‡We describe the use of singular value decomposition in transforming genome-wide expression data from genes 3 arrays space to reduced diagonalized ‘‘eigengenes’’ 3 ‘‘eigenarrays’’ space, where the eigengenes (or eigenarrays) are unique orthonormal superpositions of the genes (or arrays). Normalizing the data by filtering out the eigengenes (and eigenarrays) that are inferred to represent noise or experimental artifacts enables meaningful comparison of the expression of different genes across different arrays in different experiments. Sorting the data according to the eigengenes and eigenarrays gives a global picture of the dynamics of gene expression, in which individual genes and arrays appear to be classified into groups of similar regulation and function, or similar cellular state and biological phenotype, respectively. After normalization and sorting, the significant eigengenes and eigenarrays can be associated with observed genome-wide effects of regulators, or with measured samples, in which these regulators are overactive or underactive, respectively.

Singular Value Decomposition for Genome-Wide Expression Data Processing and Modeling

: This thesis applies neural network feature selection techniques to multivariate time series data to improve prediction of a target time series. Two approaches to feature selection are used. First, a subset enumeration method is used to determine which financial indicators are most useful for aiding in prediction of the S&P 500 futures daily price. The candidate indicators evaluated include RSI, Stochastics and several moving averages. Results indicate that the Stochastics and RSI indicators result in better prediction results than the moving averages. The second approach to feature selection is calculation of individual saliency metrics. A new decision boundary-based individual saliency metric, and a classifier independent saliency metric are developed and tested. Ruck's saliency metric, the decision boundary based saliency metric, and the classifier independent saliency metric are compared for a data set consisting of the RSI and Stochastics indicators as well as delayed closing price values. The decision based metric and the Ruck metric results are similar, but the classifier independent metric agrees with neither of the other metrics. The nine most salient features, determined by the decision boundary based metric, are used to train a neural network and the results are presented and compared to other published results. (AN)

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Nonlinear Time Series Analysis.

Since the early 1980s, short-term traffic forecasting has been an integral part of most Intelligent Transportation Systems (ITS) research and applications; most effort has gone into developing methodologies that can be used to model traffic characteristics and produce anticipated traffic conditions. Existing literature is voluminous, and has largely used single point data from motorways and has employed univariate mathematical models to predict traffic volumes or travel times. Recent developments in technology and the widespread use of powerful computers and mathematical models allow researchers an unprecedented opportunity to expand horizons and direct work in 10 challenging, yet relatively under researched, directions. It is these existing challenges that we review in this paper and offer suggestions for future work.

Short-term traffic forecasting: Where we are and where we’re going

Part I. Examples and Fundamental Concepts Introduction 1. First examples 2. Equivalence, classification, and invariants 3. Principle classes of asymptotic invariants 4. Statistical behavior of the orbits and introduction to ergodic theory 5. Smooth invariant measures and more examples Part II. Local Analysis and Orbit Growth 6. Local hyperbolic theory and its applications 7. Transversality and genericity 8. Orbit growth arising from topology 9. Variational aspects of dynamics Part III. Low-Dimensional Phenomena 10. Introduction: What is low dimensional dynamics 11. Homeomorphisms of the circle 12. Circle diffeomorphisms 13. Twist maps 14. Flows on surfaces and related dynamical systems 15. Continuous maps of the interval 16. Smooth maps of the interval Part IV. Hyperbolic Dynamical Systems 17. Survey of examples 18. Topological properties of hyperbolic sets 19. Metric structure of hyperbolic sets 20. Equilibrium states and smooth invariant measures Part V. Sopplement and Appendix 21. Dynamical systems with nonuniformly hyperbolic behavior Anatole Katok and Leonardo Mendoza.

Introduction to the Modern Theory of Dynamical Systems: EQUILIBRIUM STATES AND SMOOTH INVARIANT MEASURES

/pdf/analysis-of-observed-chaotic-data-3spe9uweeb.pdf

Analysis of observed chaotic data

Multivariate multiscale sample entropy (MMSE) is a robust method to detect the complexity of multivariate system. It is evaluated for a certain value of tolerance parameter r which is mainly calculated from common acknowledged range. This kind of selection of r is not suitable for short-term time series and may lead to the unreliable detection. To reduce the impact of limited range of r, we apply cumulative histogram method to estimate the range of r. It is data-driven and needs no parameters. Moreover, we use secondary statistics, AvgMMSE and SDMMSE rather than the single value of MMSE to detect the complexity of signals and differentiate them. Several time series, either generated from chaotic or stochastic systems, are analyzed to demonstrate the approach. The core achievement of this experiment is the stability and classification for short-term time series. Then we apply this method to financial time series. Empirical results show that the proposed method is vigorous enough to classify different stock indices over different periods.

