161,172 research outputs found
Multiscale Analysis of Spreading in a Large Communication Network
In temporal networks, both the topology of the underlying network and the
timings of interaction events can be crucial in determining how some dynamic
process mediated by the network unfolds. We have explored the limiting case of
the speed of spreading in the SI model, set up such that an event between an
infectious and susceptible individual always transmits the infection. The speed
of this process sets an upper bound for the speed of any dynamic process that
is mediated through the interaction events of the network. With the help of
temporal networks derived from large scale time-stamped data on mobile phone
calls, we extend earlier results that point out the slowing-down effects of
burstiness and temporal inhomogeneities. In such networks, links are not
permanently active, but dynamic processes are mediated by recurrent events
taking place on the links at specific points in time. We perform a multi-scale
analysis and pinpoint the importance of the timings of event sequences on
individual links, their correlations with neighboring sequences, and the
temporal pathways taken by the network-scale spreading process. This is
achieved by studying empirically and analytically different characteristic
relay times of links, relevant to the respective scales, and a set of temporal
reference models that allow for removing selected time-domain correlations one
by one
Universal features of correlated bursty behaviour
Inhomogeneous temporal processes, like those appearing in human
communications, neuron spike trains, and seismic signals, consist of
high-activity bursty intervals alternating with long low-activity periods. In
recent studies such bursty behavior has been characterized by a fat-tailed
inter-event time distribution, while temporal correlations were measured by the
autocorrelation function. However, these characteristic functions are not
capable to fully characterize temporally correlated heterogenous behavior. Here
we show that the distribution of the number of events in a bursty period serves
as a good indicator of the dependencies, leading to the universal observation
of power-law distribution in a broad class of phenomena. We find that the
correlations in these quite different systems can be commonly interpreted by
memory effects and described by a simple phenomenological model, which displays
temporal behavior qualitatively similar to that in real systems
Dynamical systems theory for music dynamics
We show that, when music pieces are cast in the form of time series of pitch
variations, the concepts and tools of dynamical systems theory can be applied
to the analysis of {\it temporal dynamics} in music. (i) Phase space portraits
are constructed from the time series wherefrom the dimensionality is evaluated
as a measure of the {\pit global} dynamics of each piece. (ii) Spectral
analysis of the time series yields power spectra () close to
{\pit red noise} () in the low frequency range. (iii) We define an
information entropy which provides a measure of the {\pit local} dynamics in
the musical piece; the entropy can be interpreted as an evaluation of the
degree of {\it complexity} in the music, but there is no evidence of an
analytical relation between local and global dynamics. These findings are based
on computations performed on eighty sequences sampled in the music literature
from the 18th to the 20th century.Comment: To appear in CHAOS. Figures and Tables (not included) can be obtained
from [email protected]
Unsupervised discovery of temporal sequences in high-dimensional datasets, with applications to neuroscience.
Identifying low-dimensional features that describe large-scale neural recordings is a major challenge in neuroscience. Repeated temporal patterns (sequences) are thought to be a salient feature of neural dynamics, but are not succinctly captured by traditional dimensionality reduction techniques. Here, we describe a software toolbox-called seqNMF-with new methods for extracting informative, non-redundant, sequences from high-dimensional neural data, testing the significance of these extracted patterns, and assessing the prevalence of sequential structure in data. We test these methods on simulated data under multiple noise conditions, and on several real neural and behavioral datas. In hippocampal data, seqNMF identifies neural sequences that match those calculated manually by reference to behavioral events. In songbird data, seqNMF discovers neural sequences in untutored birds that lack stereotyped songs. Thus, by identifying temporal structure directly from neural data, seqNMF enables dissection of complex neural circuits without relying on temporal references from stimuli or behavioral outputs
Structural Alignment of RNAs Using Profile-csHMMs and Its Application to RNA Homology Search: Overview and New Results
Systematic research on noncoding RNAs (ncRNAs) has revealed that many ncRNAs are actively involved in various biological networks. Therefore, in order to fully understand the mechanisms of these networks, it is crucial to understand the roles of ncRNAs. Unfortunately, the annotation of ncRNA genes that give rise to functional RNA molecules has begun only recently, and it is far from being complete. Considering the huge amount of genome sequence data, we need efficient computational methods for finding ncRNA genes. One effective way of finding ncRNA genes is to look for regions that are similar to known ncRNA genes. As many ncRNAs have well-conserved secondary structures, we need statistical models that can represent such structures for this purpose. In this paper, we propose a new method for representing RNA sequence profiles and finding structural alignment of RNAs based on profile context-sensitive hidden Markov models (profile-csHMMs). Unlike existing models, the proposed approach can handle any kind of RNA secondary structures, including pseudoknots. We show that profile-csHMMs can provide an effective framework for the computational analysis of RNAs and the identification of ncRNA genes
Temporal Networks
A great variety of systems in nature, society and technology -- from the web
of sexual contacts to the Internet, from the nervous system to power grids --
can be modeled as graphs of vertices coupled by edges. The network structure,
describing how the graph is wired, helps us understand, predict and optimize
the behavior of dynamical systems. In many cases, however, the edges are not
continuously active. As an example, in networks of communication via email,
text messages, or phone calls, edges represent sequences of instantaneous or
practically instantaneous contacts. In some cases, edges are active for
non-negligible periods of time: e.g., the proximity patterns of inpatients at
hospitals can be represented by a graph where an edge between two individuals
is on throughout the time they are at the same ward. Like network topology, the
temporal structure of edge activations can affect dynamics of systems
interacting through the network, from disease contagion on the network of
patients to information diffusion over an e-mail network. In this review, we
present the emergent field of temporal networks, and discuss methods for
analyzing topological and temporal structure and models for elucidating their
relation to the behavior of dynamical systems. In the light of traditional
network theory, one can see this framework as moving the information of when
things happen from the dynamical system on the network, to the network itself.
Since fundamental properties, such as the transitivity of edges, do not
necessarily hold in temporal networks, many of these methods need to be quite
different from those for static networks
Random walks on temporal networks
Many natural and artificial networks evolve in time. Nodes and connections
appear and disappear at various timescales, and their dynamics has profound
consequences for any processes in which they are involved. The first empirical
analysis of the temporal patterns characterizing dynamic networks are still
recent, so that many questions remain open. Here, we study how random walks, as
paradigm of dynamical processes, unfold on temporally evolving networks. To
this aim, we use empirical dynamical networks of contacts between individuals,
and characterize the fundamental quantities that impact any general process
taking place upon them. Furthermore, we introduce different randomizing
strategies that allow us to single out the role of the different properties of
the empirical networks. We show that the random walk exploration is slower on
temporal networks than it is on the aggregate projected network, even when the
time is properly rescaled. In particular, we point out that a fundamental role
is played by the temporal correlations between consecutive contacts present in
the data. Finally, we address the consequences of the intrinsically limited
duration of many real world dynamical networks. Considering the fundamental
prototypical role of the random walk process, we believe that these results
could help to shed light on the behavior of more complex dynamics on temporally
evolving networks.Comment: 14 pages, 13 figure
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