Generating artificial light curves: Revisited and updated

The production of artificial light curves with known statistical and variability properties is of great importance in astrophysics. Consolidating the confidence levels during cross-correlation studies, understanding the artefacts induced by sampling irregularities, establishing detection limits for future observatories are just some of the applications of simulated data sets. Currently, the widely used methodology of amplitude and phase randomisation is able to produce artificial light curves which have a given underlying power spectral density (PSD) but which are strictly Gaussian distributed. This restriction is a significant limitation, since the majority of the light curves e.g. active galactic nuclei, X-ray binaries, gamma-ray bursts show strong deviations from Gaussianity exhibiting `burst-like' events in their light curves yielding long-tailed probability distribution functions (PDFs). In this study we propose a simple method which is able to precisely reproduce light curves which match both the PSD and the PDF of either an observed light curve or a theoretical model. The PDF can be representative of either the parent distribution or the actual distribution of the observed data, depending on the study to be conducted for a given source. The final artificial light curves contain all of the statistical and variability properties of the observed source or theoretical model i.e. same PDF and PSD, respectively. Within the framework of Reproducible Research, the code, together with the illustrative example used in this manuscript, are both made publicly available in the form of an interactive Mathematica notebook.Comment: Accepted for publication in MNRAS. The paper is 23 pages long and contains 21 figures and 2 tables. The Mathematica notebook can be found in the web as part of this paper (Online Material) or at http://www.astro.soton.ac.uk/~de1e08/ArtificialLightCurves

Information transfer in signaling pathways : a study using coupled simulated and experimental data

Background: The topology of signaling cascades has been studied in quite some detail. However, how information is processed exactly is still relatively unknown. Since quite diverse information has to be transported by one and the same signaling cascade (e.g. in case of different agonists), it is clear that the underlying mechanism is more complex than a simple binary switch which relies on the mere presence or absence of a particular species. Therefore, finding means to analyze the information transferred will help in deciphering how information is processed exactly in the cell. Using the information-theoretic measure transfer entropy, we studied the properties of information transfer in an example case, namely calcium signaling under different cellular conditions. Transfer entropy is an asymmetric and dynamic measure of the dependence of two (nonlinear) stochastic processes. We used calcium signaling since it is a well-studied example of complex cellular signaling. It has been suggested that specific information is encoded in the amplitude, frequency and waveform of the oscillatory Ca2+-signal. Results: We set up a computational framework to study information transfer, e.g. for calcium signaling at different levels of activation and different particle numbers in the system. We stochastically coupled simulated and experimentally measured calcium signals to simulated target proteins and used kernel density methods to estimate the transfer entropy from these bivariate time series. We found that, most of the time, the transfer entropy increases with increasing particle numbers. In systems with only few particles, faithful information transfer is hampered by random fluctuations. The transfer entropy also seems to be slightly correlated to the complexity (spiking, bursting or irregular oscillations) of the signal. Finally, we discuss a number of peculiarities of our approach in detail. Conclusion: This study presents the first application of transfer entropy to biochemical signaling pathways. We could quantify the information transferred from simulated/experimentally measured calcium signals to a target enzyme under different cellular conditions. Our approach, comprising stochastic coupling and using the information-theoretic measure transfer entropy, could also be a valuable tool for the analysis of other signaling pathways

Information transfer in signaling pathways : a study using coupled simulated and experimental data

Background: The topology of signaling cascades has been studied in quite some detail. However, how information is processed exactly is still relatively unknown. Since quite diverse information has to be transported by one and the same signaling cascade (e.g. in case of different agonists), it is clear that the underlying mechanism is more complex than a simple binary switch which relies on the mere presence or absence of a particular species. Therefore, finding means to analyze the information transferred will help in deciphering how information is processed exactly in the cell. Using the information-theoretic measure transfer entropy, we studied the properties of information transfer in an example case, namely calcium signaling under different cellular conditions. Transfer entropy is an asymmetric and dynamic measure of the dependence of two (nonlinear) stochastic processes. We used calcium signaling since it is a well-studied example of complex cellular signaling. It has been suggested that specific information is encoded in the amplitude, frequency and waveform of the oscillatory Ca2+-signal. Results: We set up a computational framework to study information transfer, e.g. for calcium signaling at different levels of activation and different particle numbers in the system. We stochastically coupled simulated and experimentally measured calcium signals to simulated target proteins and used kernel density methods to estimate the transfer entropy from these bivariate time series. We found that, most of the time, the transfer entropy increases with increasing particle numbers. In systems with only few particles, faithful information transfer is hampered by random fluctuations. The transfer entropy also seems to be slightly correlated to the complexity (spiking, bursting or irregular oscillations) of the signal. Finally, we discuss a number of peculiarities of our approach in detail. Conclusion: This study presents the first application of transfer entropy to biochemical signaling pathways. We could quantify the information transferred from simulated/experimentally measured calcium signals to a target enzyme under different cellular conditions. Our approach, comprising stochastic coupling and using the information-theoretic measure transfer entropy, could also be a valuable tool for the analysis of other signaling pathways

