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Recurrence-plot-based recurrence networks are an approach used to analyze time series using a complex networks theory. In both approaches - recurrence plots and recurrence networks -, a threshold to identify recurrent states is required. The selection of the threshold is important in order to avoid bias of the recurrence network results. In this paper, we propose a novel method to choose a recurrence threshold adaptively. We show a comparison between the constant threshold and adaptive threshold cases to study period-chaos and even period-period transitions in the dynamics of a prototypical model system. This novel method is then used to identify climate transitions from a lake sediment record.
Extreme Rainfall of the South American Monsoon System: A Dataset Comparison Using Complex Networks
(2015)
In this study, the authors compare six different rainfall datasets for South America with a focus on their representation of extreme rainfall during the monsoon season (December February): the gauge-calibrated TRMM 3B42 V7 satellite product; the near-real-time TRMM 3B42 V7 RT, the GPCP 1 degrees daily (1DD) V1.2 satellite gauge combination product, the Interim ECMWF Re-Analysis (ERA-Interim) product; output of a high-spatial-resolution run of the ECHAM6 global circulation model; and output of the regional climate model Eta. For the latter three, this study can be understood as a model evaluation. In addition to statistical values of local rainfall distributions, the authors focus on the spatial characteristics of extreme rainfall covariability. Since traditional approaches based on principal component analysis are not applicable in the context of extreme events, they apply and further develop methods based on complex network theory. This way, the authors uncover substantial differences in extreme rainfall patterns between the different datasets: (i) The three model-derived datasets yield very different results than the satellite gauge combinations regarding the main climatological propagation pathways of extreme events as well as the main convergence zones of the monsoon system. (ii) Large discrepancies are found for the development of mesoscale convective systems in southeastern South America. (iii) Both TRMM datasets and ECHAM6 indicate a linkage of extreme rainfall events between the central Amazon basin and the eastern slopes of the central Andes, but this pattern is not reproduced by the remaining datasets. The authors' study suggests that none of the three model-derived datasets adequately captures extreme rainfall patterns in South America.
During the last glacial period, climate records from the North Atlantic region exhibit a pronounced spectral component corresponding to a period of about 1470 years, which has attracted much attention. This spectral peak is closely related to the recurrence pattern of Dansgaard-Oeschger (DO) events. In previous studies a red noise random process, more precisely a first-order autoregressive (AR1) process, was used to evaluate the statistical significance of this peak, with a reported significance of more than 99%. Here we use a simple mechanistic two-state model of DO events, which itself was derived from a much more sophisticated ocean-atmosphere model of intermediate complexity, to numerically evaluate the spectral properties of random (i.e., solely noise-driven) events. This way we find that the power spectral density of random DO events differs fundamentally from a simple red noise random process. These results question the applicability of linear spectral analysis for estimating the statistical significance of highly non-linear processes such as DO events. More precisely, to enhance our scientific understanding about the trigger of DO events, we must not consider simple "straw men" as, for example, the AR1 random process, but rather test against realistic alternative descriptions.
Nonlinear detection of paleoclimate-variability transitions possibly related to human evolution
(2011)
Potential paleoclimatic driving mechanisms acting on human evolution present an open problem of cross-disciplinary scientific interest. The analysis of paleoclimate archives encoding the environmental variability in East Africa during the past 5 Ma has triggered an ongoing debate about possible candidate processes and evolutionary mechanisms. In this work, we apply a nonlinear statistical technique, recurrence network analysis, to three distinct marine records of terrigenous dust flux. Our method enables us to identify three epochs with transitions between qualitatively different types of environmental variability in North and East Africa during the (i) Middle Pliocene (3.35-3.15 Ma B. P.), (ii) Early Pleistocene (2.25-1.6 Ma B. P.), and (iii) Middle Pleistocene (1.1-0.7 Ma B. P.). A deeper examination of these transition periods reveals potential climatic drivers, including (i) large-scale changes in ocean currents due to a spatial shift of the Indonesian throughflow in combination with an intensification of Northern Hemisphere glaciation, (ii) a global reorganization of the atmospheric Walker circulation induced in the tropical Pacific and Indian Ocean, and (iii) shifts in the dominating temporal variability pattern of glacial activity during the Middle Pleistocene, respectively. A reexamination of the available fossil record demonstrates statistically significant coincidences between the detected transition periods and major steps in hominin evolution. This result suggests that the observed shifts between more regular and more erratic environmental variability may have acted as a trigger for rapid change in the development of humankind in Africa.
