25,908 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
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
Guaranteed passive parameterized model order reduction of the partial element equivalent circuit (PEEC) method
The decrease of IC feature size and the increase of operating frequencies require 3-D electromagnetic methods, such as the partial element equivalent circuit (PEEC) method, for the analysis and design of high-speed circuits. Very large systems of equations are often produced by 3-D electromagnetic methods. During the circuit synthesis of large-scale digital or analog applications, it is important to predict the response of the system under study as a function of design parameters, such as geometrical and substrate features, in addition to frequency (or time). Parameterized model order reduction (PMOR) methods become necessary to reduce large systems of equations with respect to frequency and other design parameters. We propose an innovative PMOR technique applicable to PEEC analysis, which combines traditional passivity-preserving model order reduction methods and positive interpolation schemes. It is able to provide parametric reduced-order models, stable, and passive by construction over a user-defined range of design parameter values. Numerical examples validate the proposed approach
A taxonomy framework for unsupervised outlier detection techniques for multi-type data sets
The term "outlier" can generally be defined as an observation that is significantly different from
the other values in a data set. The outliers may be instances of error or indicate events. The
task of outlier detection aims at identifying such outliers in order to improve the analysis of
data and further discover interesting and useful knowledge about unusual events within numerous
applications domains. In this paper, we report on contemporary unsupervised outlier detection
techniques for multiple types of data sets and provide a comprehensive taxonomy framework and
two decision trees to select the most suitable technique based on data set. Furthermore, we
highlight the advantages, disadvantages and performance issues of each class of outlier detection
techniques under this taxonomy framework
Model reduction of biochemical reactions networks by tropical analysis methods
We discuss a method of approximate model reduction for networks of
biochemical reactions. This method can be applied to networks with polynomial
or rational reaction rates and whose parameters are given by their orders of
magnitude. In order to obtain reduced models we solve the problem of tropical
equilibration that is a system of equations in max-plus algebra. In the case of
networks with nonlinear fast cycles we have to solve the problem of tropical
equilibration at least twice, once for the initial system and a second time for
an extended system obtained by adding to the initial system the differential
equations satisfied by the conservation laws of the fast subsystem. The two
steps can be reiterated until the fast subsystem has no conservation laws
different from the ones of the full model. Our method can be used for formal
model reduction in computational systems biology
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