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  1. Free, publicly-accessible full text available November 17, 2024
  2. Free, publicly-accessible full text available September 1, 2024
  3. null (Ed.)
    High-throughput phenotyping enables the efficient collection of plant trait data at scale. One example involves using imaging systems over key phases of a crop growing season. Although the resulting images provide rich data for statistical analyses of plant phenotypes, image processing for trait extraction is required as a prerequisite. Current methods for trait extraction are mainly based on supervised learning with human labeled data or semisupervised learning with a mixture of human labeled data and unsupervised data. Unfortunately, preparing a sufficiently large training data is both time and labor-intensive. We describe a self-supervised pipeline (KAT4IA) that uses K -means clustering on greenhouse images to construct training data for extracting and analyzing plant traits from an image-based field phenotyping system. The KAT4IA pipeline includes these main steps: self-supervised training set construction, plant segmentation from images of field-grown plants, automatic separation of target plants, calculation of plant traits, and functional curve fitting of the extracted traits. To deal with the challenge of separating target plants from noisy backgrounds in field images, we describe a novel approach using row-cuts and column-cuts on images segmented by transform domain neural network learning, which utilizes plant pixels identified from greenhouse images to train a segmentation model for field images. This approach is efficient and does not require human intervention. Our results show that KAT4IA is able to accurately extract plant pixels and estimate plant heights. 
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  4. We consider a semiparametric additive partially linear regression model (APLM) for analysing ultra‐high‐dimensional data where both the number of linear components and the number of non‐linear components can be much larger than the sample size. We propose a two‐step approach for estimation, selection, and simultaneous inference of the components in the APLM. In the first step, the non‐linear additive components are approximated using polynomial spline basis functions, and a doubly penalized procedure is proposed to select nonzero linear and non‐linear components based on adaptive lasso. In the second step, local linear smoothing is then applied to the data with the selected variables to obtain the asymptotic distribution of the estimators of the nonparametric functions of interest. The proposed method selects the correct model with probability approaching one under regularity conditions. The estimators of both the linear part and the non‐linear part are consistent and asymptotically normal, which enables us to construct confidence intervals and make inferences about the regression coefficients and the component functions. The performance of the method is evaluated by simulation studies. The proposed method is also applied to a dataset on the shoot apical meristem of maize genotypes.

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  5. Summary

    Many methods for estimation or control of the false discovery rate (FDR) can be improved by incorporating information about π0, the proportion of all tested null hypotheses that are true. Estimates of π0 are often based on the number of p-values that exceed a threshold λ. We first give a finite sample proof for conservative point estimation of the FDR when the λ-parameter is fixed. Then we establish a condition under which a dynamic adaptive procedure, whose λ-parameter is determined by data, will lead to conservative π0- and FDR estimators. We also present asymptotic results on simultaneous conservative FDR estimation and control for a class of dynamic adaptive procedures. Simulation results show that a novel dynamic adaptive procedure achieves more power through smaller estimation errors for π0 under independence and mild dependence conditions. We conclude by discussing the connection between estimation and control of the FDR and show that several recently developed FDR control procedures can be cast in a unifying framework where the strength of the procedures can be easily evaluated.

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