scholarly journals SpaTemHTP: A Data Analysis Pipeline for Efficient Processing and Utilization of Temporal High-Throughput Phenotyping Data

2020 ◽  
Vol 11 ◽  
Author(s):  
Soumyashree Kar ◽  
Vincent Garin ◽  
Jana Kholová ◽  
Vincent Vadez ◽  
Surya S. Durbha ◽  
...  
Keyword(s):  
Time Series ◽  
Leaf Area ◽  
High Throughput ◽  
Missing Values ◽  
Time Series Data ◽  
Series Data ◽  
Genotypic Differences ◽  
Wide Range ◽  
High Throughput Phenotyping ◽  
Over Time

The rapid development of phenotyping technologies over the last years gave the opportunity to study plant development over time. The treatment of the massive amount of data collected by high-throughput phenotyping (HTP) platforms is however an important challenge for the plant science community. An important issue is to accurately estimate, over time, the genotypic component of plant phenotype. In outdoor and field-based HTP platforms, phenotype measurements can be substantially affected by data-generation inaccuracies or failures, leading to erroneous or missing data. To solve that problem, we developed an analytical pipeline composed of three modules: detection of outliers, imputation of missing values, and mixed-model genotype adjusted means computation with spatial adjustment. The pipeline was tested on three different traits (3D leaf area, projected leaf area, and plant height), in two crops (chickpea, sorghum), measured during two seasons. Using real-data analyses and simulations, we showed that the sequential application of the three pipeline steps was particularly useful to estimate smooth genotype growth curves from raw data containing a large amount of noise, a situation that is potentially frequent in data generated on outdoor HTP platforms. The procedure we propose can handle up to 50% of missing values. It is also robust to data contamination rates between 20 and 30% of the data. The pipeline was further extended to model the genotype time series data. A change-point analysis allowed the determination of growth phases and the optimal timing where genotypic differences were the largest. The estimated genotypic values were used to cluster the genotypes during the optimal growth phase. Through a two-way analysis of variance (ANOVA), clusters were found to be consistently defined throughout the growth duration. Therefore, we could show, on a wide range of scenarios, that the pipeline facilitated efficient extraction of useful information from outdoor HTP platform data. High-quality plant growth time series data is also provided to support breeding decisions. The R code of the pipeline is available at https://github.com/ICRISAT-GEMS/SpaTemHTP.

scholarly journals Jonckheere–Terpstra–Kendall-based non-parametric analysis of temporal differential gene expression

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Hitoshi Iuchi ◽  
Michiaki Hamada
Keyword(s):  
Gene Expression ◽  
Time Series ◽  
Time Course ◽  
Time Series Data ◽  
Expression Patterns ◽  
Detection Methods ◽  
Series Data ◽  
Expression Levels ◽  
Over Time ◽  
Non Parametric

Abstract Time-course experiments using parallel sequencers have the potential to uncover gradual changes in cells over time that cannot be observed in a two-point comparison. An essential step in time-series data analysis is the identification of temporal differentially expressed genes (TEGs) under two conditions (e.g. control versus case). Model-based approaches, which are typical TEG detection methods, often set one parameter (e.g. degree or degree of freedom) for one dataset. This approach risks modeling of linearly increasing genes with higher-order functions, or fitting of cyclic gene expression with linear functions, thereby leading to false positives/negatives. Here, we present a Jonckheere–Terpstra–Kendall (JTK)-based non-parametric algorithm for TEG detection. Benchmarks, using simulation data, show that the JTK-based approach outperforms existing methods, especially in long time-series experiments. Additionally, application of JTK in the analysis of time-series RNA-seq data from seven tissue types, across developmental stages in mouse and rat, suggested that the wave pattern contributes to the TEG identification of JTK, not the difference in expression levels. This result suggests that JTK is a suitable algorithm when focusing on expression patterns over time rather than expression levels, such as comparisons between different species. These results show that JTK is an excellent candidate for TEG detection.

scholarly journals An Empirical Mode-Spatial Model for Environmental Data Imputation

