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Analysis of Modular Organisation of Interaction Networks Based on Asymptotic Dynamics [chapter]

Franck Delaplace, Hanna Klaudel, Tarek Melliti, Sylvain Sené
2012 Lecture Notes in Computer Science  
We develop a discrete theoretical framework based on the analysis of the asymptotic dynamics of biological interaction networks.  ...  More precisely, we exhibit formal conditions under which agents of interaction networks can be grouped into modules, forming a modular organisation.  ...  Conclusion We developed a formal framework for the analysis of the modularity in interaction networks assuming asymptotic dynamics of modules and enabling their composition.  ... 
doi:10.1007/978-3-642-33636-2_10 fatcat:3b3cdxkizvd4naeoanxk4w53o4

Modular organisation of interaction networks based on asymptotic dynamics [article]

Franck Delaplace, Hanna Klaudel, Tarek Melliti, Sylvain Sené
2012 arXiv   pre-print
We develop a theoretical framework based on the analysis of their asymptotic dynamics.  ...  This paper investigates questions related to the modularity in discrete models of biological interaction networks.  ...  Conclusion We developed a formal framework for the analysis of the modularity in interaction networks assuming asymptotic dynamics of modules and enabling their composition.  ... 
arXiv:1111.2313v3 fatcat:rxkxvw2dcbhvrhwrcopsku7zpu

Indetermination of networks structure from the dynamics perspective [article]

Malbor Asllani, Bruno Requiao da Cunha, Ernesto Estrada, James P. Gleeson
2019 arXiv   pre-print
Networks are universally considered as complex structures of interactions of large multi-component systems.  ...  For illustration purposes, we show that for networks with different time-scale structures such as strong modularity, the existence of fast global dynamics can imply that precise inference of the community  ...  We show that the inference of networks' structural properties depends heavily on the competition between the node-based dynamics on one hand and the interactions between the nodes on the other.  ... 
arXiv:1908.06339v1 fatcat:wkumkqtasbatdphv4m575hfa4u

Dynamics impose limits to detectability of network structure

Malbor Asllani, Bruno Requiao da Cunha, Ernesto Estrada, James P Gleeson
2020 New Journal of Physics  
Networks are universally considered as complex structures of interactions of large multi-component systems.  ...  For illustration purposes, we show that for networks with different time-scale structures such as strong modularity, the existence of fast global dynamics can imply that precise inference of the community  ...  Competition between the node based dynamics and the network based one We now turn our attention to the competition between the spatial interactions and the internal dynamics of the nodes by tuning the  ... 
doi:10.1088/1367-2630/ab8ef9 fatcat:pgu44aed4jdqbmtzs4spkigbtm

Assessing the robustness of networks of spatial genetic variation

Eva M. Albert, Miguel A. Fortuna, José A. Godoy, Jordi Bascompte, Ferenc Jordan
2013 Ecology Letters  
Here, we extend recent work on the analysis of networks of spatial genetic variation to address the robustness of these networks in the face of perturbations.  ...  Our results show that while the disappearance of some spatial sites barely changes the modular structure of the genetic network, other sites have a much stronger effect.  ...  ACKNOWLEDGEMENTS We thank Jaime Bosch, Marc Antoine Marchand and the staff of the Natural Park of Cazorla, Segura y las Villas for technical support and field assistance.  ... 
doi:10.1111/ele.12061 pmid:23294521 fatcat:tbwuo4trbrb4hcbt5vp4zqibom

The Stability of a Graph Partition: A Dynamics-Based Framework for Community Detection [chapter]

Jean-Charles Delvenne, Michael T. Schaub, Sophia N. Yaliraki, Mauricio Barahona
2013 Modeling and Simulation in Science, Engineering and Technology  
Our dynamics-based approach thus serves as a unifying framework to gain a deeper understanding of different aspects and problems associated with community detection and allows us to propose new dynamically-inspired  ...  However, modular or community structure in networks has notoriously evaded rigorous definition.  ...  D. acknowledges support from the grant "Actions de recherche concertées-Large Graphs and Networks" of the Communauté Française de Belgique, the EULER project (  ... 
doi:10.1007/978-1-4614-6729-8_11 fatcat:iu6btcknozcrrhnt2yobv5dacm

Emergence and evolution of social networks through exploration of the Adjacent Possible space

Enrico Ubaldi, Raffaella Burioni, Vittorio Loreto, Francesca Tria
2021 Communications Physics  
We leverage on a recent mathematical formalisation of the Adjacent Possible space to propose a microscopic model accounting for the growth and dynamics of social networks.  ...  How people establish new connections and allocate their social interactions among them can reveal a lot of our social organisation.  ...  and analyse the output is on https://github.com/ubi15/pyUrns.  ... 
doi:10.1038/s42005-021-00527-1 fatcat:uxjk6qausjca5aidjmopo7i7qa

