scholarly journals Tracking changes in behavioural dynamics using prediction error

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0251053
Author(s):  
Tom Lorimer ◽  
Rachel Goodridge ◽  
Antonia K. Bock ◽  
Vitul Agarwal ◽  
Erik Saberski ◽  
...  
Keyword(s):  
Time Series ◽  
Escape Response ◽  
Prediction Error ◽  
Dimensional Space ◽  
Behavioural Change ◽  
Automated Analysis ◽  
High Time Resolution ◽  
Data Set ◽  
The Individual ◽  
Behavioural Dynamics

Automated analysis of video can now generate extensive time series of pose and motion in freely-moving organisms. This requires new quantitative tools to characterise behavioural dynamics. For the model roundworm Caenorhabditis elegans, body pose can be accurately quantified from video as coordinates in a single low-dimensional space. We focus on this well-established case as an illustrative example and propose a method to reveal subtle variations in behaviour at high time resolution. Our data-driven method, based on empirical dynamic modeling, quantifies behavioural change as prediction error with respect to a time-delay-embedded ‘attractor’ of behavioural dynamics. Because this attractor is constructed from a user-specified reference data set, the approach can be tailored to specific behaviours of interest at the individual or group level. We validate the approach by detecting small changes in the movement dynamics of C. elegans at the initiation and completion of delta turns. We then examine an escape response initiated by an aversive stimulus and find that the method can track return to baseline behaviour in individual worms and reveal variations in the escape response between worms. We suggest that this general approach—defining dynamic behaviours using reference attractors and quantifying dynamic changes using prediction error—may be of broad interest and relevance to behavioural researchers working with video-derived time series.

scholarly journals Tracking changes in behavioural dynamics using prediction error

2020 ◽  
Author(s):  
Tom Lorimer ◽  
Rachel Goodridge ◽  
Antonia K. Bock ◽  
Vitul Agarwal ◽  
Erik Saberski ◽  
...  
Keyword(s):  
Time Series ◽  
Escape Response ◽  
Prediction Error ◽  
Dimensional Space ◽  
Behavioural Change ◽  
Automated Analysis ◽  
High Time Resolution ◽  
Data Set ◽  
The Individual ◽  
Behavioural Dynamics

AbstractAutomated analysis of video can now generate extensive time series of pose and motion in freely-moving organisms. This requires new quantitative tools to characterize behavioural dynamics. For the model roundworm Caenorhabditis elegans, body pose can be accurately quantified from video as coordinates in a single low-dimensional space. We focus on this well-established case as an illustrative example and propose a method to reveal subtle variations in behaviour at high time resolution. Our data-driven method, based on empirical dynamic modeling, quantifies behavioural change as prediction error with respect to a time-delay-embedded ‘attractor’ of behavioural dynamics. Because this attractor is constructed from a user-specified reference data set, the approach can be tailored to specific behaviours of interest at the individual or group level. We validate the approach by detecting small changes in the movement dynamics of C. elegans at the initiation and completion of delta turns. We then examine an escape response initiated by an aversive stimulus and find that the method can track return to baseline behaviour in individual worms and reveal variations in the escape response between worms. We suggest that this general approach – defining dynamic behaviours using reference attractors and quantifying dynamic changes using prediction error – may be of broad interest and relevance to behavioural researchers working with video-derived time series.

scholarly journals Predicting Forest Cover in Distinct Ecosystems: The Potential of Multi-Source Sentinel-1 and -2 Data Fusion

2020 ◽  
Vol 12 (2) ◽  
pp. 302 ◽  
Author(s):  
Kai Heckel ◽  
Marcel Urban ◽  
Patrick Schratz ◽  
Miguel Mahecha ◽  
Christiane Schmullius
Keyword(s):  
South Africa ◽  
Time Series ◽  
Forest Cover ◽  
Short Wave ◽  
Optical Data ◽  
Biophysical Parameters ◽  
Data Set ◽  
Area Index ◽  
The Individual ◽  
Sentinel 2

