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- ItemComplex networks for climate model evaluation with application to statistical versus dynamical modeling of South American climate(Heidelberg : Springer, 2014) Feldhoff, Jan H.; Lange, Stefan; Volkholz, Jan; Donges, Jonathan F.; Kurths, Jürgen; Gerstengarbe, Friedrich-WilhelmIn this study we introduce two new node-weighted difference measures on complex networks as a tool for climate model evaluation. The approach facilitates the quantification of a model’s ability to reproduce the spatial covariability structure of climatological time series. We apply our methodology to compare the performance of a statistical and a dynamical regional climate model simulating the South American climate, as represented by the variables 2 m temperature, precipitation, sea level pressure, and geopotential height field at 500 hPa. For each variable, networks are constructed from the model outputs and evaluated against a reference network, derived from the ERA-Interim reanalysis, which also drives the models. We compare two network characteristics, the (linear) adjacency structure and the (nonlinear) clustering structure, and relate our findings to conventional methods of model evaluation. To set a benchmark, we construct different types of random networks and compare them alongside the climate model networks. Our main findings are: (1) The linear network structure is better reproduced by the statistical model statistical analogue resampling scheme (STARS) in summer and winter for all variables except the geopotential height field, where the dynamical model CCLM prevails. (2) For the nonlinear comparison, the seasonal differences are more pronounced and CCLM performs almost as well as STARS in summer (except for sea level pressure), while STARS performs better in winter for all variables.
- ItemUnraveling gene regulatory networks from time-resolved gene expression data - a measures comparison study(London : BioMed Central, 2011) Hempel, Sabrina; Koseska, Aneta; Nikoloski, Zoran; Kurths, Jürgen; Walther, DirkBackground Inferring regulatory interactions between genes from transcriptomics time-resolved data, yielding reverse engineered gene regulatory networks, is of paramount importance to systems biology and bioinformatics studies. Accurate methods to address this problem can ultimately provide a deeper insight into the complexity, behavior, and functions of the underlying biological systems. However, the large number of interacting genes coupled with short and often noisy time-resolved read-outs of the system renders the reverse engineering a challenging task. Therefore, the development and assessment of methods which are computationally efficient, robust against noise, applicable to short time series data, and preferably capable of reconstructing the directionality of the regulatory interactions remains a pressing research problem with valuable applications. Results Here we perform the largest systematic analysis of a set of similarity measures and scoring schemes within the scope of the relevance network approach which are commonly used for gene regulatory network reconstruction from time series data. In addition, we define and analyze several novel measures and schemes which are particularly suitable for short transcriptomics time series. We also compare the considered 21 measures and 6 scoring schemes according to their ability to correctly reconstruct such networks from short time series data by calculating summary statistics based on the corresponding specificity and sensitivity. Our results demonstrate that rank and symbol based measures have the highest performance in inferring regulatory interactions. In addition, the proposed scoring scheme by asymmetric weighting has shown to be valuable in reducing the number of false positive interactions. On the other hand, Granger causality as well as information-theoretic measures, frequently used in inference of regulatory networks, show low performance on the short time series analyzed in this study. Conclusions Our study is intended to serve as a guide for choosing a particular combination of similarity measures and scoring schemes suitable for reconstruction of gene regulatory networks from short time series data. We show that further improvement of algorithms for reverse engineering can be obtained if one considers measures that are rooted in the study of symbolic dynamics or ranks, in contrast to the application of common similarity measures which do not consider the temporal character of the employed data. Moreover, we establish that the asymmetric weighting scoring scheme together with symbol based measures (for low noise level) and rank based measures (for high noise level) are the most suitable choices.
- ItemSee–saw relationship of the Holocene East Asian–Australian summer monsoon(London : Nature Publishing Group, 2016) Eroglu, Deniz; McRobie, Fiona H.; Ozken, Ibrahim; Stemler, Thomas; Wyrwoll, Karl-Heinz; Breitenbach, Sebastian F.M.; Marwan, Norbert; Kurths, JürgenThe East Asian–Indonesian–Australian summer monsoon (EAIASM) links the Earth’s hemispheres and provides a heat source that drives global circulation. At seasonal and inter-seasonal timescales, the summer monsoon of one hemisphere is linked via outflows from the winter monsoon of the opposing hemisphere. Long-term phase relationships between the East Asian summer monsoon (EASM) and the Indonesian–Australian summer monsoon (IASM) are poorly understood, raising questions of long-term adjustments to future greenhouse-triggered climate change and whether these changes could ‘lock in’ possible IASM and EASM phase relationships in a region dependent on monsoonal rainfall. Here we show that a newly developed nonlinear time series analysis technique allows confident identification of strong versus weak monsoon phases at millennial to sub-centennial timescales. We find a see–saw relationship over the last 9,000 years—with strong and weak monsoons opposingly phased and triggered by solar variations. Our results provide insights into centennial- to millennial-scale relationships within the wider EAIASM regime.
