Recurrence networks - A novel paradigm for nonlinear time series analysis

This paper presents a new approach for analysing structural properties of time series from complex systems. Starting from the concept of recurrences in phase space, the recurrence matrix of a time series is interpreted as the adjacency matrix of an associated complex network which links different points in time if the evolution of the considered states is very similar. A critical comparison of these recurrence networks with similar existing techniques is presented, revealing strong conceptual benefits of the new approach which can be considered as a unifying framework for transforming time series into complex networks that also includes other methods as special cases. It is demonstrated that there are fundamental relationships between the topological properties of recurrence networks and the statistical properties of the phase space density of the underlying dynamical system. Hence, the network description yields new quantitative characteristics of the dynamical complexity of a time series, which substantially complement existing measures of recurrence quantification analysis

Networks with time structure from time series

We propose a method of constructing a network, in which its time structure is directly incorporated, based on a deterministic model from a time series. To construct such a network, we transform a linear model containing terms with different time delays into network topology. The terms in the model are translated into temporal nodes of the network. On each link connecting these nodes, we assign a positive real number representing the strength of relationship, or the "distance," between nodes specified by the parameters of the model. The method is demonstrated by a known system and applied to two actual time series.Comment: 15 pages, 5 figures, accepted to be published in Physica

Recurrence-based time series analysis by means of complex network methods

Complex networks are an important paradigm of modern complex systems sciences which allows quantitatively assessing the structural properties of systems composed of different interacting entities. During the last years, intensive efforts have been spent on applying network-based concepts also for the analysis of dynamically relevant higher-order statistical properties of time series. Notably, many corresponding approaches are closely related with the concept of recurrence in phase space. In this paper, we review recent methodological advances in time series analysis based on complex networks, with a special emphasis on methods founded on recurrence plots. The potentials and limitations of the individual methods are discussed and illustrated for paradigmatic examples of dynamical systems as well as for real-world time series. Complex network measures are shown to provide information about structural features of dynamical systems that are complementary to those characterized by other methods of time series analysis and, hence, substantially enrich the knowledge gathered from other existing (linear as well as nonlinear) approaches.Comment: To be published in International Journal of Bifurcation and Chaos (2011

Ambiguities in recurrence-based complex network representations of time series

Recently, different approaches have been proposed for studying basic properties of time series from a complex network perspective. In this work, the corresponding potentials and limitations of networks based on recurrences in phase space are investigated in some detail. We discuss the main requirements that permit a feasible system-theoretic interpretation of network topology in terms of dynamically invariant phase-space properties. Possible artifacts induced by disregarding these requirements are pointed out and systematically studied. Finally, a rigorous interpretation of the clustering coefficient and the betweenness centrality in terms of invariant objects is proposed

Horizontal visibility graphs transformed from fractional Brownian motions: Topological properties versus Hurst index

Nonlinear time series analysis aims at understanding the dynamics of stochastic or chaotic processes. In recent years, quite a few methods have been proposed to transform a single time series to a complex network so that the dynamics of the process can be understood by investigating the topological properties of the network. We study the topological properties of horizontal visibility graphs constructed from fractional Brownian motions with different Hurst index $H\in(0,1)$. Special attention has been paid to the impact of Hurst index on the topological properties. It is found that the clustering coefficient $C$ decreases when $H$ increases. We also found that the mean length $L$ of the shortest paths increases exponentially with $H$ for fixed length $N$ of the original time series. In addition, $L$ increases linearly with respect to $N$ when $H$ is close to 1 and in a logarithmic form when $H$ is close to 0. Although the occurrence of different motifs changes with $H$, the motif rank pattern remains unchanged for different $H$. Adopting the node-covering box-counting method, the horizontal visibility graphs are found to be fractals and the fractal dimension $d_B$ decreases with $H$. Furthermore, the Pearson coefficients of the networks are positive and the degree-degree correlations increase with the degree, which indicate that the horizontal visibility graphs are assortative. With the increase of $H$, the Pearson coefficient decreases first and then increases, in which the turning point is around $H=0.6$. The presence of both fractality and assortativity in the horizontal visibility graphs converted from fractional Brownian motions is different from many cases where fractal networks are usually disassortative.Comment: 12 pages, 8 figure

Beyond element-wise interactions: identifying complex interactions in biological processes

Background: Biological processes typically involve the interactions of a number of elements (genes, cells) acting on each others. Such processes are often modelled as networks whose nodes are the elements in question and edges pairwise relations between them (transcription, inhibition). But more often than not, elements actually work cooperatively or competitively to achieve a task. Or an element can act on the interaction between two others, as in the case of an enzyme controlling a reaction rate. We call “complex” these types of interaction and propose ways to identify them from time-series observations. Methodology: We use Granger Causality, a measure of the interaction between two signals, to characterize the influence of an enzyme on a reaction rate. We extend its traditional formulation to the case of multi-dimensional signals in order to capture group interactions, and not only element interactions. Our method is extensively tested on simulated data and applied to three biological datasets: microarray data of the Saccharomyces cerevisiae yeast, local field potential recordings of two brain areas and a metabolic reaction. Conclusions: Our results demonstrate that complex Granger causality can reveal new types of relation between signals and is particularly suited to biological data. Our approach raises some fundamental issues of the systems biology approach since finding all complex causalities (interactions) is an NP hard problem