3,600 research outputs found
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
Does the Rotten Child Spoil His Companion? Spatial Peer Effects Among Children in Rural India
This paper identifies the effect of neighborhood peer groups on childhood skill acquisition using observational data. We incorporate spatial peer interaction, defined as a child’s nearest geographical neighbors, into a production function of child cognitive development in Andhra Pradesh, India. Our peer group construction takes the form of directed networks, whose structure allows us to identify peer effects and enables us to disentangle endogenous effects from contextual effects. We exploit variation over time to avoid confounding correlated with social effects. Our results suggest that spatial peer and neighborhood effects are strongly positively associated with a child’s cognitive skill formation. These peer effects hold even when we consider an alternative IV-based identification strategy and different variations to network size. Further, we find that the presence of peer groups helps provide insurance against the negative impact of idiosyncratic shocks to child learning.Children, peer effects, cognitive skills, India
Learning and comparing functional connectomes across subjects
Functional connectomes capture brain interactions via synchronized
fluctuations in the functional magnetic resonance imaging signal. If measured
during rest, they map the intrinsic functional architecture of the brain. With
task-driven experiments they represent integration mechanisms between
specialized brain areas. Analyzing their variability across subjects and
conditions can reveal markers of brain pathologies and mechanisms underlying
cognition. Methods of estimating functional connectomes from the imaging signal
have undergone rapid developments and the literature is full of diverse
strategies for comparing them. This review aims to clarify links across
functional-connectivity methods as well as to expose different steps to perform
a group study of functional connectomes
Network Density of States
Spectral analysis connects graph structure to the eigenvalues and
eigenvectors of associated matrices. Much of spectral graph theory descends
directly from spectral geometry, the study of differentiable manifolds through
the spectra of associated differential operators. But the translation from
spectral geometry to spectral graph theory has largely focused on results
involving only a few extreme eigenvalues and their associated eigenvalues.
Unlike in geometry, the study of graphs through the overall distribution of
eigenvalues - the spectral density - is largely limited to simple random graph
models. The interior of the spectrum of real-world graphs remains largely
unexplored, difficult to compute and to interpret.
In this paper, we delve into the heart of spectral densities of real-world
graphs. We borrow tools developed in condensed matter physics, and add novel
adaptations to handle the spectral signatures of common graph motifs. The
resulting methods are highly efficient, as we illustrate by computing spectral
densities for graphs with over a billion edges on a single compute node. Beyond
providing visually compelling fingerprints of graphs, we show how the
estimation of spectral densities facilitates the computation of many common
centrality measures, and use spectral densities to estimate meaningful
information about graph structure that cannot be inferred from the extremal
eigenpairs alone.Comment: 10 pages, 7 figure
Efficient Physical Embedding of Topologically Complex Information Processing Networks in Brains and Computer Circuits
Nervous systems are information processing networks that evolved by natural selection, whereas very large scale integrated (VLSI) computer circuits have evolved by commercially driven technology development. Here we follow historic intuition that all physical information processing systems will share key organizational properties, such as modularity, that generally confer adaptivity of function. It has long been observed that modular VLSI circuits demonstrate an isometric scaling relationship between the number of processing elements and the number of connections, known as Rent's rule, which is related to the dimensionality of the circuit's interconnect topology and its logical capacity. We show that human brain structural networks, and the nervous system of the nematode C. elegans, also obey Rent's rule, and exhibit some degree of hierarchical modularity. We further show that the estimated Rent exponent of human brain networks, derived from MRI data, can explain the allometric scaling relations between gray and white matter volumes across a wide range of mammalian species, again suggesting that these principles of nervous system design are highly conserved. For each of these fractal modular networks, the dimensionality of the interconnect topology was greater than the 2 or 3 Euclidean dimensions of the space in which it was embedded. This relatively high complexity entailed extra cost in physical wiring: although all networks were economically or cost-efficiently wired they did not strictly minimize wiring costs. Artificial and biological information processing systems both may evolve to optimize a trade-off between physical cost and topological complexity, resulting in the emergence of homologous principles of economical, fractal and modular design across many different kinds of nervous and computational networks
Hypothesis Testing For Network Data in Functional Neuroimaging
In recent years, it has become common practice in neuroscience to use
networks to summarize relational information in a set of measurements,
typically assumed to be reflective of either functional or structural
relationships between regions of interest in the brain. One of the most basic
tasks of interest in the analysis of such data is the testing of hypotheses, in
answer to questions such as "Is there a difference between the networks of
these two groups of subjects?" In the classical setting, where the unit of
interest is a scalar or a vector, such questions are answered through the use
of familiar two-sample testing strategies. Networks, however, are not Euclidean
objects, and hence classical methods do not directly apply. We address this
challenge by drawing on concepts and techniques from geometry, and
high-dimensional statistical inference. Our work is based on a precise
geometric characterization of the space of graph Laplacian matrices and a
nonparametric notion of averaging due to Fr\'echet. We motivate and illustrate
our resulting methodologies for testing in the context of networks derived from
functional neuroimaging data on human subjects from the 1000 Functional
Connectomes Project. In particular, we show that this global test is more
statistical powerful, than a mass-univariate approach. In addition, we have
also provided a method for visualizing the individual contribution of each edge
to the overall test statistic.Comment: 34 pages. 5 figure
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