91,200 research outputs found
Probabilistic methods in the analysis of protein interaction networks
Imperial Users onl
Advancing functional connectivity research from association to causation
Cognition and behavior emerge from brain network interactions, such that investigating causal interactions should be central to the study of brain function. Approaches that characterize statistical associations among neural time series-functional connectivity (FC) methods-are likely a good starting point for estimating brain network interactions. Yet only a subset of FC methods ('effective connectivity') is explicitly designed to infer causal interactions from statistical associations. Here we incorporate best practices from diverse areas of FC research to illustrate how FC methods can be refined to improve inferences about neural mechanisms, with properties of causal neural interactions as a common ontology to facilitate cumulative progress across FC approaches. We further demonstrate how the most common FC measures (correlation and coherence) reduce the set of likely causal models, facilitating causal inferences despite major limitations. Alternative FC measures are suggested to immediately start improving causal inferences beyond these common FC measures
Perspective: network-guided pattern formation of neural dynamics
The understanding of neural activity patterns is fundamentally linked to an
understanding of how the brain's network architecture shapes dynamical
processes. Established approaches rely mostly on deviations of a given network
from certain classes of random graphs. Hypotheses about the supposed role of
prominent topological features (for instance, the roles of modularity, network
motifs, or hierarchical network organization) are derived from these
deviations. An alternative strategy could be to study deviations of network
architectures from regular graphs (rings, lattices) and consider the
implications of such deviations for self-organized dynamic patterns on the
network. Following this strategy, we draw on the theory of spatiotemporal
pattern formation and propose a novel perspective for analyzing dynamics on
networks, by evaluating how the self-organized dynamics are confined by network
architecture to a small set of permissible collective states. In particular, we
discuss the role of prominent topological features of brain connectivity, such
as hubs, modules and hierarchy, in shaping activity patterns. We illustrate the
notion of network-guided pattern formation with numerical simulations and
outline how it can facilitate the understanding of neural dynamics
Sparse neural networks with large learning diversity
Coded recurrent neural networks with three levels of sparsity are introduced.
The first level is related to the size of messages, much smaller than the
number of available neurons. The second one is provided by a particular coding
rule, acting as a local constraint in the neural activity. The third one is a
characteristic of the low final connection density of the network after the
learning phase. Though the proposed network is very simple since it is based on
binary neurons and binary connections, it is able to learn a large number of
messages and recall them, even in presence of strong erasures. The performance
of the network is assessed as a classifier and as an associative memory
Synchronization in complex networks
Synchronization processes in populations of locally interacting elements are
in the focus of intense research in physical, biological, chemical,
technological and social systems. The many efforts devoted to understand
synchronization phenomena in natural systems take now advantage of the recent
theory of complex networks. In this review, we report the advances in the
comprehension of synchronization phenomena when oscillating elements are
constrained to interact in a complex network topology. We also overview the new
emergent features coming out from the interplay between the structure and the
function of the underlying pattern of connections. Extensive numerical work as
well as analytical approaches to the problem are presented. Finally, we review
several applications of synchronization in complex networks to different
disciplines: biological systems and neuroscience, engineering and computer
science, and economy and social sciences.Comment: Final version published in Physics Reports. More information
available at http://synchronets.googlepages.com
Construction of embedded fMRI resting state functional connectivity networks using manifold learning
We construct embedded functional connectivity networks (FCN) from benchmark
resting-state functional magnetic resonance imaging (rsfMRI) data acquired from
patients with schizophrenia and healthy controls based on linear and nonlinear
manifold learning algorithms, namely, Multidimensional Scaling (MDS), Isometric
Feature Mapping (ISOMAP) and Diffusion Maps. Furthermore, based on key global
graph-theoretical properties of the embedded FCN, we compare their
classification potential using machine learning techniques. We also assess the
performance of two metrics that are widely used for the construction of FCN
from fMRI, namely the Euclidean distance and the lagged cross-correlation
metric. We show that the FCN constructed with Diffusion Maps and the lagged
cross-correlation metric outperform the other combinations
Graph analysis of functional brain networks: practical issues in translational neuroscience
The brain can be regarded as a network: a connected system where nodes, or
units, represent different specialized regions and links, or connections,
represent communication pathways. From a functional perspective communication
is coded by temporal dependence between the activities of different brain
areas. In the last decade, the abstract representation of the brain as a graph
has allowed to visualize functional brain networks and describe their
non-trivial topological properties in a compact and objective way. Nowadays,
the use of graph analysis in translational neuroscience has become essential to
quantify brain dysfunctions in terms of aberrant reconfiguration of functional
brain networks. Despite its evident impact, graph analysis of functional brain
networks is not a simple toolbox that can be blindly applied to brain signals.
On the one hand, it requires a know-how of all the methodological steps of the
processing pipeline that manipulates the input brain signals and extract the
functional network properties. On the other hand, a knowledge of the neural
phenomenon under study is required to perform physiological-relevant analysis.
The aim of this review is to provide practical indications to make sense of
brain network analysis and contrast counterproductive attitudes
Graph Theory and Networks in Biology
In this paper, we present a survey of the use of graph theoretical techniques
in Biology. In particular, we discuss recent work on identifying and modelling
the structure of bio-molecular networks, as well as the application of
centrality measures to interaction networks and research on the hierarchical
structure of such networks and network motifs. Work on the link between
structural network properties and dynamics is also described, with emphasis on
synchronization and disease propagation.Comment: 52 pages, 5 figures, Survey Pape
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