Dataset Information

Finding Structure in Time: Visualizing and Analyzing Behavioral Time Series.

ABSTRACT: The temporal structure of behavior contains a rich source of information about its dynamic organization, origins, and development. Today, advances in sensing and data storage allow researchers to collect multiple dimensions of behavioral data at a fine temporal scale both in and out of the laboratory, leading to the curation of massive multimodal corpora of behavior. However, along with these new opportunities come new challenges. Theories are often underspecified as to the exact nature of these unfolding interactions, and psychologists have limited ready-to-use methods and training for quantifying structures and patterns in behavioral time series. In this paper, we will introduce four techniques to interpret and analyze high-density multi-modal behavior data, namely, to: (1) visualize the raw time series, (2) describe the overall distributional structure of temporal events (Burstiness calculation), (3) characterize the non-linear dynamics over multiple timescales with Chromatic and Anisotropic Cross-Recurrence Quantification Analysis (CRQA), (4) and quantify the directional relations among a set of interdependent multimodal behavioral variables with Granger Causality. Each technique is introduced in a module with conceptual background, sample data drawn from empirical studies and ready-to-use Matlab scripts. The code modules showcase each technique's application with detailed documentation to allow more advanced users to adapt them to their own datasets. Additionally, to make our modules more accessible to beginner programmers, we provide a "Programming Basics" module that introduces common functions for working with behavioral timeseries data in Matlab. Together, the materials provide a practical introduction to a range of analyses that psychologists can use to discover temporal structure in high-density behavioral data.

SUBMITTER: Xu TL

PROVIDER: S-EPMC7393268 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Publications

Finding Structure in Time: Visualizing and Analyzing Behavioral Time Series.

Xu Tian Linger TL de Barbaro Kaya K Abney Drew H DH Cox Ralf F A RFA

Frontiers in psychology 20200724

The temporal structure of behavior contains a rich source of information about its dynamic organization, origins, and development. Today, advances in sensing and data storage allow researchers to collect multiple dimensions of behavioral data at a fine temporal scale both in and out of the laboratory, leading to the curation of massive multimodal corpora of behavior. However, along with these new opportunities come new challenges. Theories are often underspecified as to the exact nature of these ...[more]

PMID: 32793025

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Project description:The ability to monitor the change in expression patterns over time, and to observe the emergence of coherent temporal responses using gene expression time series, obtained from microarray experiments, is critical to advance our understanding of complex biological processes. In this context, biclustering algorithms have been recognized as an important tool for the discovery of local expression patterns, which are crucial to unravel potential regulatory mechanisms. Although most formulations of the biclustering problem are NP-hard, when working with time series expression data the interesting biclusters can be restricted to those with contiguous columns. This restriction leads to a tractable problem and enables the design of efficient biclustering algorithms able to identify all maximal contiguous column coherent biclusters.In this work, we propose e-CCC-Biclustering, a biclustering algorithm that finds and reports all maximal contiguous column coherent biclusters with approximate expression patterns in time polynomial in the size of the time series gene expression matrix. This polynomial time complexity is achieved by manipulating a discretized version of the original matrix using efficient string processing techniques. We also propose extensions to deal with missing values, discover anticorrelated and scaled expression patterns, and different ways to compute the errors allowed in the expression patterns. We propose a scoring criterion combining the statistical significance of expression patterns with a similarity measure between overlapping biclusters.We present results in real data showing the effectiveness of e-CCC-Biclustering and its relevance in the discovery of regulatory modules describing the transcriptomic expression patterns occurring in Saccharomyces cerevisiae in response to heat stress. In particular, the results show the advantage of considering approximate patterns when compared to state of the art methods that require exact matching of gene expression time series.The identification of co-regulated genes, involved in specific biological processes, remains one of the main avenues open to researchers studying gene regulatory networks. The ability of the proposed methodology to efficiently identify sets of genes with similar expression patterns is shown to be instrumental in the discovery of relevant biological phenomena, leading to more convincing evidence of specific regulatory mechanisms.A prototype implementation of the algorithm coded in Java together with the dataset and examples used in the paper is available in http://kdbio.inesc-id.pt/software/e-ccc-biclustering.

Dataset Information

Finding Structure in Time: Visualizing and Analyzing Behavioral Time Series.

Publications

Finding Structure in Time: Visualizing and Analyzing Behavioral Time Series.

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