Dataset Information

Detecting dynamic spatial correlation patterns with generalized wavelet coherence and non-stationary surrogate data.

ABSTRACT: Time series measured from real-world systems are generally noisy, complex and display statistical properties that evolve continuously over time. Here, we present a method that combines wavelet analysis and non-stationary surrogates to detect short-lived spatial coherent patterns from multivariate time-series. In contrast with standard methods, the surrogate data proposed here are realisations of a non-stationary stochastic process, preserving both the amplitude and time-frequency distributions of original data. We evaluate this framework on synthetic and real-world time series, and we show that it can provide useful insights into the time-resolved structure of spatially extended systems.

SUBMITTER: Chavez M

PROVIDER: S-EPMC6517435 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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Publications

Detecting dynamic spatial correlation patterns with generalized wavelet coherence and non-stationary surrogate data.

Chavez Mario M Cazelles Bernard B

Scientific reports 20190514 1

Time series measured from real-world systems are generally noisy, complex and display statistical properties that evolve continuously over time. Here, we present a method that combines wavelet analysis and non-stationary surrogates to detect short-lived spatial coherent patterns from multivariate time-series. In contrast with standard methods, the surrogate data proposed here are realisations of a non-stationary stochastic process, preserving both the amplitude and time-frequency distributions o ...[more]

PMID: 31089157

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Project description:MotivationSolenoid proteins are emerging as a protein class with properties intermediate between structured and intrinsically unstructured proteins. Containing repeating structural units, solenoid proteins are expected to share sequence similarities. However, in many cases, the sequence similarities are weak and non-detectable. Moreover, solenoids can be degenerated and widely vary in the number of units. So that it is difficult to detect them. Recently, several solenoid repeats detection methods have been proposed, such as self-alignment of the sequence, spectral analysis and discrete Fourier transform of sequence. Although these methods have shown good performance on certain data sets, they often fail to detect repeats with weak similarities. In this article, we propose a new approach to recognize solenoid repeats and non-solenoid proteins using stationary wavelet packet transform (SWPT). Our method associates with three advantages: (i) naturally representing five main factors of protein structure and properties by wavelet analysis technique; (ii) extracting novel wavelet features that can capture hidden components from solenoid sequence similarities and distinguish them from global proteins; (iii) obtaining statistics features that capture repeating motifs of solenoid proteins.ResultsOur method analyzes the characteristics of amino acid sequence in both spectral and temporal domains using SWPT. Both global and local information of proteins are captured by SWPT coefficients. We obtain and integrate wavelet-based features and statistics-based features of amino acid sequence to improve the classification task. Our proposed method is evaluated by comparing to state-of-the-art methods such as HHrepID and REPETITA. The experimental results show that our algorithm consistently outperforms them in areas under ROC curve. At the same false positive rate, the sensitivity of our WAVELET method is higher than other methods.Availabilityhttp://www.naaan.org/anvo/Software/Software.htm.

Dataset Information

Detecting dynamic spatial correlation patterns with generalized wavelet coherence and non-stationary surrogate data.

Publications

Detecting dynamic spatial correlation patterns with generalized wavelet coherence and non-stationary surrogate data.

Similar Datasets

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