicious network traffic which can then be investigated by a cybersecurity operations centre. State-of-the-art approaches utilise supervised machine…

Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees…