TY - GEN A1 - Hempel, Sabrina A1 - Koseska, Aneta A1 - Nikoloski, Zoran A1 - Kurths, Jürgen T1 - Unraveling gene regulatory networks from time-resolved gene expression data BT - a measures comparison study N2 - 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 371 KW - unferring cellular networks KW - mutual information KW - Escherichia-coli KW - cluster-analysis KW - series KW - algorithms KW - inference KW - models KW - recognition KW - variables Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-400924 ER - TY - JOUR A1 - Ramos, Antonio M. T. A1 - Builes-Jaramillo, Alejandro A1 - Poveda, German A1 - Goswami, Bedartha A1 - Macau, Elbert E. N. A1 - Kurths, Jürgen A1 - Marwan, Norbert T1 - Recurrence measure of conditional dependence and applications JF - Physical review : E, Statistical, nonlinear and soft matter physics N2 - Identifying causal relations from observational data sets has posed great challenges in data-driven causality inference studies. One of the successful approaches to detect direct coupling in the information theory framework is transfer entropy. However, the core of entropy-based tools lies on the probability estimation of the underlying variables. Herewe propose a data-driven approach for causality inference that incorporates recurrence plot features into the framework of information theory. We define it as the recurrence measure of conditional dependence (RMCD), and we present some applications. The RMCD quantifies the causal dependence between two processes based on joint recurrence patterns between the past of the possible driver and present of the potentially driven, excepting the contribution of the contemporaneous past of the driven variable. Finally, it can unveil the time scale of the influence of the sea-surface temperature of the Pacific Ocean on the precipitation in the Amazonia during recent major droughts. Y1 - 2017 U6 - https://doi.org/10.1103/PhysRevE.95.052206 SN - 2470-0045 SN - 2470-0053 VL - 95 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Marwan, Norbert A1 - Kurths, Jürgen T1 - Line structures in recurrence plots N2 - Recurrence plots exhibit line structures which represent typical behaviour of the investigated system. The local slope of these line structures is connected with a specific transformation of the time scales of different segments of the phase-space trajectory. This provides us a better understanding of the structures occurring in recurrence plots. The relationship between the time-scales and line structures are of practical importance in cross recurrence plots. Using this relationship within cross recurrence plots, the time-scales of differently sampled or time- transformed measurements can be adjusted. An application to geophysical measurements illustrates the capability of this method for the adjustment of time-scales in different measurements. (C) 2005 Elsevier B.V. All rights reserved Y1 - 2005 SN - 0375-9601 ER - TY - JOUR A1 - Marwan, Norbert A1 - Trauth, Martin H. A1 - Vuille, Mathias A1 - Kurths, Jürgen T1 - Comparing modern and Pleistocene ENSO-like influences in NW Argentina using nonlinear time series analysis methods N2 - Higher variability in rainfall and river discharge could be of major importance in landslide generation in the north-western Argentine Andes. Annual layered (varved) deposits of a landslide dammed lake in the Santa Maria Basin (26°S, 66°W) with an age of 30,000 14C years provide an archive of precipitation variability during this time. The comparison of these data with present-day rainfall observations tests the hypothesis that increased rainfall variability played a major role in landslide generation. A potential cause of such variability is the El Niño/ Southern Oscillation (ENSO). The causal link between ENSO and local rainfall is quantified by using a new method of nonlinear data analysis, the quantitative analysis of cross recurrence plots (CRP). This method seeks similarities in the dynamics of two different processes, such as an ocean-atmosphere oscillation and local rainfall. Our analysis reveals significant similarities in the statistics of both modern and palaeo-precipitation data. The similarities in the data suggest that an ENSO-like influence on local rainfall was present at around 30,000 14C years ago. Increased rainfall, which was inferred from a lake balance modeling in a previous study, together with ENSO-like cyclicities could help to explain the clustering of landslides at around 30,000 14C years ago. Y1 - 2003 UR - http://arxiv.org/abs/nlin.CD/0303056 ER - TY - JOUR A1 - Marwan, Norbert A1 - Wessel, Niels A1 - Meyerfeldt, Udo A1 - Schirdewan, Alexander A1 - Kurths, Jürgen T1 - Recurrence-plot-based measures of complexity and its application to heart-rate-variability data N2 - The knowledge of transitions between regular, laminar or chaotic behavior is essential to understand the underlying mechanisms behind complex systems. While several linear approaches are often insufficient to describe such processes, there are several nonlinear methods which however require rather long time observations. To overcome these difficulties, we propose measures of complexity based on vertical structures in recurrence plots and apply them to the logistic map as well as to heart rate variability data. For the logistic map these measures enable us not only to detect transitions between chaotic and periodic states, but also to identify laminar states, i.e. chaos-chaos transitions. The