A new method for tolerance estimation of multivariate multiscale sample entropy and its application for short-term time series

The recognition of complex systems plays a vital role in system dynamics. To distinguish chaotic systems and stochastic processes, the complex-entropy causality plane (CECP) was proposed and received considerable attention. However, few methods have been applied to the identification of fractional order chaotic systems. In this paper, we propose multiscale multivariate fractional dispersion entropy (MMFDE) and MMFDE plane to study the structural complexity of multivariate nonlinear systems. Unlike the ordinal pattern in CECP, the dispersion pattern is used in MMFDE plane to solve the computational burden in fractional order systems. Moreover, the fractional order α in MMFDE can be used to adjust the ability of MMFDE plane to distinguish between different systems. Through simulation data, we find that the MMFDE plane can classify not only chaotic systems and stochastic processes but also different fractional order chaotic systems even if adding noise to the signals. It is then applied to financial time series and epileptic EEG recordings. The results show that the MMFDE plane can identify developed and emerging markets. For epileptic EEG recordings, both the EEG subbands and the original data without filtering can be used to distinguish different states of healthy subjects and patients with epilepsy. The coarse-graining process is also discussed to demonstrate the consequences further.

The identification of fractional order systems by multiscale multivariate analysis

This letter is devoted to the cross-correlation analysis of non-stationary multivariate data, in which the detrended cross-correlation matrix based on the detrended cross-correlation coefficient is studied. The relationship between Pearson's cross-correlation coefficient and the detrended cross-correlation coefficient is analyzed. As a special case of random matrix theory, the distribution of the eigenvalues of the detrended cross-correlation matrix for purely random variables is derived.

https://iopscience.iop.org/article/10.1209/0295-5075/107/40008/pdf

Distribution of eigenvalues of detrended cross-correlation matrix

In this paper, we propose the multiscale joint permutation entropy (MJPE) to study the synchronism between two complex time series from the view of ordinal pattern and multiple scales. First, we use the Rossler system using active control, two-component ARFIMA processes to test the effectiveness of MJPE and also add some noise to the ARFIMA time series and apply MJPE to find the effect of noise. The results show the necessity of investigating the synchronism on the multiple scales, prove the effectiveness of MJPE method and show the sensitiveness of MJPE method to noise. Then MJPE method is employed to financial time series and traffic time series to validate the applicability of the proposed MJPE method for the complex time series in the real world. The conclusion from these MJPE results for financial time series is consistent with the actual situation of the synchronism and correlation between stock indices. Meanwhile, the results for traffic time series suggest the need for study the synchronism from the perspective of multiple scales and point out the different synchronisms for traffic time series of weekdays and weekends. MJPE method has a broad application prospect on the investigation of synchronism on the complex time series from different fields.

Multiscale joint permutation entropy for complex time series

In this work, we analyze time series on the basis of the visibility graph algorithm that maps the original series into a graph. By taking into account the all-round information carried by the signals, the time irreversibility and fractal behavior of series are evaluated from a complex network perspective, and considered signals are further classified from different aspects. The reliability of the proposed analysis is supported by numerical simulations on synthesized uncorrelated random noise, short-term correlated chaotic systems and long-term correlated fractal processes, and by the empirical analysis on daily closing prices of eleven worldwide stock indices. Obtained results suggest that finite size has a significant effect on the evaluation, and that there might be no direct relation between the time irreversibility and long-range correlation of series. Similarity and dissimilarity between stock indices are also indicated from respective regional and global perspectives, showing the existence of multiple features of underlying systems.

Pengjian Shang

Papers

A new method for tolerance estimation of multivariate multiscale sample entropy and its application for short-term time series

The identification of fractional order systems by multiscale multivariate analysis

Distribution of eigenvalues of detrended cross-correlation matrix

Multiscale joint permutation entropy for complex time series

Time irreversibility and intrinsics revealing of series with complex network approach