Related papers: Comparing and simplifying distinct-cluster phyloge…
Symmetries in a network connectivity regulate how the graph's functioning organizes into clustered states. Classical methods for tracing the symmetry group of a network require very high computational costs, and therefore they are of hard,…
Compound graphs are networks in which vertices can be grouped into larger subsets, with these subsets capable of further grouping, resulting in a nesting that can be many levels deep. In several applications, including biological workflows,…
A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…
A phylogenetic tree is a graphical representation of an evolutionary history of taxa in which the leaves correspond to the taxa and the non-leaves correspond to speciations. One of important problems in phylogenetic analysis is to assemble…
For a phylogenetic tree, the phylogenetic diversity of a set A of taxa is the total weight of edges on paths to A. Finding small sets of maximal diversity is crucial for conservation planning, as it indicates where limited resources can be…
Grouping the nodes of a graph into clusters is a standard technique for studying networks. We study a problem where we are given a directed network and are asked to partition the graph into a sequence of coherent groups. We assume that…
A classical result, fundamental to evolutionary biology, states that an edge-weighted tree $T$ with leaf set $X$, positive edge weights, and no vertices of degree 2 can be uniquely reconstructed from the set of leaf-to-leaf distances…
Network models provide a powerful and flexible framework for analyzing a wide range of structured data sources. In many situations of interest, however, multiple networks can be constructed to capture different aspects of an underlying…
Phylogenetic networks provide a framework for representing evolutionary histories involving reticulate events such as hybridization or horizontal gene transfer. A central problem is to infer such networks from local structural information.…
Community detection, which focuses on clustering nodes or detecting communities in (mostly) a single network, is a problem of considerable practical interest and has received a great deal of attention in the research community. While being…
Network reconstruction lies at the heart of phylogenetic research. Two well studied classes of phylogenetic networks include tree-child networks and level-$k$ networks. In a tree-child network, every non-leaf node has a child that is a tree…
The paper tackles the problem of clustering multiple networks, directed or not, that do not share the same set of vertices, into groups of networks with similar topology. A statistical model-based approach based on a finite mixture of…
Subject of research is complex networks and network systems. The network system is defined as a complex network in which flows are moved. Classification of flows in the network is carried out on the basis of ordering and continuity. It is…
Structure and dynamics of complex networks usually deal with degree distributions, clustering, shortest path lengths and other graph properties. Although these concepts have been analysed for graphs on abstract spaces, many networks happen…
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…
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,…
Phylogenetic mixture models are statistical models of character evolution allowing for heterogeneity. Each of the classes in some unknown partition of the characters may evolve by different processes, or even along different trees. The…
A new method for identifying communities in networks is proposed. Reference nodes, either selected using a priory information about the network or according to relevant node measurements, are obtained so as to indicate putative communities.…
The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…
In the framework of coupled cell systems, a coupled cell network describes graphically the dynamical dependencies between individual dynamical systems, the cells. The fundamental network of a network reveals the hidden symmetries of that…