Related papers: Genetic Networks Encode Secrets of Their Past
In this paper, we develop the idea to partition the edges of a weighted graph in order to uncover overlapping communities of its nodes. Our approach is based on the construction of different types of weighted line graphs, i.e. graphs whose…
Many real-world complex networks arise as a result of a competition between growth and rewiring processes. Usually the initial part of the evolution is dominated by growth while the later one rather by rewiring. The initial growth allows…
Graph are a ubiquitous data representation, as they represent a flexible and compact representation. For instance, the 3D structure of RNA can be efficiently represented as $\textit{2.5D graphs}$, graphs whose nodes are nucleotides and…
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.…
Trends change rapidly in today's world, prompting this key question: What is the mechanism behind the emergence of new trends? By representing real-world dynamic systems as complex networks, the emergence of new trends can be symbolized by…
Network embeddings learn to represent nodes as low-dimensional vectors to preserve the proximity between nodes and communities of the network for network analysis. The temporal edges (e.g., relationships, contacts, and emails) in dynamic…
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 $X$…
Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…
Phylogenetic networks are used to represent the evolutionary history of species. Recently, the new class of orchard networks was introduced, which were later shown to be interpretable as trees with additional horizontal arcs. This makes the…
Phylogenetic networks are a type of leaf-labelled, acyclic, directed graph used by biologists to represent the evolutionary history of species whose past includes reticulation events. A phylogenetic network is tree-child if each non-leaf…
Inferring missing links or detecting spurious ones based on observed graphs, known as link prediction, is a long-standing challenge in graph data analysis. With the recent advances in deep learning, graph neural networks have been used for…
In this work, we introduce a novel evaluation framework for generative models of graphs, emphasizing the importance of model-generated graph overlap (Chanpuriya et al., 2021) to ensure both accuracy and edge-diversity. We delineate a…
This work introduces NetDiff, an expressive graph denoising diffusion probabilistic architecture that generates wireless ad hoc network link topologies. Such networks, with directional antennas, can achieve unmatched performance when the…
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…
We demonstrate that graphs embedded on surfaces are a powerful and practical tool to generate, characterize and simulate networks with a broad range of properties. Remarkably, the study of topologically embedded graphs is non-restrictive…
The interplay between topology and dynamics in complex networks is a fundamental but widely unexplored problem. Here, we study this phenomenon on a prototype model in which the network is shaped by a dynamical variable. We couple the…
The problem of inferring unknown graph edges from numerical data at a graph's nodes appears in many forms across machine learning. We study a version of this problem that arises in the field of \emph{landscape genetics}, where genetic…
We develop random graph models where graphs are generated by connecting not only pairs of vertices by edges but also larger subsets of vertices by copies of small atomic subgraphs of arbitrary topology. This allows the for the generation of…
In many networks, vertices have hidden attributes, or types, that are correlated with the networks topology. If the topology is known but these attributes are not, and if learning the attributes is costly, we need a method for choosing…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…