- ItemStatistical mechanics and information-theoretic perspectives on complexity in the Earth system(Basel : MDPI, 2013) Balasis, Georgios; Donner, Reik V.; Potirakis, Stelios M.; Runge, Jakob; Papadimitriou, Constantinos; Daglis, Ioannis A.; Eftaxias, Konstantinos; Kurths, JürgenThis review provides a summary of methods originated in (non-equilibrium) statistical mechanics and information theory, which have recently found successful applications to quantitatively studying complexity in various components of the complex system Earth. Specifically, we discuss two classes of methods: (i) entropies of different kinds (e.g., on the one hand classical Shannon and R´enyi entropies, as well as non-extensive Tsallis entropy based on symbolic dynamics techniques and, on the other hand, approximate entropy, sample entropy and fuzzy entropy); and (ii) measures of statistical interdependence and causality (e.g., mutual information and generalizations thereof, transfer entropy, momentary information transfer). We review a number of applications and case studies utilizing the above-mentioned methodological approaches for studying contemporary problems in some exemplary fields of the Earth sciences, highlighting the potentials of different techniques.
- ItemExploring brain function from anatomical connectivity(Lausanne : Frontiers Media, 2011) Zamora-López, Gorka; Zhou, Changsong; Kurths, JürgenThe intrinsic relationship between the architecture of the brain and the range of sensory and behavioral phenomena it produces is a relevant question in neuroscience. Here, we review recent knowledge gained on the architecture of the anatomical connectivity by means of complex network analysis. It has been found that cortico-cortical networks display a few prominent characteristics: (i) modular organization, (ii) abundant alternative processing paths, and (iii) the presence of highly connected hubs. Additionally, we present a novel classification of cortical areas of the cat according to the role they play in multisensory connectivity. All these properties represent an ideal anatomical substrate supporting rich dynamical behaviors, facilitating the capacity of the brain to process sensory information of different modalities segregated and to integrate them toward a comprehensive perception of the real world. The results here exposed are mainly based on anatomical data of cats’ brain, but further observations suggest that, from worms to humans, the nervous system of all animals might share these fundamental principles of organization.
- ItemCortical hubs form a module for multisensory integration on top of the hierarchy of cortical networks(Lausanne : Frontiers Media, 2010) Zamora-López, Gorka; Zhou, Changsong; Kurths, JürgenSensory stimuli entering the nervous system follow particular paths of processing, typically separated (segregated) from the paths of other modal information. However, sensory perception, awareness and cognition emerge from the combination of information (integration). The corticocortical networks of cats and macaque monkeys display three prominent characteristics: (i) modular organisation (facilitating the segregation), (ii) abundant alternative processing paths and (iii) the presence of highly connected hubs. Here, we study in detail the organisation and potential function of the cortical hubs by graph analysis and information theoretical methods. We find that the cortical hubs form a spatially delocalised, but topologically central module with the capacity to integrate multisensory information in a collaborative manner. With this, we resolve the underlying anatomical substrate that supports the simultaneous capacity of the cortex to segregate and to integrate multisensory information.
