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Various hypotheses exist about the paths used for communication between the nodes of complex networks. Most studies simply suppose that communication goes via shortest paths, while others have more explicit assumptions about how routing…
In mathematical phylogenetics, evolutionary relationships are often represented by trees and networks. The latter are typically used whenever the relationships cannot be adequately described by a tree, which happens when so-called…
We propose a dynamical process for network evolution, aiming at explaining the emergence of the small world phenomenon, i.e., the statistical observation that any pair of individuals are linked by a short chain of acquaintances computable…
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…
This paper studies the relationship between undirected (unrooted) and directed (rooted) phylogenetic networks. We describe a polynomial-time algorithm for deciding whether an undirected nonbinary phylogenetic network, given the locations of…
We comprehensively studied the morphology of the self-organized effective network structures that form in simple coupled maps with interelement synchronization-dependent connection changes. Based on the parameter values, the spontaneous…
In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…
We consider the neighborhood tree induced by alternating the use of different neighborhood structures within a local search descent. We investigate the issue of designing a search strategy operating at the neighborhood tree level by…
Traditional approaches to neuroevolution often start from scratch. This becomes prohibitively expensive in terms of computational and data requirements when targeting modern, deep neural networks. Using a warm start could be highly…
C. elegans is commonly used in neuroscience for behaviour analysis because of it's compact nervous system with well-described connectivity. Localizing the animal and distinguishing between its head and tail are important tasks to track the…
Recurrent Neural Networks (RNNs) were recently successfully used to model the way neural activity drives task-related behavior in animals, operating under the implicit assumption that the obtained solutions are universal. Observations in…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
Networks embedded in space can display all sorts of transitions when their structure is modified. The nature of these transitions (and in some cases crossovers) can differ from the usual appearance of a giant component as observed for the…
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 directed acyclic graphs that depict the genomic evolution of related taxa. Reticulation nodes in such networks (nodes with more than one parent) represent reticulate evolutionary events, such as recombination,…
Hybrid evolution and horizontal gene transfer (HGT) are processes where evolutionary relationships may more accurately be described by a reticulated network than by a tree. In such a network, there will often be several paths between any…
The displayed tree phylogenetic network model is shown to sit as a natural submodel of the graphical model associated to a directed acyclic graph (DAG). This representation allows to derive a number of results about the displayed tree…
Today, the human brain can be studied as a whole. Electroencephalography, magnetoencephalography, or functional magnetic resonance imaging techniques provide functional connectivity patterns between different brain areas, and during…
Good representations for phylogenetic trees and networks are important for optimizing storage efficiency and implementation of scalable methods for the inference and analysis of evolutionary trees for genes, genomes and species. We…
Phylogenetic network is an evolutionary model that uses a rooted directed acyclic graph (instead of a tree) to model an evolutionary history of species in which reticulate events (e.g., hybrid speciation or horizontal gene transfer)…