The South American Andes are frequently exposed to intense rainfall events with varying moisture sources and precipitation-forming processes. In this study, we assess the spatiotemporal characteristics and geographical origins of rainfall over the South American continent. Using high-spatiotemporal resolution satellite data (TRMM 3B42 V7), we define four different types of rainfall events based on their (1) high magnitude, (2) long temporal extent, (3) large spatial extent, and (4) high magnitude, long temporal and large spatial extent combined. In a first step, we analyze the spatiotemporal characteristics of these events over the entire South American continent and integrate their impact for the main Andean hydrologic catchments. Our results indicate that events of type 1 make the overall highest contributions to total seasonal rainfall (up to 50%). However, each consecutive episode of the infrequent events of type 4 still accounts for up to 20% of total seasonal rainfall in the subtropical Argentinean plains. In a second step, we employ complex network theory to unravel possibly non-linear and long-ranged climatic linkages for these four event types on the high-elevation Altiplano-Puna Plateau as well as in the main river catchments along the foothills of the Andes. Our results suggest that one to two particularly large squall lines per season, originating from northern Brazil, indirectly trigger large, long-lasting thunderstorms on the Altiplano Plateau. In general, we observe that extreme rainfall in the catchments north of approximately 20 degrees S typically originates from the Amazon Basin, while extreme rainfall at the eastern Andean foothills south of 20 degrees S and the Puna Plateau originates from southeastern South America.
Non-linear time series analysis of precipitation events using regional climate networks for Germany
(2016)
Synchronous occurrences of heavy rainfall events and the study of their relation in time and space are of large socio-economical relevance, for instance for the agricultural and insurance sectors, but also for the general well-being of the population. In this study, the spatial synchronization structure is analyzed as a regional climate network constructed from precipitation event series. The similarity between event series is determined by the number of synchronous occurrences. We propose a novel standardization of this number that results in synchronization scores which are not biased by the number of events in the respective time series. Additionally, we introduce a new version of the network measure directionality that measures the spatial directionality of weighted links by also taking account of the effects of the spatial embedding of the network. This measure provides an estimate of heavy precipitation isochrones by pointing out directions along which rainfall events synchronize. We propose a climatological interpretation of this measure in terms of propagating fronts or event traces and confirm it for Germany by comparing our results to known atmospheric circulation patterns.
Background: 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.
Spatiotemporal dynamics of the Calvin cycle multistationarity and symmetry breaking instabilities
(2011)
The possibility of controlling the Calvin cycle has paramount implications for increasing the production of biomass. Multistationarity, as a dynamical feature of systems, is the first obvious candidate whose control could find biotechnological applications. Here we set out to resolve the debate on the multistationarity of the Calvin cycle. Unlike the existing simulation-based studies, our approach is based on a sound mathematical framework, chemical reaction network theory and algebraic geometry, which results in provable results for the investigated model of the Calvin cycle in which we embed a hierarchy of realistic kinetic laws. Our theoretical findings demonstrate that there is a possibility for multistationarity resulting from two sources, homogeneous and inhomogeneous instabilities, which partially settle the debate on multistability of the Calvin cycle. In addition, our tractable analytical treatment of the bifurcation parameters can be employed in the design of validation experiments.
Identifying causal links (couplings) is a fundamental problem that facilitates the understanding of emerging structures in complex networks. We propose and analyze inner composition alignment-a novel, permutation-based asymmetric association measure to detect regulatory links from very short time series, currently applied to gene expression. The measure can be used to infer the direction of couplings, detect indirect (superfluous) links, and account for autoregulation. Applications to the gene regulatory network of E. coli are presented.
The analysis of palaeoclimate time series is usually affected by severe methodological problems, resulting primarily from non-equidistant sampling and uncertain age models. As an alternative to existing methods of time series analysis, in this paper we argue that the statistical properties of recurrence networks - a recently developed approach - are promising candidates for characterising the system's nonlinear dynamics and quantifying structural changes in its reconstructed phase space as time evolves. In a first order approximation, the results of recurrence network analysis are invariant to changes in the age model and are not directly affected by non-equidistant sampling of the data. Specifically, we investigate the behaviour of recurrence network measures for both paradigmatic model systems with non-stationary parameters and four marine records of long-term palaeoclimate variations. We show that the obtained results are qualitatively robust under changes of the relevant parameters of our method, including detrending, size of the running window used for analysis, and embedding delay. We demonstrate that recurrence network analysis is able to detect relevant regime shifts in synthetic data as well as in problematic geoscientific time series. This suggests its application as a general exploratory tool of time series analysis complementing existing methods.