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Internal links and pairs as a new tool for the analysis of bipartite complex networks [article]

Oussama Allali, Lionel Tabourier, Clémence Magnien, Matthieu Latapy
2011 arXiv   pre-print
We introduce here internal links and pairs as a new notion useful for such analysis: it gives insights on the information lost by projecting the bipartite graph.  ...  Many real-world complex networks are best modeled as bipartite (or 2-mode) graphs, where nodes are divided into two sets with links connecting one side to the other.  ...  Acknowledgements This work is supported in part by the French ANR MAPE project.  ... 
arXiv:1104.4418v2 fatcat:rgtdtsgsszc7xcmjtelemjihae

Internal links and pairs as a new tool for the analysis of bipartite complex networks

Oussama Allali, Lionel Tabourier, Clémence Magnien, Matthieu Latapy
2012 Social Network Analysis and Mining  
We introduce here internal links and pairs as a new notion useful for a bipartite analysis, and which gives insights on the information lost by projecting the bipartite graph.  ...  Many real-world complex networks are best modeled as bipartite (or 2-mode) graphs, where nodes are divided into two sets with links connecting one side to the other.  ...  Acknowledgements This work is supported in part by the French ANR MAPE project.  ... 
doi:10.1007/s13278-012-0053-0 fatcat:ppolhphax5berobkw5h2srzmmi

The Study About the Analysis of Responsiveness Pair Clustering Tosocial Network Bipartite Graph

Akira Otsuki, Masayoshi Kawamura
2013 Advanced Computing An International Journal  
Then, the "The regional information" and "The information of purchase history (Where and what bought information)" are captured as bipartite graph, and Responsiveness Pair Clustering analysis (a clustering  ...  In this study, since it was found to be difficult to analyze a network such as bipartite graph having limitations in links by using modularity Q, responsiveness is used instead of modularity Q as similarity  ...  As a result, there are three nodes and two links in the network.  ... 
doi:10.5121/acij.2013.4601 fatcat:546lhsjz6jeqxllfgz2gcfxadm

Bipartite Graph Analysis as an Alternative to Reveal Clusterization in Complex Systems

Vasyl Palchykov, Yurij Holovatch
2018 2018 IEEE Second International Conference on Data Stream Mining & Processing (DSMP)  
As a case study we consider scientific knowledge, which is represented as a complex bipartite network of articles and related concepts.  ...  We demonstrate how analysis of co-clustering in bipartite networks may be used as a bridge to connect, compare and complement clustering results about community structure in two different spaces: single-mode  ...  A pair of numbers in a bipartite network gives the number of concepts and the number of articles in each cluster of a bipartite network.  ... 
doi:10.1109/dsmp.2018.8478505 fatcat:foguoixjlfconhjwuusj2yvowe

NETZCOPE: A TOOL FOR DISPLAYING AND ANALYZING COMPLEX NETWORKS [chapter]

MICHAEL J. BARBER, LUDWIG STREIT, OLEG STROGAN
2011 Quantum Bio-Informatics IV  
We present NetzCope, a software application for the display and analysis of networks.  ...  Networks are a natural and popular mechanism for the representation and investigation of a broad class of systems. But extracting information from a network can present significant challenges.  ...  In this work, we present NetzCope, a software application for the display and analysis of complex networks.  ... 
doi:10.1142/9789814343763_0034 fatcat:kyymavomzffd5ips6ssl5x2qt4

Modularity in Protein Complex and Drug Interactions Reveals New Polypharmacological Properties

Jose C. Nacher, Jean-Marc Schwartz, John Parkinson
2012 PLoS ONE  
Network medicine has emerged as a new paradigm to deal with complex diseases. Connections between protein complexes and key diseases have been suggested for decades.  ...  The network structure is characterized by a high modularity, both in the bipartite graph and in its projections, indicating that its topology is highly distinct from a random network and that it contains  ...  Acknowledgments The authors thank Dr. R. Guimerà for fruitful discussions. Author Contributions  ... 
doi:10.1371/journal.pone.0030028 pmid:22279562 pmcid:PMC3261189 fatcat:ei4n7zfkizda3fpxaxjd7lwm5e

NeMo: Network Module identification in Cytoscape

Corban G Rivera, Rachit Vakil, Joel S Bader
2010 BMC Bioinformatics  
As the size of the known human interactome grows, biologists increasingly rely on computational tools to identify patterns that represent protein complexes and pathways.  ...  In this work, we present a novel method to identify densely connected and bipartite network modules based on a log odds score for shared neighbours.  ...  Acknowledgements The authors would like to thank Gary Bader for the MCODE source code and helpful comments on the manuscript.  ... 
doi:10.1186/1471-2105-11-s1-s61 pmid:20122237 pmcid:PMC3009535 fatcat:d3kwtelrqvakleduhugfapkgq4

A network perspective on the virus world

Jaime Iranzo, Mart Krupovic, Eugene V. Koonin
2017 Communicative & Integrative Biology  
As new tools for network analysis are developed, we expect that novel insights into virus evolution will result from the study of more complex representations of the virus world.  ...  Here we discuss 3 network representations of the virus world with decreasing levels of complexity, from a multilayer network that integrates sequence conservation and patterns of gene sharing to a classic  ...  As new tools for analysis of bipartite networks are developed, it soon will become possible to extend the network analyses to the entire virosphere and compare the findings from this approach with the  ... 
doi:10.1080/19420889.2017.1296614 pmid:28451057 pmcid:PMC5398231 fatcat:3vdnqswglzhbhkusxeotoe7rwe

