2,646 research outputs found
Multilayer Networks
In most natural and engineered systems, a set of entities interact with each
other in complicated patterns that can encompass multiple types of
relationships, change in time, and include other types of complications. Such
systems include multiple subsystems and layers of connectivity, and it is
important to take such "multilayer" features into account to try to improve our
understanding of complex systems. Consequently, it is necessary to generalize
"traditional" network theory by developing (and validating) a framework and
associated tools to study multilayer systems in a comprehensive fashion. The
origins of such efforts date back several decades and arose in multiple
disciplines, and now the study of multilayer networks has become one of the
most important directions in network science. In this paper, we discuss the
history of multilayer networks (and related concepts) and review the exploding
body of work on such networks. To unify the disparate terminology in the large
body of recent work, we discuss a general framework for multilayer networks,
construct a dictionary of terminology to relate the numerous existing concepts
to each other, and provide a thorough discussion that compares, contrasts, and
translates between related notions such as multilayer networks, multiplex
networks, interdependent networks, networks of networks, and many others. We
also survey and discuss existing data sets that can be represented as
multilayer networks. We review attempts to generalize single-layer-network
diagnostics to multilayer networks. We also discuss the rapidly expanding
research on multilayer-network models and notions like community structure,
connected components, tensor decompositions, and various types of dynamical
processes on multilayer networks. We conclude with a summary and an outlook.Comment: Working paper; 59 pages, 8 figure
Interdisciplinary and physics challenges of Network Theory
Network theory has unveiled the underlying structure of complex systems such
as the Internet or the biological networks in the cell. It has identified
universal properties of complex networks, and the interplay between their
structure and dynamics. After almost twenty years of the field, new challenges
lie ahead. These challenges concern the multilayer structure of most of the
networks, the formulation of a network geometry and topology, and the
development of a quantum theory of networks. Making progress on these aspects
of network theory can open new venues to address interdisciplinary and physics
challenges including progress on brain dynamics, new insights into quantum
technologies, and quantum gravity.Comment: (7 pages, 4 figures
Mathematical Formulation of Multi-Layer Networks
A network representation is useful for describing the structure of a large
variety of complex systems. However, most real and engineered systems have
multiple subsystems and layers of connectivity, and the data produced by such
systems is very rich. Achieving a deep understanding of such systems
necessitates generalizing "traditional" network theory, and the newfound deluge
of data now makes it possible to test increasingly general frameworks for the
study of networks. In particular, although adjacency matrices are useful to
describe traditional single-layer networks, such a representation is
insufficient for the analysis and description of multiplex and time-dependent
networks. One must therefore develop a more general mathematical framework to
cope with the challenges posed by multi-layer complex systems. In this paper,
we introduce a tensorial framework to study multi-layer networks, and we
discuss the generalization of several important network descriptors and
dynamical processes --including degree centrality, clustering coefficients,
eigenvector centrality, modularity, Von Neumann entropy, and diffusion-- for
this framework. We examine the impact of different choices in constructing
these generalizations, and we illustrate how to obtain known results for the
special cases of single-layer and multiplex networks. Our tensorial approach
will be helpful for tackling pressing problems in multi-layer complex systems,
such as inferring who is influencing whom (and by which media) in multichannel
social networks and developing routing techniques for multimodal transportation
systems.Comment: 15 pages, 5 figure
Flow-Based Network Analysis of the Caenorhabditis elegans Connectome
We exploit flow propagation on the directed neuronal network of the nematode C. elegans to reveal dynamically relevant features of its connectome. We find flow-based groupings of neurons at different levels of granularity, which we relate to functional and anatomical constituents of its nervous system. A systematic in silico evaluation of the full set of single and double neuron ablations is used to identify deletions that induce the most severe disruptions of the multi-resolution flow structure. Such ablations are linked to functionally relevant neurons, and suggest potential candidates for further in vivo investigation. In addition, we use the directional patterns of incoming and outgoing network flows at all scales to identify flow profiles for the neurons in the connectome, without pre-imposing a priori categories. The four flow roles identified are linked to signal propagation motivated by biological input-response scenarios
Rigidity and flexibility of biological networks
The network approach became a widely used tool to understand the behaviour of
complex systems in the last decade. We start from a short description of
structural rigidity theory. A detailed account on the combinatorial rigidity
analysis of protein structures, as well as local flexibility measures of
proteins and their applications in explaining allostery and thermostability is
given. We also briefly discuss the network aspects of cytoskeletal tensegrity.
Finally, we show the importance of the balance between functional flexibility
and rigidity in protein-protein interaction, metabolic, gene regulatory and
neuronal networks. Our summary raises the possibility that the concepts of
flexibility and rigidity can be generalized to all networks.Comment: 21 pages, 4 figures, 1 tabl
The physics of spreading processes in multilayer networks
The study of networks plays a crucial role in investigating the structure,
dynamics, and function of a wide variety of complex systems in myriad
disciplines. Despite the success of traditional network analysis, standard
networks provide a limited representation of complex systems, which often
include different types of relationships (i.e., "multiplexity") among their
constituent components and/or multiple interacting subsystems. Such structural
complexity has a significant effect on both dynamics and function. Throwing
away or aggregating available structural information can generate misleading
results and be a major obstacle towards attempts to understand complex systems.
The recent "multilayer" approach for modeling networked systems explicitly
allows the incorporation of multiplexity and other features of realistic
systems. On one hand, it allows one to couple different structural
relationships by encoding them in a convenient mathematical object. On the
other hand, it also allows one to couple different dynamical processes on top
of such interconnected structures. The resulting framework plays a crucial role
in helping achieve a thorough, accurate understanding of complex systems. The
study of multilayer networks has also revealed new physical phenomena that
remain hidden when using ordinary graphs, the traditional network
representation. Here we survey progress towards attaining a deeper
understanding of spreading processes on multilayer networks, and we highlight
some of the physical phenomena related to spreading processes that emerge from
multilayer structure.Comment: 25 pages, 4 figure
Protein multi-scale organization through graph partitioning and robustness analysis: Application to the myosin-myosin light chain interaction
Despite the recognized importance of the multi-scale spatio-temporal
organization of proteins, most computational tools can only access a limited
spectrum of time and spatial scales, thereby ignoring the effects on protein
behavior of the intricate coupling between the different scales. Starting from
a physico-chemical atomistic network of interactions that encodes the structure
of the protein, we introduce a methodology based on multi-scale graph
partitioning that can uncover partitions and levels of organization of proteins
that span the whole range of scales, revealing biological features occurring at
different levels of organization and tracking their effect across scales.
Additionally, we introduce a measure of robustness to quantify the relevance of
the partitions through the generation of biochemically-motivated surrogate
random graph models. We apply the method to four distinct conformations of
myosin tail interacting protein, a protein from the molecular motor of the
malaria parasite, and study properties that have been experimentally addressed
such as the closing mechanism, the presence of conserved clusters, and the
identification through computational mutational analysis of key residues for
binding.Comment: 13 pages, 7 Postscript figure
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