Related papers: Making a Network Orchard by Adding Leaves
Modeling networks can serve as a means of summarizing high-dimensional complex systems. Adapting an approach devised for dense, weighted networks, we propose a new method for generating and estimating unweighted networks. This approach can…
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…
Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level-1 phylogenetic network displaying a given set $\mathcal{T}$ of binary binets or…
Sum-Product Networks with complex probability distribution at the leaves have been shown to be powerful tractable-inference probabilistic models. However, while learning the internal parameters has been amply studied, learning complex leaf…
Galled trees are widely studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into galled networks by relaxing a structural condition. In this work, a linear recurrence formula is given…
Collaboration networks are studied as an example of growing bipartite networks. These have been previously observed to have structure such as positive correlations between nearest-neighbour degrees. However, a detailed understanding of the…
Latent Euclidean embedding models a given network by representing each node in a Euclidean space, where the probability of two nodes sharing an edge is a function of the distances between the nodes. This implies that for two nodes to share…
Network visualization allows a quick glance at how nodes (or actors) are connected by edges (or ties). A conventional network diagram of "contact tree" maps out a root and branches that represent the structure of nodes and edges, often…
We study a class of growth algorithms for directed graphs that are candidate models for the evolution of genetic regulatory networks. The algorithms involve partial duplication of nodes and their links, together with innovation of new…
Many popular algorithms for searching the space of leaf-labelled trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are…
Phylogenetic networks provide a means of describing the evolutionary history of sets of species believed to have undergone hybridization or gene flow during their evolution. The mutation process for a set of such species can be modeled as a…
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…
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…
The neighbor-joining algorithm is a popular phylogenetics method for constructing trees from dissimilarity maps. The neighbor-net algorithm is an extension of the neighbor-joining algorithm and is used for constructing split networks. We…
In this article we study the treewidth of the \emph{display graph}, an auxiliary graph structure obtained from the fusion of phylogenetic (i.e., evolutionary) trees at their leaves. Earlier work has shown that the treewidth of the display…
Generated networks are widely used in network-based research as a convenient simulation environment. Generating universal networks that more accurately reflect real-world patterns is a cornerstone task. This study proposes a vari-linear…
We study the min-cost seed selection problem in online social networks, where the goal is to select a set of seed nodes with the minimum total cost such that the expected number of influenced nodes in the network exceeds a predefined…
Analyzing relational data consisting of multiple samples or layers involves critical challenges: How many networks are required to capture the variety of structures in the data? And what are the structures of these representative networks?…
Phylogenetic trees are leaf-labelled trees, where the leaves correspond to extant species (taxa), and the internal vertices represent ancestral species. The evolutionary history of a set of species can be explained by more than one…
The effort to understand network systems in increasing detail has resulted in a diversity of methods designed to extract their large-scale structure from data. Unfortunately, many of these methods yield diverging descriptions of the same…