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Subject: methodology × WGL Institute: PIK ×

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Now showing 1 - 4 of 4
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    Topological data analysis of contagion maps for examining spreading processes on networks
    ([London] : Nature Publishing Group UK, 2015) Taylor, Dane; Klimm, Florian; Harrington, Heather A.; Kramár, Miroslav; Mischaikow, Konstantin; Porter, Mason A.; Mucha, Peter J.
    Social and biological contagions are influenced by the spatial embeddedness of networks. Historically, many epidemics spread as a wave across part of the Earth’s surface; however, in modern contagions long-range edges—for example, due to airline transportation or communication media—allow clusters of a contagion to appear in distant locations. Here we study the spread of contagions on networks through a methodology grounded in topological data analysis and nonlinear dimension reduction. We construct ‘contagion maps’ that use multiple contagions on a network to map the nodes as a point cloud. By analysing the topology, geometry and dimensionality of manifold structure in such point clouds, we reveal insights to aid in the modelling, forecast and control of spreading processes. Our approach highlights contagion maps also as a viable tool for inferring low-dimensional structure in networks.
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    Partial cross mapping eliminates indirect causal influences
    ([London] : Nature Publishing Group UK, 2020) Leng, Siyang; Ma, Huanfei; Kurths, Jürgen; Lai, Ying-Cheng; Lin, Wei; Aihara, Kazuyuki; Chen, Luonan
    Causality detection likely misidentifies indirect causations as direct ones, due to the effect of causation transitivity. Although several methods in traditional frameworks have been proposed to avoid such misinterpretations, there still is a lack of feasible methods for identifying direct causations from indirect ones in the challenging situation where the variables of the underlying dynamical system are non-separable and weakly or moderately interacting. Here, we solve this problem by developing a data-based, model-independent method of partial cross mapping based on an articulated integration of three tools from nonlinear dynamics and statistics: phase-space reconstruction, mutual cross mapping, and partial correlation. We demonstrate our method by using data from different representative models and real-world systems. As direct causations are keys to the fundamental underpinnings of a variety of complex dynamics, we anticipate our method to be indispensable in unlocking and deciphering the inner mechanisms of real systems in diverse disciplines from data.
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    The complexity of gene expression dynamics revealed by permutation entropy
    (London : BioMed Central Ltd., 2010) Sun, Xiaoliang; Zou, Yong; Nikiforova, Victoria; Kurths, Jürgen; Walther, Dirk
    Background: High complexity is considered a hallmark of living systems. Here we investigate the complexity of temporal gene expression patterns using the concept of Permutation Entropy (PE) first introduced in dynamical systems theory. The analysis of gene expression data has so far focused primarily on the identification of differentially expressed genes, or on the elucidation of pathway and regulatory relationships. We aim to study gene expression time series data from the viewpoint of complexity.Results: Applying the PE complexity metric to abiotic stress response time series data in Arabidopsis thaliana, genes involved in stress response and signaling were found to be associated with the highest complexity not only under stress, but surprisingly, also under reference, non-stress conditions. Genes with house-keeping functions exhibited lower PE complexity. Compared to reference conditions, the PE of temporal gene expression patterns generally increased upon stress exposure. High-complexity genes were found to have longer upstream intergenic regions and more cis-regulatory motifs in their promoter regions indicative of a more complex regulatory apparatus needed to orchestrate their expression, and to be associated with higher correlation network connectivity degree. Arabidopsis genes also present in other plant species were observed to exhibit decreased PE complexity compared to Arabidopsis specific genes.Conclusions: We show that Permutation Entropy is a simple yet robust and powerful approach to identify temporal gene expression profiles of varying complexity that is equally applicable to other types of molecular profile data.
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    Correlating the ancient Maya and modern european calendars with high-precision AMS 14C dating
    (London : Nature Publishing Group, 2013) Kennett, D.J.; Hajdas, I.; Culleton, B.J.; Belmecheri, S.; Martin, S.; Neff, H.; Awe, J.; Graham, H.V.; Freeman, K.H.; Newsom, L.; Lentz, D.L.; Anselmetti, F.S.; Robinson, M.; Marwan, N.; Southon, J.; Hodell, D.A.; Haug, G.H.
    The reasons for the development and collapse of Maya civilization remain controversial and historical events carved on stone monuments throughout this region provide a remarkable source of data about the rise and fall of these complex polities. Use of these records depends on correlating the Maya and European calendars so that they can be compared with climate and environmental datasets. Correlation constants can vary up to 1000 years and remain controversial.Wereport a series of high-resolution AMS14C dates on a wooden lintel collected from the Classic Period city of Tikal bearing Maya calendar dates. The radiocarbon dates were calibrated using a Bayesian statistical model and indicate that the dates were carved on the lintel betweenAD 658-696. This strongly supports the Goodman-Mart?nez-Thompson (GMT) correlation and the hypothesis that climate change played an important role in the development and demise of this complex civilization.