92 research outputs found
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
An evolving network model with community structure
Many social and biological networks consist of communities—groups of nodes within which connections are dense, but between which connections are sparser. Recently, there has been considerable interest in designing algorithms for detecting community structures in real-world complex networks. In this paper, we propose an evolving network model which exhibits community structure. The network model is based on the inner-community preferential attachment and inter-community preferential attachment mechanisms. The degree distributions of this network model are analysed based on a mean-field method. Theoretical results and numerical simulations indicate that this network model has community structure and scale-free properties
Node-weighted measures for complex networks with spatially embedded, sampled, or differently sized nodes
When network and graph theory are used in the study of complex systems, a
typically finite set of nodes of the network under consideration is frequently
either explicitly or implicitly considered representative of a much larger
finite or infinite region or set of objects of interest. The selection
procedure, e.g., formation of a subset or some kind of discretization or
aggregation, typically results in individual nodes of the studied network
representing quite differently sized parts of the domain of interest. This
heterogeneity may induce substantial bias and artifacts in derived network
statistics. To avoid this bias, we propose an axiomatic scheme based on the
idea of node splitting invariance to derive consistently weighted variants of
various commonly used statistical network measures. The practical relevance and
applicability of our approach is demonstrated for a number of example networks
from different fields of research, and is shown to be of fundamental importance
in particular in the study of spatially embedded functional networks derived
from time series as studied in, e.g., neuroscience and climatology.Comment: 21 pages, 13 figure
Modelling Students’ Thematically Associated Knowledge : Networked Knowledge from Affinity Statistics
Peer reviewe
Hierarchy measure for complex networks
Nature, technology and society are full of complexity arising from the
intricate web of the interactions among the units of the related systems (e.g.,
proteins, computers, people). Consequently, one of the most successful recent
approaches to capturing the fundamental features of the structure and dynamics
of complex systems has been the investigation of the networks associated with
the above units (nodes) together with their relations (edges). Most complex
systems have an inherently hierarchical organization and, correspondingly, the
networks behind them also exhibit hierarchical features. Indeed, several papers
have been devoted to describing this essential aspect of networks, however,
without resulting in a widely accepted, converging concept concerning the
quantitative characterization of the level of their hierarchy. Here we develop
an approach and propose a quantity (measure) which is simple enough to be
widely applicable, reveals a number of universal features of the organization
of real-world networks and, as we demonstrate, is capable of capturing the
essential features of the structure and the degree of hierarchy in a complex
network. The measure we introduce is based on a generalization of the m-reach
centrality, which we first extend to directed/partially directed graphs. Then,
we define the global reaching centrality (GRC), which is the difference between
the maximum and the average value of the generalized reach centralities over
the network. We investigate the behavior of the GRC considering both a
synthetic model with an adjustable level of hierarchy and real networks.
Results for real networks show that our hierarchy measure is related to the
controllability of the given system. We also propose a visualization procedure
for large complex networks that can be used to obtain an overall qualitative
picture about the nature of their hierarchical structure.Comment: 29 pages, 9 figures, 4 table
Investigating the topology of interacting networks - Theory and application to coupled climate subnetworks
Network theory provides various tools for investigating the structural or
functional topology of many complex systems found in nature, technology and
society. Nevertheless, it has recently been realised that a considerable number
of systems of interest should be treated, more appropriately, as interacting
networks or networks of networks. Here we introduce a novel graph-theoretical
framework for studying the interaction structure between subnetworks embedded
within a complex network of networks. This framework allows us to quantify the
structural role of single vertices or whole subnetworks with respect to the
interaction of a pair of subnetworks on local, mesoscopic and global
topological scales.
Climate networks have recently been shown to be a powerful tool for the
analysis of climatological data. Applying the general framework for studying
interacting networks, we introduce coupled climate subnetworks to represent and
investigate the topology of statistical relationships between the fields of
distinct climatological variables. Using coupled climate subnetworks to
investigate the terrestrial atmosphere's three-dimensional geopotential height
field uncovers known as well as interesting novel features of the atmosphere's
vertical stratification and general circulation. Specifically, the new measure
"cross-betweenness" identifies regions which are particularly important for
mediating vertical wind field interactions. The promising results obtained by
following the coupled climate subnetwork approach present a first step towards
an improved understanding of the Earth system and its complex interacting
components from a network perspective
Giraffe (Giraffa camelopardalis) social networks in areas of contrasting human activity and lion density
Using Transcription Modules to Identify Expression Clusters Perturbed in Williams-Beuren Syndrome
The genetic dissection of the phenotypes associated with Williams-Beuren Syndrome (WBS) is advancing thanks to the study of individuals carrying typical or atypical structural rearrangements, as well as in vitro and animal studies. However, little is known about the global dysregulations caused by the WBS deletion. We profiled the transcriptomes of skin fibroblasts from WBS patients and compared them to matched controls. We identified 868 differentially expressed genes that were significantly enriched in extracellular matrix genes, major histocompatibility complex (MHC) genes, as well as genes in which the products localize to the postsynaptic membrane. We then used public expression datasets from human fibroblasts to establish transcription modules, sets of genes coexpressed in this cell type. We identified those sets in which the average gene expression was altered in WBS samples. Dysregulated modules are often interconnected and share multiple common genes, suggesting that intricate regulatory networks connected by a few central genes are disturbed in WBS. This modular approach increases the power to identify pathways dysregulated in WBS patients, thus providing a testable set of additional candidates for genes and their interactions that modulate the WBS phenotypes
A Hybrid of Metabolic Flux Analysis and Bayesian Factor Modeling for Multiomic Temporal Pathway Activation.
The
growing availability of multiomic data provides a highly comprehensive
view of cellular processes at the levels of mRNA, proteins, metabolites,
and reaction fluxes. However, due to probabilistic interactions between
components depending on the environment and on the time course, casual,
sometimes rare interactions may cause important effects in the cellular
physiology. To date, interactions at the pathway level cannot be measured
directly, and methodologies to predict pathway cross-correlations
from reaction fluxes are still missing. Here, we develop a multiomic
approach of flux-balance analysis combined with Bayesian factor modeling
with the aim of detecting pathway cross-correlations and predicting
metabolic pathway activation profiles. Starting from gene expression
profiles measured in various environmental conditions, we associate
a flux rate profile with each condition. We then infer pathway cross-correlations
and identify the degrees of pathway activation with respect to the
conditions and time course using Bayesian factor modeling. We test
our framework on the most recent metabolic reconstruction of Escherichia coli in both static and dynamic environments,
thus predicting the functionality of particular groups of reactions
and how it varies over time. In a dynamic environment, our method
can be readily used to characterize the temporal progression of pathway
activation in response to given stimuli
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