- ItemDiminished heart beat non-stationarities in congestive heart failure(Lausanne : Frontiers Media, 2013) Camargo, Sabrina; Riedl, Maik; Anteneodo, Celia; Kurths, Jürgen; Wessel, NielsStudies on heart rate variability (HRV) have become popular and the possibility of diagnosis based on non-invasive techniques compels us to overcome the difficulties originated on the environmental changes that can affect the signal. We perform a non-parametric segmentation which consists of locating the points where the signal can be split into stationary segments. By finding stationary segments we are able to analyze the size of these segments and evaluate how the signal changes from one segment to another, looking at the statistical moments given in each patch, for example, mean and variance. We analyze HRV data for 15 patients with congestive heart failure (CHF; 11 males, 4 females, age 56±11 years), 18 elderly healthy subjects (EH; 11 males, 7 females, age 50±7 years), and 15 young healthy subjects (YH; 11 females, 4 males, age 31±6 years). Our results confirm higher variance for YH, and EH, while CHF displays diminished variance with p-values <0.01, when compared to the healthy groups, presenting higher HRV in healthy subjects. Moreover, it is possible to distinguish between YH and EH with p < 0.05 through the segmentation outcomes. We found high correlations between the results of segmentation and standard measures of HRV analysis and a connection to results of detrended fluctuation analysis (DFA). The segmentation applied to HRV studies detects aging and pathological conditions effects on the non-stationary behavior of the analyzed groups, promising to contribute in complexity analysis and providing risk stratification measures.
- ItemSystems Medicine of Cancer: Bringing Together Clinical Data and Nonlinear Dynamics of Genetic Networks(London : Hindawi, 2016) Blyuss, Konstantin B.; Manchanda, Ranjit; Kurths, Jürgen; Alsaedi, Ahmed; Zaikin, AlexeyEditorial
- ItemModification of brain oscillations via rhythmic light stimulation provides evidence for entrainment but not for superposition of event-related responses(Lausanne : Frontiers Media, 2016) Notbohm, Annika; Kurths, Jürgen; Herrmann, Christoph S.The functional relevance of brain oscillations in the alpha frequency range (8–13 Hz) has been repeatedly investigated through the use of rhythmic visual stimulation. The underlying mechanism of the steady-state visual evoked potential (SSVEP) measured in EEG during rhythmic stimulation, however, is not known. There are two hypotheses on the origin of SSVEPs: entrainment of brain oscillations and superposition of event-related responses (ERPs). The entrainment but not the superposition hypothesis justifies rhythmic visual stimulation as a means to manipulate brain oscillations, because superposition assumes a linear summation of single responses, independent from ongoing brain oscillations. Here, we stimulated participants with a rhythmic flickering light of different frequencies and intensities. We measured entrainment by comparing the phase coupling of brain oscillations stimulated by rhythmic visual flicker with the oscillations induced by arrhythmic jittered stimulation, varying the time, stimulation frequency, and intensity conditions. In line with a theoretical concept of entrainment (the so called Arnold tongue), we found the phase coupling to be more pronounced with increasing stimulation intensity as well as at stimulation frequencies closer to each participant's intrinsic frequency. Only inside the Arnold tongue did the conditions significantly differ from the jittered stimulation. Furthermore, even in a single sequence of an SSVEP, we found non-linear features (intermittency of phase locking) that contradict the linear summation of single responses, as assumed by the superposition hypothesis. Our findings provide unequivocal evidence that visual rhythmic stimulation entrains brain oscillations, thus validating the approach of rhythmic stimulation as a manipulation of brain oscillations.
- ItemReliability of inference of directed climate networks using conditional mutual information(Basel : MDPI, 2013) Hlinka, Jaroslav; Hartman, David; Vejmelka, Martin; Runge, Jakob; Marwan, Norbert; Kurths, Jürgen; Paluš, MilanAcross geosciences, many investigated phenomena relate to specific complex systems consisting of intricately intertwined interacting subsystems. Such dynamical complex systems can be represented by a directed graph, where each link denotes an existence of a causal relation, or information exchange between the nodes. For geophysical systems such as global climate, these relations are commonly not theoretically known but estimated from recorded data using causality analysis methods. These include bivariate nonlinear methods based on information theory and their linear counterpart. The trade-off between the valuable sensitivity of nonlinear methods to more general interactions and the potentially higher numerical reliability of linear methods may affect inference regarding structure and variability of climate networks. We investigate the reliability of directed climate networks detected by selected methods and parameter settings, using a stationarized model of dimensionality-reduced surface air temperature data from reanalysis of 60-year global climate records. Overall, all studied bivariate causality methods provided reproducible estimates of climate causality networks, with the linear approximation showing higher reliability than the investigated nonlinear methods. On the example dataset, optimizing the investigated nonlinear methods with respect to reliability increased the similarity of the detected networks to their linear counterparts, supporting the particular hypothesis of the near-linearity of the surface air temperature reanalysis data.