traditional recurrence quantification analysis fails to detect the latter transitions. Applying our new measures to the heart rate variability data, we are able to detect and quantify the laminar phases before a life-threatening cardiac arrhythmia occurs thereby facilitating a prediction of such an event. Our findings could be of importance for the therapy of malignant cardiac arrhythmias. Y1 - 2002 UR - http://arxiv.org/abs/physics/0201064 ER - TY - JOUR A1 - Donges, Jonathan A1 - Donner, Reik Volker A1 - Trauth, Martin H. A1 - Marwan, Norbert A1 - Schellnhuber, Hans Joachim A1 - Kurths, Jürgen T1 - Nonlinear detection of paleoclimate-variability transitions possibly related to human evolution JF - Proceedings of the National Academy of Sciences of the United States of America N2 - 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. KW - African climate KW - Plio-Pleistocene KW - climate-driven evolution KW - dynamical transitions KW - nonlinear time series analysis Y1 - 2011 U6 - https://doi.org/10.1073/pnas.1117052108 SN - 0027-8424 VL - 108 IS - 51 SP - 20422 EP - 20427 PB - National Acad. of Sciences CY - Washington ER - TY - JOUR A1 - Donges, Jonathan A1 - Zou, Yong A1 - Marwan, Norbert A1 - Kurths, Jürgen T1 - Complex networks in climate dynamics : comparing linear and nonlinear network construction methods N2 - Complex network theory provides a powerful framework to statistically investigate the topology of local and non- local statistical interrelationships, i.e. teleconnections, in the climate system. Climate networks constructed from the same global climatological data set using the linear Pearson correlation coefficient or the nonlinear mutual information as a measure of dynamical similarity between regions, are compared systematically on local, mesoscopic and global topological scales. A high degree of similarity is observed on the local and mesoscopic topological scales for surface air temperature fields taken from AOGCM and reanalysis data sets. We find larger differences on the global scale, particularly in the betweenness centrality field. The global scale view on climate networks obtained using mutual information offers promising new perspectives for detecting network structures based on nonlinear physical processes in the climate system. Y1 - 2009 UR - http://www.springerlink.com/content/1951-6355 U6 - https://doi.org/10.1140/epjst/e2009-01098-2 SN - 1951-6355 ER - TY - INPR A1 - Engbert, Ralf A1 - Scheffczyk, Christian A1 - Krampe, Ralf-Thomas A1 - Rosenblum, Mikhael A1 - Kurths, Jürgen A1 - Kliegl, Reinhold T1 - Tempo-induced transitions in polyrhythmic hand movements N2 - We investigate the cognitive control in polyrhythmic hand movements as a model paradigm for bimanual coordination. Using a symbolic coding of the recorded time series, we demonstrate the existence of qualitative transitions induced by experimental manipulation of the tempo. A nonlinear model with delayed feedback control is proposed, which accounts for these dynamical transitions in terms of bifurcations resulting from variation of the external control parameter. Furthermore, it is shown that transitions can also be observed due to fluctuations in the timing control level. We conclude that the complexity of coordinated bimanual movements results from interactions between nonlinear control mechanisms with delayed feedback and stochastic timing components. T3 - NLD Preprints - 41 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-14380 ER - TY - GEN A1 - Thiel, Marco A1 - Romano, Maria Carmen A1 - Kurths, Jürgen A1 - Rolfs, Martin A1 - Kliegl, Reinhold T1 - Generating Surrogates from Recurrences N2 - In this paper we present an approach to recover the dynamics from recurrences of a system and then generate (multivariate) twin surrogate (TS) trajectories. In contrast to other approaches, such as the linear-like surrogates, this technique produces surrogates which correspond to an independent copy of the underlying system, i. e. they induce a trajectory of the underlying system visiting the attractor in a different way. We show that these surrogates are well suited to test for complex synchronization, which makes it possible to systematically assess the reliability of synchronization analyses. We then apply the TS to study binocular fixational movements and find strong indications that the fixational movements of the left and right eye are phase synchronized. This result indicates that there might be one centre only in the brain that produces the fixational movements in both eyes or a close link between two centres. T3 - Zweitveröffentlichungen der Universität Potsdam : Humanwissenschaftliche Reihe - paper 238 KW - Æ Recurrence Plots KW - Surrogate Data KW - Hypothesis Test KW - Phase Synchronization Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-56906 ER - TY - JOUR A1 - Scheffczyk, Christian A1 - Engbert, Ralf A1 - Kurths, Jürgen A1 - Krampe, Ralf-Thomas A1 - Kliegl, Reinhold T1 - Nonlinear Phenomena in Polyrhythmic Hand Movements N2 - In this paper we apply symbolic transformations as a visualisation technique for analysing rhythm production. It is shown that qualitative information can be extracted from the experimental data. This approach may provide new insights into the organisation of temporal order by the brain on different levels of description. A simple phenomenological model for the explanation of the observed phenomena is proposed. Y1 - 1995 SN - 981-02-2689-6 ER -