The fusion of microwave and optical data sets is expected to provide great potential for the derivation of forest cover around the globe. As Sentinel-1 and Sentinel-2 are now both operating in twin mode, they can provide an unprecedented data source to build dense spatial and temporal high-resolution time series across a variety of wavelengths. This study investigates (i) the ability of the individual sensors and (ii) their joint potential to delineate forest cover for study sites in two highly varied landscapes located in Germany (temperate dense mixed forests) and South Africa (open savanna woody vegetation and forest plantations). We used multi-temporal Sentinel-1 and single time steps of Sentinel-2 data in combination to derive accurate forest/non-forest (FNF) information via machine-learning classifiers. The forest classification accuracies were 90.9% and 93.2% for South Africa and Thuringia, respectively, estimated while using autocorrelation corrected spatial cross-validation (CV) for the fused data set. Sentinel-1 only classifications provided the lowest overall accuracy of 87.5%, while Sentinel-2 based classifications led to higher accuracies of 91.9%. Sentinel-2 short-wave infrared (SWIR) channels, biophysical parameters (Leaf Area Index (LAI), and Fraction of Absorbed Photosynthetically Active Radiation (FAPAR)) and the lower spectrum of the Sentinel-1 synthetic aperture radar (SAR) time series were found to be most distinctive in the detection of forest cover. In contrast to homogenous forests sites, Sentinel-1 time series information improved forest cover predictions in open savanna-like environments with heterogeneous regional features. The presented approach proved to be robust and it displayed the benefit of fusing optical and SAR data at high spatial resolution.

scholarly journals The SPARC water vapour assessment II: Profile-to-profile comparisons of stratospheric and lower mesospheric water vapour data sets obtained from satellites

2018 ◽  
Author(s):  
Stefan Lossow ◽  
Farahnaz Khosrawi ◽  
Michael Kiefer ◽  
Kaley A. Walker ◽  
Jean-Loup Bertaux ◽  
...  
Keyword(s):  
Time Series ◽  
Water Vapour ◽  
Data Sets ◽  
General Behaviour ◽  
Data Set ◽  
Observational Database ◽  
Comparison Results ◽  
Wide Range ◽  
The Individual ◽  
Mean Time

Abstract. Within the framework of the second SPARC (Stratosphere-troposphere Processes And their Role in Climate) water vapour assessment (WAVAS-II), profile-to-profile comparisons of stratospheric and lower mesospheric water vapour were performed considering 33 data sets derived from satellite observations of 15 different instruments. These comparisons aimed to provide a picture of the typical biases and drifts in the observational database and to identify data set specific problems. The observational database typically exhibits the largest biases below 70 hPa, both in absolute and relative terms. The smallest biases are often found between 50 hPa and 5 hPa. Typically, they range from 0.25 ppmv to 0.5 ppmv (5 % to 10 %) in this altitude region, based on the 50 % percentile over the different comparison results. Higher up, the biases are overall increasing with altitude but this general behaviour is accompanied by considerable variations. Characteristic values vary between 0.3 ppmv and 1 ppmv (4 % to 20 %). Obvious data set specific bias issues are found for a number of data sets. In our work we performed a drift analysis for data sets overlapping for a period of at least 36 months. This assessment shows a wide range of drifts among the different data sets that are statistically significant at the 2σ uncertainty level. In general, the smallest drifts are found in the altitude range between about 30 hPa to 10 hPa. Histograms considering results from all altitudes indicate the largest occurrence for drifts between 0.05 ppmv decade−1 and 0.3 ppmv decade−1. Comparisons of our drift estimates to those derived from comparisons of zonal mean time series only exhibit statistically significant differences in slightly more than 3 % of the comparisons. Hence, drift estimates from profile-to-profile and zonal mean time series comparisons are largely interchangeable. Like for the biases, a number of data sets exhibit prominent drift issues. In our analyses we found that the large number of MIPAS data sets included in the assessment affects our general results as well as the bias summaries we provide for the individual data sets. This is because these data sets exhibit a relative similarity with respect to the remaining data sets, despite that they are based on different measurement modes and different processors implementing different retrieval choices. Because of that, we have by default considered an aggregation of the comparison results obtained from MIPAS data sets. Results without this aggregation are provided on multiple occasions to characterise the effects due to the numerous MIPAS data sets. Among other effects, they cause a reduction of the typical biases in the observational database.

scholarly journals The SPARC water vapour assessment II: profile-to-profile comparisons of stratospheric and lower mesospheric water vapour data sets obtained from satellites

2019 ◽  
Vol 12 (5) ◽  
pp. 2693-2732 ◽  
Author(s):  
Stefan Lossow ◽  
Farahnaz Khosrawi ◽  
Michael Kiefer ◽  
Kaley A. Walker ◽  
Jean-Loup Bertaux ◽  
...  
Keyword(s):  
Time Series ◽  
Water Vapour ◽  
Data Sets ◽  
General Behaviour ◽  
Data Set ◽  
Observational Database ◽  
Comparison Results ◽  
Wide Range ◽  
The Individual ◽  
Mean Time

