316 research outputs found
Modular analysis of gene expression data with R
Summary: Large sets of data, such as expression profiles from many samples, require analytic tools to reduce their complexity. The Iterative Signature Algorithm (ISA) is a biclustering algorithm. It was designed to decompose a large set of data into so-called ‘modules'. In the context of gene expression data, these modules consist of subsets of genes that exhibit a coherent expression profile only over a subset of microarray experiments. Genes and arrays may be attributed to multiple modules and the level of required coherence can be varied resulting in different ‘resolutions' of the modular mapping. In this short note, we introduce two BioConductor software packages written in GNU R: The isa2 package includes an optimized implementation of the ISA and the eisa package provides a convenient interface to run the ISA, visualize its output and put the biclusters into biological context. Potential users of these packages are all R and BioConductor users dealing with tabular (e.g. gene expression) data. Availability: http://www.unil.ch/cbg/ISA Contact: [email protected]
Ambiguities in recurrence-based complex network representations of time series
Recently, different approaches have been proposed for studying basic
properties of time series from a complex network perspective. In this work, the
corresponding potentials and limitations of networks based on recurrences in
phase space are investigated in some detail. We discuss the main requirements
that permit a feasible system-theoretic interpretation of network topology in
terms of dynamically invariant phase-space properties. Possible artifacts
induced by disregarding these requirements are pointed out and systematically
studied. Finally, a rigorous interpretation of the clustering coefficient and
the betweenness centrality in terms of invariant objects is proposed
Recurrence-based time series analysis by means of complex network methods
Complex networks are an important paradigm of modern complex systems sciences
which allows quantitatively assessing the structural properties of systems
composed of different interacting entities. During the last years, intensive
efforts have been spent on applying network-based concepts also for the
analysis of dynamically relevant higher-order statistical properties of time
series. Notably, many corresponding approaches are closely related with the
concept of recurrence in phase space. In this paper, we review recent
methodological advances in time series analysis based on complex networks, with
a special emphasis on methods founded on recurrence plots. The potentials and
limitations of the individual methods are discussed and illustrated for
paradigmatic examples of dynamical systems as well as for real-world time
series. Complex network measures are shown to provide information about
structural features of dynamical systems that are complementary to those
characterized by other methods of time series analysis and, hence,
substantially enrich the knowledge gathered from other existing (linear as well
as nonlinear) approaches.Comment: To be published in International Journal of Bifurcation and Chaos
(2011
Large-scale structure of time evolving citation networks
In this paper we examine a number of methods for probing and understanding
the large-scale structure of networks that evolve over time. We focus in
particular on citation networks, networks of references between documents such
as papers, patents, or court cases. We describe three different methods of
analysis, one based on an expectation-maximization algorithm, one based on
modularity optimization, and one based on eigenvector centrality. Using the
network of citations between opinions of the United States Supreme Court as an
example, we demonstrate how each of these methods can reveal significant
structural divisions in the network, and how, ultimately, the combination of
all three can help us develop a coherent overall picture of the network's
shape.Comment: 10 pages, 6 figures; journal names for 4 references fixe
IGraph/M: graph theory and network analysis for Mathematica
IGraph/M is an efficient general purpose graph theory and network analysis
package for Mathematica. IGraph/M serves as the Wolfram Language interfaces to
the igraph C library, and also provides several unique pieces of functionality
not yet present in igraph, but made possible by combining its capabilities with
Mathematica's. The package is designed to support both graph theoretical
research as well as the analysis of large-scale empirical networks.Comment: submitted to Journal of Open Source Software on August 30, 202
ExpressionView—an interactive viewer for modules identified in gene expression data
