4,993 research outputs found
Internal links and pairs as a new tool for the analysis of bipartite complex networks
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. However, there is currently a lack of methods to analyze properly
such graphs as most existing measures and methods are suited to classical
graphs. A usual but limited approach consists in deriving 1-mode graphs (called
projections) from the underlying bipartite structure, though it causes
important loss of information and data storage issues. 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. We
illustrate the relevance of theses concepts on several real-world instances
illustrating how it enables to discriminate behaviors among various cases when
we compare them to a benchmark of random networks. Then, we show that we can
draw benefit from this concept for both modeling complex networks and storing
them in a compact format
Network-based approaches to explore complex biological systems towards network medicine
Network medicine relies on different types of networks: from the molecular level of protein–protein interactions to gene regulatory network and correlation studies of gene expression. Among network approaches based on the analysis of the topological properties of protein–protein interaction (PPI) networks, we discuss the widespread DIAMOnD (disease module detection) algorithm. Starting from the assumption that PPI networks can be viewed as maps where diseases can be identified with localized perturbation within a specific neighborhood (i.e., disease modules), DIAMOnD performs a systematic analysis of the human PPI network to uncover new disease-associated genes by exploiting the connectivity significance instead of connection density. The past few years have witnessed the increasing interest in understanding the molecular mechanism of post-transcriptional regulation with a special emphasis on non-coding RNAs since they are emerging as key regulators of many cellular processes in both physiological and pathological states. Recent findings show that coding genes are not the only targets that microRNAs interact with. In fact, there is a pool of different RNAs—including long non-coding RNAs (lncRNAs) —competing with each other to attract microRNAs for interactions, thus acting as competing endogenous RNAs (ceRNAs). The framework of regulatory networks provides a powerful tool to gather new insights into ceRNA regulatory mechanisms. Here, we describe a data-driven model recently developed to explore the lncRNA-associated ceRNA activity in breast invasive carcinoma. On the other hand, a very promising example of the co-expression network is the one implemented by the software SWIM (switch miner), which combines topological properties of correlation networks with gene expression data in order to identify a small pool of genes—called switch genes—critically associated with drastic changes in cell phenotype. Here, we describe SWIM tool along with its applications to cancer research and compare its predictions with DIAMOnD disease genes
NetzCope: A Tool for Displaying and Analyzing Complex 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. We present NetzCope, a software
application for the display and analysis of networks. Its key features include
the visualization of networks in two or three dimensions, the organization of
vertices to reveal structural similarity, and the detection and visualization
of network communities by modularity maximization.Comment: 16 pages, Proceedings of ICQBIC2010; minor improvements to wording in
v
Searching for Communities in Bipartite Networks
Bipartite networks are a useful tool for representing and investigating
interaction networks. We consider methods for identifying communities in
bipartite networks. Intuitive notions of network community groups are made
explicit using Newman's modularity measure. A specialized version of the
modularity, adapted to be appropriate for bipartite networks, is presented; a
corresponding algorithm is described for identifying community groups through
maximizing this measure. The algorithm is applied to networks derived from the
EU Framework Programs on Research and Technological Development. Community
groups identified are compared using information-theoretic methods.Comment: 12 pages, 4 figures, to appear in "Proceedings of the 5th Jagna
International Workshop: Stochastic and Quantum Dynamics of Biomolecular
Systems," C. C. Bernido and M. V. Carpio-Bernido, editors. A version with
full-quality figures and larger file size is available at
http://ccm.uma.pt/publications/Barber-Faria-Streit-Strogan-2008.pd
Identifying Overlapping and Hierarchical Thematic Structures in Networks of Scholarly Papers: A Comparison of Three Approaches
We implemented three recently proposed approaches to the identification of
overlapping and hierarchical substructures in graphs and applied the
corresponding algorithms to a network of 492 information-science papers coupled
via their cited sources. The thematic substructures obtained and overlaps
produced by the three hierarchical cluster algorithms were compared to a
content-based categorisation, which we based on the interpretation of titles
and keywords. We defined sets of papers dealing with three topics located on
different levels of aggregation: h-index, webometrics, and bibliometrics. We
identified these topics with branches in the dendrograms produced by the three
cluster algorithms and compared the overlapping topics they detected with one
another and with the three pre-defined paper sets. We discuss the advantages
and drawbacks of applying the three approaches to paper networks in research
fields.Comment: 18 pages, 9 figure
Non-parametric Bayesian modeling of complex networks
Modeling structure in complex networks using Bayesian non-parametrics makes
it possible to specify flexible model structures and infer the adequate model
complexity from the observed data. This paper provides a gentle introduction to
non-parametric Bayesian modeling of complex networks: Using an infinite mixture
model as running example we go through the steps of deriving the model as an
infinite limit of a finite parametric model, inferring the model parameters by
Markov chain Monte Carlo, and checking the model's fit and predictive
performance. We explain how advanced non-parametric models for complex networks
can be derived and point out relevant literature
- …