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Despite their widespread utility across domains, basic network models face fundamental limitations when applied to complex biological systems, particularly in neuroscience. This paper critically examines these limitations and explores…

Other Quantitative Biology · Quantitative Biology 2024-11-07 Luiz Pessoa

A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes,…

Molecular Networks · Quantitative Biology 2007-09-12 Reka Albert

Understanding the structural complexity and predictability of complex networks is a central challenge in network science. Although recent studies have revealed a relationship between compression-based entropy and link prediction…

Social and Information Networks · Computer Science 2025-10-14 Sebastián Brzovic , Cristóbal Rojas , Andrés Abeliuk

We study the evolution of the network properties of a populated network embedded in a genotype space characterised by either a low or a high number of potential links, with particular emphasis on the connectivity and clustering. Evolution…

Statistical Mechanics · Physics 2007-05-23 Paul Anderson , Henrik Jeldtoft Jensen

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…

Physics and Society · Physics 2017-02-13 Olexandr Polishchuk

A typical complex system should be described by a supernetwork or a network of networks, in which the networks are coupled to some other networks. As the first step to understanding the complex systems on such more systematic level,…

Physics and Society · Physics 2015-05-20 Xiu-Lian Xu , Yan-Qin Qu , Shan Guan , Yu-Mei Jiang , Da-Ren He

Cooperation is observed widely in nature and is thought an essential component of many evolutionary processes, yet the mechanisms by which it arises and persists are still unclear. Among several theories, network reciprocity -- a model of…

Computer Science and Game Theory · Computer Science 2016-05-10 Steve Miller , Joshua Knowles

A complexity-theoretic approach to studying biological networks is proposed. A simple graph representation is used where molecules (DNA, RNA, proteins and chemicals) are vertices and relations between them are directed and signed…

Social and Information Networks · Computer Science 2018-04-25 Ali Atiia , François Major , Jérôme Waldispühl

The concept of multilayer networks has become recently integrated into complex systems modeling since it encapsulates a very general concept of complex relationships. Biological pathways are an example of complex real-world networks, where…

Human-Computer Interaction · Computer Science 2021-10-12 Hsiang-Yun Wu , Martin Nöllenburg , Ivan Viola

Systems of dynamical interactions between competing species can be used to model many complex systems, and can be mathematically described by {\em random} networks. Understanding how patterns of activity arise in such systems is important…

Adaptation and Self-Organizing Systems · Physics 2016-01-21 Nick McCullen , Thomas Wagenknecht

Mechanisms of pattern formation---of which the Turing instability is an archetype---constitute an important class of dynamical processes occurring in biological, ecological and chemical systems. Recently, it has been shown that the Turing…

Disordered Systems and Neural Networks · Physics 2019-06-19 Sayat Mimar , Mariamo Mussa Juane , Juyong Park , Alberto P. Munuzuri , Gourab Ghoshal

We constructs a new network by superposition of hexahedron , which are scale-free, highly sparse,disassortative ,and maximal planar graphs. The network degree distribution, agglomeration coefficient and degree of correlation are computed…

Physics and Society · Physics 2021-04-12 Li Haijun , Lu Qingping

Many real-world complex systems such as social, biological, information as well as technological systems results of a decentralized and unplanned evolution which leads to a common structuration. Irrespective of their origin, these so-called…

Social and Information Networks · Computer Science 2013-05-03 Chantal Cherifi , Jean-François Santucci

It is now generally assumed that the heterogeneity of most networks in nature probably arises via preferential attachment of some sort. However, the origin of various other topological features, such as degree-degree correlations and…

Adaptation and Self-Organizing Systems · Physics 2010-03-05 Samuel Johnson , J. Marro , Joaquin J. Torres

A central issue in the study of large complex network systems, such as power grids, financial networks, and ecological systems, is to understand their response to dynamical perturbations. Recent studies recognize that many real networks…

Adaptation and Self-Organizing Systems · Physics 2022-07-26 Chao Duan , Takashi Nishikawa , Deniz Eroglu , Adilson E. Motter

Hierarchical tree structures are common in many real-world systems, from tree roots and branches to neuronal dendrites and biologically inspired artificial neural networks, as well as in technological networks for organizing and searching…

Statistical Mechanics · Physics 2025-02-04 Davide Cipollini , Lambert Schomaker

The network density matrix formalism allows for describing the dynamics of information on top of complex structures and it has been successfully used to analyze from system's robustness to perturbations to coarse graining multilayer…

Physics and Society · Physics 2023-05-03 Arsham Ghavasieh , Manlio De Domenico

Turing's theory of pattern formation is a universal model for self-organization, applicable to many systems in physics, chemistry and biology. Essential properties of a Turing system, such as the conditions for the existence of patterns and…

Adaptation and Self-Organizing Systems · Physics 2018-08-02 Xavier Diego , Luciano Marcon , Patrick Müller , James Sharpe

We review the main tools which allow for the statistical characterization of weighted networks. We then present two case studies, the airline connection network and the scientific collaboration network, which are representative of critical…

Statistical Mechanics · Physics 2009-11-10 Marc Barthelemy , Alain Barrat , Romualdo Pastor-Satorras , Alessandro Vespignani

Each complex network (or class of networks) presents specific topological features which characterize its connectivity and highly influence the dynamics of processes executed on the network. The analysis, discrimination, and synthesis of…

Disordered Systems and Neural Networks · Physics 2009-09-29 Luciano da F. Costa , Francisco A. Rodrigues , Gonzalo Travieso , P. R. Villas Boas