Abstract. Within the framework of the second SPARC (Stratosphere-troposphere Processes And their Role in Climate) water vapour assessment (WAVAS-II), profile-to-profile comparisons of stratospheric and lower mesospheric water vapour were performed by considering 33 data sets derived from satellite observations of 15 different instruments. These comparisons aimed to provide a picture of the typical biases and drifts in the observational database and to identify data-set-specific problems. The observational database typically exhibits the largest biases below 70 hPa, both in absolute and relative terms. The smallest biases are often found between 50 and 5 hPa. Typically, they range from 0.25 to 0.5 ppmv (5 % to 10 %) in this altitude region, based on the 50 % percentile over the different comparison results. Higher up, the biases increase with altitude overall but this general behaviour is accompanied by considerable variations. Characteristic values vary between 0.3 and 1 ppmv (4 % to 20 %). Obvious data-set-specific bias issues are found for a number of data sets. In our work we performed a drift analysis for data sets overlapping for a period of at least 36 months. This assessment shows a wide range of drifts among the different data sets that are statistically significant at the 2σ uncertainty level. In general, the smallest drifts are found in the altitude range between about 30 and 10 hPa. Histograms considering results from all altitudes indicate the largest occurrence for drifts between 0.05 and 0.3 ppmv decade−1. Comparisons of our drift estimates to those derived from comparisons of zonal mean time series only exhibit statistically significant differences in slightly more than 3 % of the comparisons. Hence, drift estimates from profile-to-profile and zonal mean time series comparisons are largely interchangeable. As for the biases, a number of data sets exhibit prominent drift issues. In our analyses we found that the large number of MIPAS data sets included in the assessment affects our general results as well as the bias summaries we provide for the individual data sets. This is because these data sets exhibit a relative similarity with respect to the remaining data sets, despite the fact that they are based on different measurement modes and different processors implementing different retrieval choices. Because of that, we have by default considered an aggregation of the comparison results obtained from MIPAS data sets. Results without this aggregation are provided on multiple occasions to characterise the effects due to the numerous MIPAS data sets. Among other effects, they cause a reduction of the typical biases in the observational database.

scholarly journals Brain Density Clustering Analysis: A New Approach to Brain Functional Dynamics

2021 ◽  
Vol 15 ◽  
Author(s):  
Ashkan Faghiri ◽  
Eswar Damaraju ◽  
Aysenil Belger ◽  
Judith M. Ford ◽  
Daniel Mathalon ◽  
...  
Keyword(s):  
Time Series ◽  
Dimensional Space ◽  
Real Data ◽  
High Dimensional ◽  
Data Set ◽  
High Dimensional Space ◽  
New Approach ◽  
Oscillatory Pattern ◽  
Functional Dynamics ◽  
Novel Approach

BackgroundA number of studies in recent years have explored whole-brain dynamic connectivity using pairwise approaches. There has been less focus on trying to analyze brain dynamics in higher dimensions over time.MethodsWe introduce a new approach that analyzes time series trajectories to identify high traffic nodes in a high dimensional space. First, functional magnetic resonance imaging (fMRI) data are decomposed using spatial ICA to a set of maps and their associated time series. Next, density is calculated for each time point and high-density points are clustered to identify a small set of high traffic nodes. We validated our method using simulations and then implemented it on a real data set.ResultsWe present a novel approach that captures dynamics within a high dimensional space and also does not use any windowing in contrast to many existing approaches. The approach enables one to characterize and study the time series in a potentially high dimensional space, rather than looking at each component pair separately. Our results show that schizophrenia patients have a lower dynamism compared to healthy controls. In addition, we find patients spend more time in nodes associated with the default mode network and less time in components strongly correlated with auditory and sensorimotor regions. Interestingly, we also found that subjects oscillate between state pairs that show opposite spatial maps, suggesting an oscillatory pattern.ConclusionOur proposed method provides a novel approach to analyze the data in its native high dimensional space and can possibly provide new information that is undetectable using other methods.

