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Diverse biological networks exhibit universal features distinguished from those of random networks, calling much attention to their origins and implications. Here we propose a minimal evolution model of Boolean regulatory networks, which…

Molecular Networks · Quantitative Biology 2014-11-26 Deok-Sun Lee

Traditional network generation models attempt to replicate global structural properties (degree distribution, average distance, clustering coefficient, communities, etc.) through synthetic link formation mechanisms such as triadic closure…

Social and Information Networks · Computer Science 2013-10-14 Erick Stattner , Martine Collard

One of interesting phenomena due to topological heterogeneities in complex networks is the friendship paradox: Your friends have on average more friends than you do. Recently, this paradox has been generalized for arbitrary node attributes,…

Physics and Society · Physics 2014-08-26 Hang-Hyun Jo , Young-Ho Eom

We study the temporal co-variation of network co-evolution via the cross-link structure of networks, for which we take advantage of the formalism of hypergraphs to map cross-link structures back to network nodes. We investigate two sets of…

Disordered Systems and Neural Networks · Physics 2015-06-16 Danielle S. Bassett , Nicholas F. Wymbs , Mason A. Porter , Peter J. Mucha , Scott T. Grafton

This paper investigates how the compositional structure of neural networks shapes their optimization landscape and training dynamics. We analyze the gradient flow associated with overparameterized optimization problems, which can be…

Machine Learning · Computer Science 2025-11-14 Arthur Castello Branco de Oliveira , Dhruv Jatkar , Eduardo Sontag

Many important real-world networks manifest "small-world" properties such as scale-free degree distributions, small diameters, and clustering. The most common model of growth for these networks is "preferential attachment", where nodes…

Quantitative Methods · Quantitative Biology 2009-11-13 Samarth Swarup , Les Gasser

Although the origin of the fat-tail characteristic of the degree distribution in complex networks has been extensively researched, the underlying cause of the degree distribution characteristic across the complete range of degrees remains…

Physics and Society · Physics 2023-11-07 Bin Zhou , Petter Holme , Zaiwu Gong , Choujun Zhan , Yao Huang , Xin Lu , Xiangyi Meng

Constructing systems that exhibit time-scales much longer than those of the underlying components, as well as emergent dynamical and collective behavior, is a key goal in fields such as synthetic biology and materials self-assembly.…

Statistical Mechanics · Physics 2021-07-22 Evelyn Tang , Jaime Agudo-Canalejo , Ramin Golestanian

Animal behaviors are sometimes decomposable into discrete, stereotyped elements. In one model, such behaviors are triggered by specific commands; in the extreme case, the discreteness of behavior is traced to the discreteness of action…

Neurons and Cognition · Quantitative Biology 2009-12-31 Greg J. Stephens , William S. Ryu , William Bialek

We study collaboration networks in terms of evolving, self-organizing bipartite graph models. We propose a model of a growing network, which combines preferential edge attachment with the bipartite structure, generic for collaboration…

Statistical Mechanics · Physics 2009-11-10 Jose J. Ramasco , S. N. Dorogovtsev , Romualdo Pastor-Satorras

Large-scale white matter pathways crisscrossing the cortex create a complex pattern of connectivity that underlies human cognitive function. Generative mechanisms for this architecture have been difficult to identify in part because little…

Neurons and Cognition · Quantitative Biology 2015-06-16 Florian Klimm , Danielle S. Bassett , Jean M. Carlson , Peter J. Mucha

We present analytical results for the emerging structure of networks that evolve via a combination of growth (by node addition and random attachment) and contraction (by random node deletion). To this end we consider a network model in…

Statistical Mechanics · Physics 2022-10-25 Barak Budnick , Ofer Biham , Eytan Katzav

The first part of this paper studies the evolution of gradient flow for homogeneous neural networks near a class of saddle points exhibiting a sparsity structure. The choice of these saddle points is motivated from previous works on…

Machine Learning · Computer Science 2025-09-16 Akshay Kumar , Jarvis Haupt

This paper proposes a novel topological learning framework that integrates networks of different sizes and topology through persistent homology. Such challenging task is made possible through the introduction of a computationally efficient…

Neurons and Cognition · Quantitative Biology 2023-01-30 Tananun Songdechakraiwut , Moo K. Chung

We study the evolution of a random weighted network with complex nonlinear dynamics at each node, whose activity may cease as a result of interactions with other nodes. Starting from a knowledge of the micro-level behaviour at each node, we…

Statistical Mechanics · Physics 2007-05-23 Sitabhra Sinha , Sudeshna Sinha

We present a new model of the evolutionary dynamics and the growth of on-line social networks. The model emulates people's strategies for acquiring information in social networks, emphasising the local subjective view of an individual and…

Social and Information Networks · Computer Science 2013-10-01 Emanuele Massaro , Henrik Olsson , Andrea Guazzini , Franco Bagnoli

Network theory provides novel concepts that promise an improved characterization of interacting dynamical systems. Within this framework, evolving networks can be considered as being composed of nodes, representing systems, and of…

Neurons and Cognition · Quantitative Biology 2014-08-26 Klaus Lehnertz , Gerrit Ansmann , Stephan Bialonski , Henning Dickten , Christian Geier , Stephan Porz

Preferential attachment is often suggested to be the underlying mechanism of the growth of a network, largely due to that many real networks are, to a certain extent, scale-free. However, such attribution is usually made under debatable…

Applications · Statistics 2025-09-16 Clement Lee

Neural systems show a modular and typically also a hierarchical organisation across different levels and across different species. Topology relates to function, but it is also influences dynamics as earlier studies showed its effect on…

Neurons and Cognition · Quantitative Biology 2014-05-15 Marcus Kaiser

We present and discuss the results of an experimental analysis in the design of Boolean networks by means of genetic algorithms. A population of networks is evolved with the aim of finding a network such that the attractor it reaches is of…

Neural and Evolutionary Computing · Computer Science 2011-02-01 Andrea Roli , Cristian Arcaroli , Marco Lazzarini , Stefano Benedettini