Hydrology ◽  
2018 ◽  
Vol 5 (4) ◽  
pp. 63 ◽  
Author(s):  
Benjamin Nelsen ◽  
D. Williams ◽  
Gustavious Williams ◽  
Candace Berrett
Keyword(s):  
Time Series ◽  
Spatial Data ◽  
Missing Values ◽  
Time Series Data ◽  
Environmental Data ◽  
Series Data ◽  
Data Imputation ◽  
Accurate Data ◽  
Target Station ◽  
Periodic Components

Complete and accurate data are necessary for analyzing and understanding trends in time-series datasets; however, many of the available time-series datasets have gaps that affect the analysis, especially in the earth sciences. As most available data have missing values, researchers use various interpolation methods or ad hoc approaches to data imputation. Since the analysis based on inaccurate data can lead to inaccurate conclusions, more accurate data imputation methods can provide accurate analysis. We present a spatial-temporal data imputation method using Empirical Mode Decomposition (EMD) based on spatial correlations. We call this method EMD-spatial data imputation or EMD-SDI. Though this method is applicable to other time-series data sets, here we demonstrate the method using temperature data. The EMD algorithm decomposes data into periodic components called intrinsic mode functions (IMF) and exactly reconstructs the original signal by summing these IMFs. EMD-SDI initially decomposes the data from the target station and other stations in the region into IMFs. EMD-SDI evaluates each IMF from the target station in turn and selects the IMF from other stations in the region with periodic behavior most correlated to target IMF. EMD-SDI then replaces a section of missing data in the target station IMF with the section from the most closely correlated IMF from the regional stations. We found that EMD-SDI selects the IMFs used for reconstruction from different stations throughout the region, not necessarily the station closest in the geographic sense. EMD-SDI accurately filled data gaps from 3 months to 5 years in length in our tests and favorably compares to a simple temporal method. EMD-SDI leverages regional correlation and the fact that different stations can be subject to different periodic behaviors. In addition to data imputation, the EMD-SDI method provides IMFs that can be used to better understand regional correlations and processes.

scholarly journals Evidence Graphs: Supporting Transparent and FAIR Computation, with Defeasible Reasoning on Data, Methods and Results

2021 ◽  
Author(s):  
Sadnan Al Manir ◽  
Justin Niestroy ◽  
Maxwell Adam Levinson ◽  
Timothy Clark
Keyword(s):  
Time Series ◽  
Large Scale ◽  
Time Series Data ◽  
Predictive Analytics ◽  
Defeasible Reasoning ◽  
Series Data ◽  
Inference Rules ◽  
Deep Networks ◽  
Evidence Graph ◽  
Over Time

Introduction: Transparency of computation is a requirement for assessing the validity of computed results and research claims based upon them; and it is essential for access to, assessment, and reuse of computational components. These components may be subject to methodological or other challenges over time. While reference to archived software and/or data is increasingly common in publications, a single machine-interpretable, integrative representation of how results were derived, that supports defeasible reasoning, has been absent. Methods: We developed the Evidence Graph Ontology, EVI, in OWL 2, with a set of inference rules, to provide deep representations of supporting and challenging evidence for computations, services, software, data, and results, across arbitrarily deep networks of computations, in connected or fully distinct processes. EVI integrates FAIR practices on data and software, with important concepts from provenance models, and argumentation theory. It extends PROV for additional expressiveness, with support for defeasible reasoning. EVI treats any com- putational result or component of evidence as a defeasible assertion, supported by a DAG of the computations, software, data, and agents that produced it. Results: We have successfully deployed EVI for very-large-scale predictive analytics on clinical time-series data. Every result may reference its own evidence graph as metadata, which can be extended when subsequent computations are executed. Discussion: Evidence graphs support transparency and defeasible reasoning on results. They are first-class computational objects, and reference the datasets and software from which they are derived. They support fully transparent computation, with challenge and support propagation. The EVI approach may be extended to include instruments, animal models, and critical experimental reagents.

scholarly journals Time Series Imputation via L1 Norm-Based Singular Spectrum Analysis

2018 ◽  
Vol 17 (02) ◽  
pp. 1850017 ◽  
Author(s):  
Mahdi Kalantari ◽  
Masoud Yarmohammadi ◽  
Hossein Hassani ◽  
Emmanuel Sirimal Silva
Keyword(s):  
Time Series ◽  
Spectrum Analysis ◽  
Missing Values ◽  
Time Series Data ◽  
Singular Spectrum Analysis ◽  
Series Data ◽  
L1 Norm ◽  
Nonparametric Approach ◽  
Singular Spectrum ◽  
Simulated Time