Linear and Nonlinear Smooth Orthogonal Decomposition to Reconstruct Local Fatigue Dynamics: A Comparison

2010 ◽  
Author(s):  
David B. Segala ◽  
David Chelidze ◽  
Deanna Gates ◽  
Jonathan Dingwell
Keyword(s):  
Time Series ◽  
Muscle Fatigue ◽  
Power Spectra ◽  
Dimensional Subspace ◽  
Orthogonal Decomposition ◽  
Muscle Injuries ◽  
Data Set ◽  
Individual Muscle ◽  
The Individual ◽  
Smooth Orthogonal Decomposition

Identifying physiological fatigue is important for the development of more robust training protocols, better energy supplements, and/or reduction of muscle injuries. Current fatigue measurement technologies are usually invasive and/or impractical, and may not be realizable in out of laboratory settings. A fatigue identification methodology that only uses motion kinematics measurements has a great potential for field applications. Phase space warping (PSW) features of motion kinematic time series analyzed through smooth orthogonal decomposition (SOD) have tracked individual muscle fatigue. In this paper, the performance of a standard SOD analysis is compared to its nonlinear extension using a new experimental data set. Ten healthy right-handed subjects (27 ± 2.8 years; 1.71 ± 0.10 m height; and 69.91 ± 18.26 kg body mass) perform a sawing motion by pushing a weighted handle back and forth until voluntary exhaustion. Three sets of joint kinematic angles are measured from the elbow, wrist and shoulder as well as surface Electromyography (EMG) from ten different muscle groups. A vector-valued feature time series is generated using PSW metrics estimated from movement kinematics. Dominant SOD coordinates of these features are extracted to track the individual muscle fatigue trends as indicated by mean and median frequencies of the corresponding EMG power spectra. Cross subject variability shows that considerably fewer nonlinear SOD coordinates are needed to track EMG-based fatigue markers, and that nonlinear SOD methodology captures fatigue dynamics in a lower-dimensional subspace than its linear counterpart.

scholarly journals Bootstrapping and Empirical Bayes Methods Improve Rhythm Detection in Sparsely Sampled Data

2018 ◽  
Vol 33 (4) ◽  
pp. 339-349 ◽  
Author(s):  
Alan L. Hutchison ◽  
Ravi Allada ◽  
Aaron R. Dinner
Keyword(s):  
Time Series ◽  
Empirical Bayes ◽  
High Time Resolution ◽  
Periodic Patterns ◽  
Data Set ◽  
Bayes Methods ◽  
Genome Wide ◽  
Empirical Bayes Methods ◽  
Genome Wide Expression ◽  
Expression Time

There is much interest in using genome-wide expression time series to identify circadian genes. However, the cost and effort of such measurements often limit data collection. Consequently, it is difficult to assess the experimental uncertainty in the measurements and, in turn, to detect periodic patterns with statistical confidence. We show that parametric bootstrapping and empirical Bayes methods for variance shrinkage can improve rhythm detection in genome-wide expression time series. We demonstrate these approaches by building on the empirical JTK_CYCLE method (eJTK) to formulate a method that we term BooteJTK. Our procedure rapidly and accurately detects cycling time series by combining information about measurement uncertainty with information about the rank order of the time series values. We exploit a publicly available genome-wide data set with high time resolution to show that BooteJTK provides more consistent rhythm detection than existing methods at typical sampling frequencies. Then, we apply BooteJTK to genome-wide expression time series from multiple tissues and show that it reveals biologically sensible tissue relationships that eJTK misses. BooteJTK is implemented in Python and is freely available on GitHub at https://github.com/alanlhutchison/BooteJTK .

Algorithms for automated montage synthesis of images from laser-scanning confocal microscopes

1995 ◽  
Vol 53 ◽  
pp. 650-651
Author(s):  
D. E. Becker
Keyword(s):  
Image Analysis ◽  
High Resolution ◽  
Laser Scanning ◽  
Cell Counting ◽  
Wide Area ◽  
Data Set ◽  
Computational Synthesis ◽  
Automated Cell Counting ◽  
Partial View ◽  
The Individual

An efficient, robust, and widely-applicable technique is presented for computational synthesis of high-resolution, wide-area images of a specimen from a series of overlapping partial views. This technique can also be used to combine the results of various forms of image analysis, such as segmentation, automated cell counting, deblurring, and neuron tracing, to generate representations that are equivalent to processing the large wide-area image, rather than the individual partial views. This can be a first step towards quantitation of the higher-level tissue architecture. The computational approach overcomes mechanical limitations, such as hysterisis and backlash, of microscope stages. It also automates a procedure that is currently done manually. One application is the high-resolution visualization and/or quantitation of large batches of specimens that are much wider than the field of view of the microscope.The automated montage synthesis begins by computing a concise set of landmark points for each partial view. The type of landmarks used can vary greatly depending on the images of interest. In many cases, image analysis performed on each data set can provide useful landmarks. Even when no such “natural” landmarks are available, image processing can often provide useful landmarks.

