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Since proteins carry out biological processes by interacting with other proteins, analyzing the structure of protein-protein interaction (PPI) networks could explain complex biological mechanisms, evolution, and disease. Similarly, studying…
Structure inference is an important task for network data processing and analysis in data science. In recent years, quite a few approaches have been developed to learn the graph structure underlying a set of observations captured in a data…
The behavior of many complex systems is determined by a core of densely interconnected units. While many methods are available to identify the core of a network when connections between nodes are all of the same type, a principled approach…
Proteins interact with other proteins within biological pathways, forming connected subgraphs in the protein-protein interactome (PPI). Proteins are often involved in multiple biological pathways which complicates interpretation of…
Antifragility is a property from which systems are able to resist stress and furthermore benefit from it. Even though antifragile dynamics is found in various real-world complex systems where multiple subsystems interact with each other,…
Multiplex networks are a type of multilayer network in which entities are connected to each other via multiple types of connections. We propose a method, based on computing pairwise similarities between layers and then doing community…
Many systems are naturally represented by a multilayer network in which edges exist in multiple layers that encode different, but potentially related, types of interactions, and it is important to understand limitations on the detectability…
We study properties of multi-layered, interconnected networks from an ensemble perspective, i.e. we analyze ensembles of multi-layer networks that share similar aggregate characteristics. Using a diffusive process that evolves on a…
The interactions between particles in particulate systems are organized in `force networks', mesoscale features that bridge between the particle scale and the scale of the system as a whole. While such networks are known to be crucial in…
Some networked systems can be better modelled by multilayer structure where the individual nodes develop relationships in multiple layers. Multilayer networks with similar nodes across layers are also known as multiplex networks. This…
The analysis and interpretation of relationships between biological molecules is done with the help of networks. Networks are used ubiquitously throughout biology to represent the relationships between genes and gene products. Network…
Network theorists have developed methods to characterize the complex interactions in natural phenomena. The structure of the network of interactions between proteins is important in the field of proteomics, and has been subject to intensive…
In this perspective article, we present a multidisciplinary approach for characterizing protein structure networks. We first place our approach in its historical context and describe the manner in which it synthesizes concepts from quantum…
Analytical approaches to model the structure of complex networks can be distinguished into two groups according to whether they consider an intensive (e.g., fixed degree sequence and random otherwise) or an extensive (e.g., adjacency…
Many real-world networks represent dynamic systems with interactions that change over time, often in uncoordinated ways and at irregular intervals. For example, university students connect in intermittent groups that repeatedly form and…
In a multiplex network, a set of nodes is connected by different types of interactions, each represented as a separate layer within the network. Multiplexes have emerged as a key instrument for modeling large-scale complex systems, due to…
Network theory provides various tools for investigating the structural or functional topology of many complex systems found in nature, technology and society. Nevertheless, it has recently been realised that a considerable number of systems…
Many natural, engineered, and social systems can be represented using the framework of a layered network, where each layer captures a different type of interaction between the same set of nodes. The study of such multiplex networks is a…
Many complex systems in nature and society can be described in terms of networks capturing the intricate web of connections among the units they are made of. A key question is how to interpret the global organization of such networks as the…
Many network systems are composed of interdependent but distinct types of interactions, which cannot be fully understood in isolation. These different types of interactions are often represented as layers, attributes on the edges or as a…