Applying graph-based data mining concepts to the educational sphere

András London, Áron Pelyhe, Csaba Holló, Tamás Németh
2015 Proceedings of the 16th International Conference on Computer Systems and Technologies - CompSysTech '15  
Since a huge amount of data (which is detailed as well) is produced by the complex administration systems of educational institutes, instead of the classical statistical methods, new types of data processing  ...  In this study, we discuss the possible application of the ubiquitous complex network approach for information extraction from educational data.  ...  This work is supported by the European Union and cofunded by the European Social Fund. Project title: The denouement of talent in favour of the excellence of the University of Szeged.  ... 
doi:10.1145/2812428.2812436 dblp:conf/compsystech/LondonPHN15 fatcat:yagrbxqndbddxl4qtx6ty72d7y

The Methodology Behind Network Thinking: Graphs to Analyze Microbial Complexity and Evolution [chapter]

Andrew K. Watson, Romain Lannes, Jananan S. Pathmanathan, Raphaël Méheust, Slim Karkar, Philippe Colson, Eduardo Corel, Philippe Lopez, Eric Bapteste
2019 Msphere  
In recent years, development of new methods for the construction and analysis of networks has helped to broaden the availability of these approaches from programmers to a diversity of users.  ...  networks and bipartite graphs, and a guide for their construction and analyses.  ...  Visualization of networks can be performed with programs such as Cytoscape [54] or Gephi [55] , both of which also have a range of internal tools and external plugins for network analysis.  ... 
doi:10.1007/978-1-4939-9074-0_9 pmid:31278668 fatcat:xcwsltl35bfk7enmoobtt5asr4

Colombian export capabilities: building the firms-products network [article]

Matteo Bruno, Fabio Saracco, Tiziano Squartini, Marco Dueñas
2018 Entropy   accepted
Interestingly, this finding is refined by applying a recently-proposed algorithm for projecting bipartite networks on the layer of interest and, then, running the Louvain algorithm on the resulting monopartite  ...  In this paper we analyse the bipartite Colombian firms-products network, throughout a period of five years, from 2010 to 2014.  ...  More precisely, we analyze the bipartite network of Colombian exports using data at the firm level for the period 2010-2014 by employing tools developed within the field of information theory and complex  ... 
doi:10.3390/e20100785 pmid:33265873 pmcid:PMC7512347 arXiv:1809.03222v2 fatcat:w2b4kglbnfhn7mzwuzwve4irzu

Embedding technique and network analysis of scientific innovations emergence in an arXiv-based concept network [article]

Serhii Brodiuk, Vasyl Palchykov, Yurij Holovatch
2020 arXiv   pre-print
Combining approaches developed in complex networks science and graph embedding, we discuss the predictability of edges (links) on the scientific knowledge landscape where the innovations may appear.  ...  Novelty is an inherent part of innovations and discoveries. Such processes may be considered as an appearance of new ideas or as an emergence of atypical connections between the existing ones.  ...  A part of this work has been performed in the frames of the Master thesis by S.B. in Ukrainian Catholic University (Lviv, Ukraine).  ... 
arXiv:2003.10289v1 fatcat:hibdyv3h5fcjbnmdql52spdqt4

Complex networks analysis in socioeconomic models [article]

Luis M. Varela, Giulia Rotundo, Marcel Ausloos, Jesus Carrete
2014 arXiv   pre-print
This chapter aims at reviewing complex networks models and methods that were either developed for or applied to socioeconomic issues, and pertinent to the theme of New Economic Geography.  ...  As the most frequently used model for interacting agent-based systems, a brief description of the statistical mechanics of the classical Ising model on regular lattices, together with recent extensions  ...  Acknowledgment: This work has been performed in the framework of COST Action IS1104 "The EU in the new economic complex geography: models, tools and policy evaluation".  ... 
arXiv:1403.6767v2 fatcat:hv6223ai7vf5tpnekb52ku2ypa

Network-Based Approaches to Explore Complex Biological Systems towards Network Medicine

Giulia Fiscon, Federica Conte, Lorenzo Farina, Paola Paci
2018 Genes  
The framework of regulatory networks provides a powerful tool to gather new insights into ceRNA regulatory mechanisms.  ...  a systematic analysis of the human PPI network to uncover new disease-associated genes by exploiting the connectivity significance instead of connection density.  ...  The representation of complex systems as networks is of paramount importance for visualizing the interactome underlying structure, revealing new functional roles, and proposing new and fresh interpretations  ... 
doi:10.3390/genes9090437 pmid:30200360 pmcid:PMC6162385 fatcat:hkrmpxhfizbbjcdtdhxdrhfzd4

AN INTEGRATED NETWORK APPROACH TO IDENTIFYING BIOLOGICAL PATHWAYS AND ENVIRONMENTAL EXPOSURE INTERACTIONS IN COMPLEX DISEASES

CHRISTIAN DARABOS, JINGYA QIU, JASON H. MOORE
2015 Biocomputing 2016  
The integrated network approach is a novel method for detecting the biological effects of environmental exposures.  ...  To better capture the intricacies of the interactions between environmental exposure and the biological pathways in complex disorders, we integrate both aspects into a single "tripartite" network.  ...  Acknowledgments This work was supported by the National Institute of Health (NIH) grants R01 EY022300, LM009012, LM010098, AI59694. Pacific Symposium on Biocomputing 2016  ... 
doi:10.1142/9789814749411_0002 fatcat:abuecin2ynarjiea3t4bzk6fja
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