Temporal stability of network partitions

Giovanni Petri, Paul Expert
2014 Physical Review E  
This method is based on random walkers coevolving with the network and as such constitutes a generalization of partition stability to the case of temporal networks.  ...  a network mesoscopic structures.  ...  structure of the network, the other on dynamics.  ... 
doi:10.1103/physreve.90.022813 pmid:25215787 fatcat:njnhye33tbhk5laf4ksshhsvfa

Emergence of Structural Patterns in Neutral Trophic Networks

Elsa Canard, Nicolas Mouquet, Lucile Marescot, Kevin J. Gaston, Dominique Gravel, David Mouillot, Timothy Ravasi
2012 PLoS ONE  
High nestedness and low modularity values observed in neutral networks fall in the range of those from empirical antagonist bipartite networks.  ...  However, the study of interaction networks still lacks a comprehensive neutral theory.  ...  Leibold for helpful discussion. and an anonymous reviewer for helpful comments on previous versions of this manuscript. Author Contributions  ... 
doi:10.1371/journal.pone.0038295 pmid:22899987 pmcid:PMC3416803 fatcat:rf6wooody5bhtnsoptat5mizle

Emergence of spontaneous assembly activity in developing neural networks without afferent input

Marcus A. Triplett, Lilach Avitan, Geoffrey J. Goodhill, Francesco P. Battaglia
2018 PLoS Computational Biology  
Here we show that a recurrent network of binary threshold neurons with initially random weights can form neural assemblies based on a simple Hebbian learning rule.  ...  Effects of modularity on the structure of spontaneous activity. (A) Stochastic binary neuron model. Each neuron computes a weighted sum of network activity in the previous timestep.  ...  Structural analysis of network development We then performed a more complete analysis of the structural properties of the network during its development.  ... 
doi:10.1371/journal.pcbi.1006421 fatcat:56w7h75w45gonpzj3qy34iyo4y

Systems-level insights into cellular regulation: inferring, analysing, and modelling intracellular networks

C. Christensen, R. Albert, J. Thakar
2007 IET Systems Biology  
analysis of these networks, and the extension of static networks into various dynamic models capable of providing a new layer of insight into the functioning of cellular systems is discussed.  ...  Genes and gene products interact on several levels, forming transcriptional regulatory-, protein interaction-, metabolic-and signal transduction networks.  ...  A dynamical model of an interacting system is based on the premise of locality in the network space and consists of a set of equations indicating how the state of each node changes in response to changes  ... 
doi:10.1049/iet-syb:20060071 pmid:17441550 fatcat:ttoq55gpxzaszbmjvctrtcitqe

Dynamics of Cluster Synchronisation in Modular Networks: Implications for Structural and Functional Networks [chapter]

Jake Stroud, Mauricio Barahona, Tiago Pereira
2015 Understanding Complex Systems  
From the dynamics of the nodes one then constructs a network of functional relations, termed the functional network.  ...  A fundamental question in the analysis of complex systems concerns the relation between functional and structural networks.  ...  Our model is based on the following assumptions: • The network has a modular structure such that nodes in one module have few connections to nodes outside the module. • Within modules, nodes have a high  ... 
doi:10.1007/978-3-319-17037-4_4 fatcat:y53thwymnndy7k6v4dvkdmajre

A recursive network approach can identify constitutive regulatory circuits in gene expression data

Monica Francesca Blasi, Ida Casorelli, Alfredo Colosimo, Francesco Simone Blasi, Margherita Bignami, Alessandro Giuliani
2005 Physica A: Statistical Mechanics and its Applications  
Giuliani). the constitutive regulatory networks involved in the generic organisation of the cell display a high degree of clustering depending on a modular architecture. r  ...  The activity of the cell is often coordinated by the organisation of proteins into regulatory circuits that share a common function.  ...  Italo Capuzzo Dolcetta, Mathematics Department, University of Roma ''La Sapienza''.  ... 
doi:10.1016/j.physa.2004.09.005 fatcat:ahyvppnqxzgz3h3jltwqiht7om

Real and virtual relationships in tourism digital ecosystems

Rodolfo Baggio, Giacomo Del Chiappa
2013 Information Technology & Tourism  
Figure 1 Cumulative degree distributions for the physical and the virtual components of the Elba and Livigno networks (color online)  ...  The present study argues that two components can be considered when assessing the relationships among stakeholders within a tourism destination: a real and a virtual one.  ...  The first part of the analysis was conducted in order to assess the self-organisation characteristics of the networks.  ... 
doi:10.1007/s40558-013-0001-5 fatcat:dldfhcr5nzfz7m4hnqzp5atxcu

A synthesis of animal-mediated seed dispersal of palms reveals distinct biogeographical differences in species interactions

Gabriel Muñoz, Kristian Trøjelsgaard, W. Daniel Kissling
2019 Journal of Biogeography  
H ij is a null model matrix that describes the probability of occurrence of an interaction between i and j based on the degree distributions of A ij .  ...  potential publication selection biases based on author name, journal, or year of study).  ... 
doi:10.1111/jbi.13493 fatcat:lul5b5ppkrga3cguuifheeu3gy
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