EXTREME VALUES OF SEA SURFACE TEMPERATURE ASSOCIATED WITH LONG-PERIOD PHENOMENA OCCURRED DURING 1960-2015 IN THE COLOMBIAN PACIFIC OCEAN

2017 ◽  
Author(s):  
Diaz Juan Navia ◽  
Diaz Juan Navia ◽  
Bolaños Nancy Villegas ◽  
Bolaños Nancy Villegas ◽  
Igor Malikov ◽  
...  
Keyword(s):  
Time Series ◽  
Pacific Ocean ◽  
Surface Temperature ◽  
Sea Surface Temperature ◽  
Extreme Values ◽  
Sea Surface ◽  
Absolute Maximum ◽  
Data Set ◽  
Arctic Oscillation Index ◽  
Colombian Pacific

Sea Surface Temperature Anomalies (SSTA), in four coastal hydrographic stations of Colombian Pacific Ocean, were analyzed. The selected hydrographic stations were: Tumaco (1°48'N-78°45'W), Gorgona island (2°58'N-78°11'W), Solano Bay (6°13'N-77°24'W) and Malpelo island (4°0'N-81°36'W). SSTA time series for 1960-2015 were calculated from monthly Sea Surface Temperature obtained from International Comprehensive Ocean Atmosphere Data Set (ICOADS). SSTA time series, Oceanic Nino Index (ONI), Pacific Decadal Oscillation index (PDO), Arctic Oscillation index (AO) and sunspots number (associated to solar activity), were compared. It was found that the SSTA absolute minimum has occurred in Tumaco (-3.93°C) in March 2009, in Gorgona (-3.71°C) in October 2007, in Solano Bay (-4.23°C) in April 2014 and Malpelo (-4.21°C) in December 2005. The SSTA absolute maximum was observed in Tumaco (3.45°C) in January 2002, in Gorgona (5.01°C) in July 1978, in Solano Bay (5.27°C) in March 1998 and Malpelo (3.64°C) in July 2015. A high correlation between SST and ONI in large part of study period, followed by a good correlation with PDO, was identified. The AO and SSTA have showed an inverse relationship in some periods. Solar Cycle has showed to be a modulator of behavior of SSTA in the selected stations. It was determined that extreme values of SST are related to the analyzed large scale oscillations.

Territorial Distribution of Alcohol and Drug Addictions Mortality Concerning Regional Disparities in the Slovak Republic from Year 1996 to Year 2015

2020 ◽  
Keyword(s):  
Mortality Rate ◽  
Slovak Republic ◽  
Regional Disparities ◽  
Point Of View ◽  
Extreme Position ◽  
Data Set ◽  
Female Sex ◽  
Male Sex ◽  
The Individual ◽  
High Level

BACKGROUND: This paper deals with territorial distribution of the alcohol and drug addictions mortality at a level of the districts of the Slovak Republic. AIM: The aim of the paper is to explore the relations within the administrative territorial division of the Slovak Republic, that is, between the individual districts and hence, to reveal possibly hidden relation in alcohol and drug mortality. METHODS: The analysis is divided and executed into the two fragments – one belongs to the female sex, the other one belongs to the male sex. The standardised mortality rate is computed according to a sequence of the mathematical relations. The Euclidean distance is employed to compute the similarity within each pair of a whole data set. The cluster analysis examines is performed. The clusters are created by means of the mutual distances of the districts. The data is collected from the database of the Statistical Office of the Slovak Republic for all the districts of the Slovak Republic. The covered time span begins in the year 1996 and ends in the year 2015. RESULTS: The most substantial point is that the Slovak Republic possesses the regional disparities in a field of mortality expressed by the standardised mortality rate computed particularly for the diagnoses assigned to the alcohol and drug addictions at a considerably high level. However, the female sex and the male sex have the different outcome. The Bratislava III District keeps absolutely the most extreme position. It forms an own cluster for the both sexes too. The Topoľčany District bears a similar extreme position from a point of view of the male sex. All the Bratislava districts keep their mutual notable dissimilarity. Contrariwise, evaluation of a development of the regional disparities among the districts looks like notably heterogeneously. CONCLUSIONS: There are considerable regional discrepancies throughout the districts of the Slovak Republic. Hence, it is necessary to create a common platform how to proceed with the solution of this issue.

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