Missing values in time series data is a well-known and important problem which many researchers have studied extensively in various fields. In this paper, a new nonparametric approach for missing value imputation in time series is proposed. The main novelty of this research is applying the [Formula: see text] norm-based version of Singular Spectrum Analysis (SSA), namely [Formula: see text]-SSA which is robust against outliers. The performance of the new imputation method has been compared with many other established methods. The comparison is done by applying them to various real and simulated time series. The obtained results confirm that the SSA-based methods, especially [Formula: see text]-SSA can provide better imputation in comparison to other methods.

scholarly journals Co-eye: a multi-resolution ensemble classifier for symbolically approximated time series

2020 ◽  
Vol 109 (11) ◽  
pp. 2029-2061
Author(s):  
Zahraa S. Abdallah ◽  
Mohamed Medhat Gaber
Keyword(s):  
Time Series ◽  
Time Series Data ◽  
Ensemble Classifier ◽  
Series Data ◽  
New Classification ◽  
Symbolic Representations ◽  
Classification Technique ◽  
Field Of Vision ◽  
Main Challenge ◽  
Wide Range

Abstract Time series classification (TSC) is a challenging task that attracted many researchers in the last few years. One main challenge in TSC is the diversity of domains where time series data come from. Thus, there is no “one model that fits all” in TSC. Some algorithms are very accurate in classifying a specific type of time series when the whole series is considered, while some only target the existence/non-existence of specific patterns/shapelets. Yet other techniques focus on the frequency of occurrences of discriminating patterns/features. This paper presents a new classification technique that addresses the inherent diversity problem in TSC using a nature-inspired method. The technique is stimulated by how flies look at the world through “compound eyes” that are made up of thousands of lenses, called ommatidia. Each ommatidium is an eye with its own lens, and thousands of them together create a broad field of vision. The developed technique similarly uses different lenses and representations to look at the time series, and then combines them for broader visibility. These lenses have been created through hyper-parameterisation of symbolic representations (Piecewise Aggregate and Fourier approximations). The algorithm builds a random forest for each lens, then performs soft dynamic voting for classifying new instances using the most confident eyes, i.e., forests. We evaluate the new technique, coined Co-eye, using the recently released extended version of UCR archive, containing more than 100 datasets across a wide range of domains. The results show the benefits of bringing together different perspectives reflecting on the accuracy and robustness of Co-eye in comparison to other state-of-the-art techniques.

On the Constancy of Hedonic Wine Price Coefficients over Time

2019 ◽  
Vol 14 (2) ◽  
pp. 182-207 ◽  
Author(s):  
Benoît Faye ◽  
Eric Le Fur
Keyword(s):  
Time Series ◽  
Literature Review ◽  
Time Series Data ◽  
Hedonic Model ◽  
Series Data ◽  
Extensive Literature ◽  
Long Run ◽  
The Stability ◽  
Over Time ◽  
Jel Classifications

AbstractThis article tests the stability of the main hedonic wine price coefficients over time. We draw on an extensive literature review to identify the most frequently used methodology and define a standard hedonic model. We estimate this model on monthly subsamples of a worldwide auction database of the most commonly exchanged fine wines. This provides, for each attribute, a monthly time series of hedonic coefficients time series data from 2003 to 2014. Using a multivariate autoregressive model, we then study the stability of these coefficients over time and test the existence of structural or cyclical changes related to fluctuations in general price levels. We find that most hedonic coefficients are variable and either exhibit structural or cyclical variations over time. These findings shed doubt on the relevance of both short- and long-run hedonic estimations. (JEL Classifications: C13, C22, D44, G11)

Estimation of the seasonal leaf area index in urban oak forests using Sentinel-2 time series data

2019 ◽  
Author(s):  
A. Kozlova ◽  
I. Piestova ◽  
L. Patrusheva ◽  
M. Lubsky ◽  
A. Nikulina ◽  
...  
Keyword(s):  
Time Series ◽  
Leaf Area Index ◽  
Leaf Area ◽  
Time Series Data ◽  
Series Data ◽  
Oak Forests ◽  
Area Index ◽  
Sentinel 2
Sign in / Sign up

Export Citation Format

Share Document