Summary: ExpressionView is an R package that provides an interactive graphical environment to explore transcription modules identified in gene expression data. A sophisticated ordering algorithm is used to present the modules with the expression in a visually appealing layout that provides an intuitive summary of the results. From this overview, the user can select individual modules and access biologically relevant metadata associated with them. Availability: http://www.unil.ch/cbg/ExpressionView. Screenshots, tutorials and sample data sets can be found on the ExpressionView web site. Contact: [email protected]
Geometric and dynamic perspectives on phase-coherent and noncoherent chaos
Statistically distinguishing between phase-coherent and noncoherent chaotic
dynamics from time series is a contemporary problem in nonlinear sciences. In
this work, we propose different measures based on recurrence properties of
recorded trajectories, which characterize the underlying systems from both
geometric and dynamic viewpoints. The potentials of the individual measures for
discriminating phase-coherent and noncoherent chaotic oscillations are
discussed. A detailed numerical analysis is performed for the chaotic R\"ossler
system, which displays both types of chaos as one control parameter is varied,
and the Mackey-Glass system as an example of a time-delay system with
noncoherent chaos. Our results demonstrate that especially geometric measures
from recurrence network analysis are well suited for tracing transitions
between spiral- and screw-type chaos, a common route from phase-coherent to
noncoherent chaos also found in other nonlinear oscillators. A detailed
explanation of the observed behavior in terms of attractor geometry is given.Comment: 12 pages, 13 figure
Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package
We introduce the \texttt{pyunicorn} (Pythonic unified complex network and
recurrence analysis toolbox) open source software package for applying and
combining modern methods of data analysis and modeling from complex network
theory and nonlinear time series analysis. \texttt{pyunicorn} is a fully
object-oriented and easily parallelizable package written in the language
Python. It allows for the construction of functional networks such as climate
networks in climatology or functional brain networks in neuroscience
representing the structure of statistical interrelationships in large data sets
of time series and, subsequently, investigating this structure using advanced
methods of complex network theory such as measures and models for spatial
networks, networks of interacting networks, node-weighted statistics or network
surrogates. Additionally, \texttt{pyunicorn} provides insights into the
nonlinear dynamics of complex systems as recorded in uni- and multivariate time
series from a non-traditional perspective by means of recurrence quantification
analysis (RQA), recurrence networks, visibility graphs and construction of
surrogate time series. The range of possible applications of the library is
outlined, drawing on several examples mainly from the field of climatology.Comment: 28 pages, 17 figure
Worldwide food recall patterns over an eleven month period: A country perspective.
<p>Abstract</p> <p>Background</p> <p>Following the World Health Organization Forum in November 2007, the Beijing Declaration recognized the importance of food safety along with the rights of all individuals to a safe and adequate diet. The aim of this study is to retrospectively analyze the patterns in food alert and recall by countries to identify the principal hazard generators and gatekeepers of food safety in the eleven months leading up to the Declaration.</p> <p>Methods</p> <p>The food recall data set was collected by the Laboratory of the Government Chemist (LGC, UK) over the period from January to November 2007. Statistics were computed with the focus reporting patterns by the 117 countries. The complexity of the recorded interrelations was depicted as a network constructed from structural properties contained in the data. The analysed network properties included degrees, weighted degrees, modularity and <it>k</it>-core decomposition. Network analyses of the reports, based on 'country making report' (<it>detector</it>) and 'country reported on' (<it>transgressor</it>), revealed that the network is organized around a dominant core.</p> <p>Results</p> <p>Ten countries were reported for sixty per cent of all faulty products marketed, with the top 5 countries having received between 100 to 281 reports. Further analysis of the dominant core revealed that out of the top five transgressors three made no reports (in the order China > Turkey > Iran). The top ten detectors account for three quarters of reports with three > 300 (Italy: 406, Germany: 340, United Kingdom: 322).</p> <p>Conclusion</p> <p>Of the 117 countries studied, the vast majority of food reports are made by 10 countries, with EU countries predominating. The majority of the faulty foodstuffs originate in ten countries with four major producers making no reports. This pattern is very distant from that proposed by the Beijing Declaration which urges all countries to take responsibility for the provision of safe and adequate diets for their nationals.</p
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