Surrogate time series

Before we apply nonlinear techniques, for example those inspired by chaos theory, to dynamical phenomena occurring in nature, it is necessary to first ask if the use of such advanced techniques is justified "by the data". While many processes in nature seem very unlikely a priori to be linear, the possible nonlinear nature might not be evident in specific aspects of their dynamics. The method of surrogate data has become a very popular tool to address such a question. However, while it was meant to provide a statistically rigorous, foolproof framework, some limitations and caveats have shown up in its practical use. In this paper, recent efforts to understand the caveats, avoid the pitfalls, and to overcome some of the limitations, are reviewed and augmented by new material. In particular, we will discuss specific as well as more general approaches to constrained randomisation, providing a full range of examples. New algorithms will be introduced for unevenly sampled and multivariate data and for surrogate spike trains. The main limitation, which lies in the interpretability of the test results, will be illustrated through instructive case studies. We will also discuss some implementational aspects of the realisation of these methods in the TISEAN (http://www.mpipks-dresden.mpg.de/~tisean) software package.Comment: 28 pages, 23 figures, software at http://www.mpipks-dresden.mpg.de/~tisea

Machine-learning nonstationary noise out of gravitational-wave detectors

Signal extraction out of background noise is a common challenge in high-precision physics experiments, where the measurement output is often a continuous data stream. To improve the signal-to-noise ratio of the detection, witness sensors are often used to independently measure background noises and subtract them from the main signal. If the noise coupling is linear and stationary, optimal techniques already exist and are routinely implemented in many experiments. However, when the noise coupling is nonstationary, linear techniques often fail or are suboptimal. Inspired by the properties of the background noise in gravitational wave detectors, this work develops a novel algorithm to efficiently characterize and remove nonstationary noise couplings, provided there exist witnesses of the noise source and of the modulation. In this work, the algorithm is described in its most general formulation, and its efficiency is demonstrated with examples from the data of the Advanced LIGO gravitational-wave observatory, where we could obtain an improvement of the detector gravitational-wave reach without introducing any bias on the source parameter estimation

Informative and misinformative interactions in a school of fish

It is generally accepted that, when moving in groups, animals process information to coordinate their motion. Recent studies have begun to apply rigorous methods based on Information Theory to quantify such distributed computation. Following this perspective, we use transfer entropy to quantify dynamic information flows locally in space and time across a school of fish during directional changes around a circular tank, i.e. U-turns. This analysis reveals peaks in information flows during collective U-turns and identifies two different flows: an informative flow (positive transfer entropy) based on fish that have already turned about fish that are turning, and a misinformative flow (negative transfer entropy) based on fish that have not turned yet about fish that are turning. We also reveal that the information flows are related to relative position and alignment between fish, and identify spatial patterns of information and misinformation cascades. This study offers several methodological contributions and we expect further application of these methodologies to reveal intricacies of self-organisation in other animal groups and active matter in general

Measuring information-transfer delays

In complex networks such as gene networks, traffic systems or brain circuits it is important to understand how long it takes for the different parts of the network to effectively influence one another. In the brain, for example, axonal delays between brain areas can amount to several tens of milliseconds, adding an intrinsic component to any timing-based processing of information. Inferring neural interaction delays is thus needed to interpret the information transfer revealed by any analysis of directed interactions across brain structures. However, a robust estimation of interaction delays from neural activity faces several challenges if modeling assumptions on interaction mechanisms are wrong or cannot be made. Here, we propose a robust estimator for neuronal interaction delays rooted in an information-theoretic framework, which allows a model-free exploration of interactions. In particular, we extend transfer entropy to account for delayed source-target interactions, while crucially retaining the conditioning on the embedded target state at the immediately previous time step. We prove that this particular extension is indeed guaranteed to identify interaction delays between two coupled systems and is the only relevant option in keeping with Wiener’s principle of causality. We demonstrate the performance of our approach in detecting interaction delays on finite data by numerical simulations of stochastic and deterministic processes, as well as on local field potential recordings. We also show the ability of the extended transfer entropy to detect the presence of multiple delays, as well as feedback loops. While evaluated on neuroscience data, we expect the estimator to be useful in other fields dealing with network dynamics

Exploring the movement dynamics of deception

Both the science and the everyday practice of detecting a lie rest on the same assumption: hidden cognitive states that the liar would like to remain hidden nevertheless influence observable behavior. This assumption has good evidence. The insights of professional interrogators, anecdotal evidence, and body language textbooks have all built up a sizeable catalog of non-verbal cues that have been claimed to distinguish deceptive and truthful behavior. Typically, these cues are discrete, individual behaviors—a hand touching a mouth, the rise of a brow—that distinguish lies from truths solely in terms of their frequency or duration. Research to date has failed to establish any of these non-verbal cues as a reliable marker of deception. Here we argue that perhaps this is because simple tallies of behavior can miss out on the rich but subtle organization of behavior as it unfolds over time. Research in cognitive science from a dynamical systems perspective has shown that behavior is structured across multiple timescales, with more or less regularity and structure. Using tools that are sensitive to these dynamics, we analyzed body motion data from an experiment that put participants in a realistic situation of choosing, or not, to lie to an experimenter. Our analyses indicate that when being deceptive, continuous fluctuations of movement in the upper face, and somewhat in the arms, are characterized by dynamical properties of less stability, but greater complexity. For the upper face, these distinctions are present despite no apparent differences in the overall amount of movement between deception and truth. We suggest that these unique dynamical signatures of motion are indicative of both the cognitive demands inherent to deception and the need to respond adaptively in a social context