5,114 research outputs found
A statistical model for brain networks inferred from large-scale electrophysiological signals
Network science has been extensively developed to characterize structural
properties of complex systems, including brain networks inferred from
neuroimaging data. As a result of the inference process, networks estimated
from experimentally obtained biological data, represent one instance of a
larger number of realizations with similar intrinsic topology. A modeling
approach is therefore needed to support statistical inference on the bottom-up
local connectivity mechanisms influencing the formation of the estimated brain
networks. We adopted a statistical model based on exponential random graphs
(ERGM) to reproduce brain networks, or connectomes, estimated by spectral
coherence between high-density electroencephalographic (EEG) signals. We
validated this approach in a dataset of 108 healthy subjects during eyes-open
(EO) and eyes-closed (EC) resting-state conditions. Results showed that the
tendency to form triangles and stars, reflecting clustering and node
centrality, better explained the global properties of the EEG connectomes as
compared to other combinations of graph metrics. Synthetic networks generated
by this model configuration replicated the characteristic differences found in
brain networks, with EO eliciting significantly higher segregation in the alpha
frequency band (8-13 Hz) as compared to EC. Furthermore, the fitted ERGM
parameter values provided complementary information showing that clustering
connections are significantly more represented from EC to EO in the alpha
range, but also in the beta band (14-29 Hz), which is known to play a crucial
role in cortical processing of visual input and externally oriented attention.
These findings support the current view of the brain functional segregation and
integration in terms of modules and hubs, and provide a statistical approach to
extract new information on the (re)organizational mechanisms in healthy and
diseased brains.Comment: Due to the limitation "The abstract field cannot be longer than 1,920
characters", the abstract appearing here is slightly shorter than that in the
PDF fil
Mapping multiplex hubs in human functional brain network
Typical brain networks consist of many peripheral regions and a few highly
central ones, i.e. hubs, playing key functional roles in cerebral
inter-regional interactions. Studies have shown that networks, obtained from
the analysis of specific frequency components of brain activity, present
peculiar architectures with unique profiles of region centrality. However, the
identification of hubs in networks built from different frequency bands
simultaneously is still a challenging problem, remaining largely unexplored.
Here we identify each frequency component with one layer of a multiplex network
and face this challenge by exploiting the recent advances in the analysis of
multiplex topologies. First, we show that each frequency band carries unique
topological information, fundamental to accurately model brain functional
networks. We then demonstrate that hubs in the multiplex network, in general
different from those ones obtained after discarding or aggregating the measured
signals as usual, provide a more accurate map of brain's most important
functional regions, allowing to distinguish between healthy and schizophrenic
populations better than conventional network approaches.Comment: 11 pages, 8 figures, 2 table
Maximum Fidelity
The most fundamental problem in statistics is the inference of an unknown
probability distribution from a finite number of samples. For a specific
observed data set, answers to the following questions would be desirable: (1)
Estimation: Which candidate distribution provides the best fit to the observed
data?, (2) Goodness-of-fit: How concordant is this distribution with the
observed data?, and (3) Uncertainty: How concordant are other candidate
distributions with the observed data? A simple unified approach for univariate
data that addresses these traditionally distinct statistical notions is
presented called "maximum fidelity". Maximum fidelity is a strict frequentist
approach that is fundamentally based on model concordance with the observed
data. The fidelity statistic is a general information measure based on the
coordinate-independent cumulative distribution and critical yet previously
neglected symmetry considerations. An approximation for the null distribution
of the fidelity allows its direct conversion to absolute model concordance (p
value). Fidelity maximization allows identification of the most concordant
model distribution, generating a method for parameter estimation, with
neighboring, less concordant distributions providing the "uncertainty" in this
estimate. Maximum fidelity provides an optimal approach for parameter
estimation (superior to maximum likelihood) and a generally optimal approach
for goodness-of-fit assessment of arbitrary models applied to univariate data.
Extensions to binary data, binned data, multidimensional data, and classical
parametric and nonparametric statistical tests are described. Maximum fidelity
provides a philosophically consistent, robust, and seemingly optimal foundation
for statistical inference. All findings are presented in an elementary way to
be immediately accessible to all researchers utilizing statistical analysis.Comment: 66 pages, 32 figures, 7 tables, submitte
Higher order assortativity in complex networks
Assortativity was first introduced by Newman and has been extensively studied
and applied to many real world networked systems since then. Assortativity is a
graph metrics and describes the tendency of high degree nodes to be directly
connected to high degree nodes and low degree nodes to low degree nodes. It can
be interpreted as a first order measure of the connection between nodes, i.e.
the first autocorrelation of the degree-degree vector. Even though
assortativity has been used so extensively, to the author's knowledge, no
attempt has been made to extend it theoretically. This is the scope of our
paper. We will introduce higher order assortativity by extending the Newman
index based on a suitable choice of the matrix driving the connections. Higher
order assortativity will be defined for paths, shortest paths, random walks of
a given time length, connecting any couple of nodes. The Newman assortativity
is achieved for each of these measures when the matrix is the adjacency matrix,
or, in other words, the correlation is of order 1. Our higher order
assortativity indexes can be used for describing a variety of real networks,
help discriminating networks having the same Newman index and may reveal new
topological network features.Comment: 24 pages, 16 figure
Comparing the writing style of real and artificial papers
Recent years have witnessed the increase of competition in science. While
promoting the quality of research in many cases, an intense competition among
scientists can also trigger unethical scientific behaviors. To increase the
total number of published papers, some authors even resort to software tools
that are able to produce grammatical, but meaningless scientific manuscripts.
Because automatically generated papers can be misunderstood as real papers, it
becomes of paramount importance to develop means to identify these scientific
frauds. In this paper, I devise a methodology to distinguish real manuscripts
from those generated with SCIGen, an automatic paper generator. Upon modeling
texts as complex networks (CN), it was possible to discriminate real from fake
papers with at least 89\% of accuracy. A systematic analysis of features
relevance revealed that the accessibility and betweenness were useful in
particular cases, even though the relevance depended upon the dataset. The
successful application of the methods described here show, as a proof of
principle, that network features can be used to identify scientific gibberish
papers. In addition, the CN-based approach can be combined in a straightforward
fashion with traditional statistical language processing methods to improve the
performance in identifying artificially generated papers.Comment: To appear in Scientometrics (2015
Structuprint: a scalable and extensible tool for two-dimensional representation of protein surfaces
© 2016 Kontopoulos et al.Background: The term molecular cartography encompasses a family of computational methods for two-dimensional transformation of protein structures and analysis of their physicochemical properties. The underlying algorithms comprise multiple manual steps, whereas the few existing implementations typically restrict the user to a very limited set of molecular descriptors. Results: We present Structuprint, a free standalone software that fully automates the rendering of protein surface maps, given - at the very least - a directory with a PDB file and an amino acid property. The tool comes with a default database of 328 descriptors, which can be extended or substituted by user-provided ones. The core algorithm comprises the generation of a mould of the protein surface, which is subsequently converted to a sphere and mapped to two dimensions, using the Miller cylindrical projection. Structuprint is partly optimized for multicore computers, making the rendering of animations of entire molecular dynamics simulations feasible. Conclusions: Structuprint is an efficient application, implementing a molecular cartography algorithm for protein surfaces. According to the results of a benchmark, its memory requirements and execution time are reasonable, allowing it to run even on low-end personal computers. We believe that it will be of use - primarily but not exclusively - to structural biologists and computational biochemists
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