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A Bayesian Updating Framework for Long-term Multi-Environment Trial Data in Plant Breeding

Bark, Stephan, Malik, Waqas Ahmed, Prus, Maryna, Piepho, Hans-Peter, Schmid, Volker

arXiv.org Machine Learning

In variety testing, multi-environment trials (MET) are essential for evaluating the genotypic performance of crop plants. A persistent challenge in the statistical analysis of MET data is the estimation of variance components, which are often still inaccurately estimated or shrunk to exactly zero when using residual (restricted) maximum likelihood (REML) approaches. At the same time, institutions conducting MET typically possess extensive historical data that can, in principle, be leveraged to improve variance component estimation. However, these data are rarely incorporated sufficiently. The purpose of this paper is to address this gap by proposing a Bayesian framework that systematically integrates historical information to stabilize variance component estimation and better quantify uncertainty. Our Bayesian linear mixed model (BLMM) reformulation uses priors and Markov chain Monte Carlo (MCMC) methods to maintain the variance components as positive, yielding more realistic distributional estimates. Furthermore, our model incorporates historical prior information by managing MET data in successive historical data windows. Variance component prior and posterior distributions are shown to be conjugate and belong to the inverse gamma and inverse Wishart families. While Bayesian methodology is increasingly being used for analyzing MET data, to the best of our knowledge, this study comprises one of the first serious attempts to objectively inform priors in the context of MET data. This refers to the proposed Bayesian updating approach. To demonstrate the framework, we consider an application where posterior variance component samples are plugged into an A-optimality experimental design criterion to determine the average optimal allocations of trials to agro-ecological zones in a sub-divided target population of environments (TPE).


Why spring smells like semen and rotting fish

Popular Science

More information Adding us as a Preferred Source in Google by using this link indicates that you would like to see more of our content in Google News results. While beautiful, Bradford pear trees also stink. Breakthroughs, discoveries, and DIY tips sent six days a week. The sun is out, the streets are humming, the days are getting longer, and the air smells like like um say, can anyone else smell that? All over America, spring is getting smellier every year, and the culprit is the Bradford pear, a tree that gained popularity in the mid-20 century for its ornamental properties.


Biodegradable wash keeps grapes fresh for 2 weeks at room temperature

Popular Science

More information Adding us as a Preferred Source in Google by using this link indicates that you would like to see more of our content in Google News results. The estimated commercial cost is also comparable to existing industry rinses. Breakthroughs, discoveries, and DIY tips sent six days a week. While rinsing really does help clean fruits and vegetables of harmful pesticides and bacteria, washing produce with water alone doesn't ensure a longer shelf life or guard against decay. With millions of pounds of fresh food wasted annually in the United States alone, agricultural researchers at the University of British Columbia (UBC) in Canada are investigating new ways to extend freshness and rid produce of unwanted pesticides.


Gradient Boosting for Spatial Panel Models with Random and Fixed Effects

Balzer, Michael, Benlahlou, Adhen

arXiv.org Machine Learning

Due to the increase in data availability in urban and regional studies, various spatial panel models have emerged to model spatial panel data, which exhibit spatial patterns and spatial dependencies between observations across time. Although estimation is usually based on maximum likelihood or generalized method of moments, these methods may fail to yield unique solutions if researchers are faced with high-dimensional settings. This article proposes a model-based gradient boosting algorithm, which enables estimation with interpretable results that is feasible in low- and high-dimensional settings. Due to its modular nature, the flexible model-based gradient boosting algorithm is suitable for a variety of spatial panel models, which can include random and fixed effects. The general framework also enables data-driven model and variable selection as well as implicit regularization where the bias-variance trade-off is controlled for, thereby enhancing accuracy of prediction on out-of-sample spatial panel data. Monte Carlo experiments concerned with the performance of estimation and variable selection confirm proper functionality in low- and high-dimensional settings while real-world applications including non-life insurance in Italian districts, rice production in Indonesian farms and life expectancy in German districts illustrate the potential application.


Rice cheese may be the next big thing

Popular Science

Early test batches contained 12 percent protein. Food scientists with the Arkansas Agricultural Experiment Station investigated proteins from three parts of a single rice cultivar for plant-based cheesemaking and discovered each source offered different qualities. Breakthroughs, discoveries, and DIY tips sent six days a week. There are a lot of non-dairy and vegan cheese alternatives on the market today. But while the tastes and textures of many of them almost pass for the real thing, they usually lack one major component: protein .


Weed that smells like paint thinner takes over Arizona

Popular Science

Stinknet is an invasive weed that can disperse thousands of seeds at a time. An invasive yellow weed called stinknet surrounding desert plants. Breakthroughs, discoveries, and DIY tips sent six days a week. Invasive plants can be just as destructive as animals --and often fly more under the radar until it's too late. The noxious yellow weed gives off more than just an offensive smell; it's also destroying native wildflowers critical to the ecosystem.



WildfireSpreadTS: A dataset of multi-modal time series for wildfire spread prediction

Neural Information Processing Systems

We present a multi-temporal, multi-modal remote-sensing dataset for predicting how active wildfires will spread at a resolution of 24 hours. The dataset consists of 13 607 images across 607 fire events in the United States from January 2018 to October 2021. For each fire event, the dataset contains a full time series of daily observations, containing detected active fires and variables related to fuel, topography and weather conditions. The dataset is challenging due to: a) its inputs being multi-temporal, b) the high number of 23 multi-modal input channels, c) highly imbalanced labels and d) noisy labels, due to smoke, clouds, and inaccuracies in the active fire detection.



SSL4EO-L: Datasets and Foundation Models for Landsat Imagery Adam J. Stewart

Neural Information Processing Systems

The Landsat program is the longest-running Earth observation program in history, with 50+ years of data acquisition by 8 satellites. The multispectral imagery captured by sensors onboard these satellites is critical for a wide range of scientific fields. Despite the increasing popularity of deep learning and remote sensing, the majority of researchers still use decision trees and random forests for Landsat image analysis due to the prevalence of small labeled datasets and lack of foundation models. In this paper, we introduce SSL4EO-L, the first ever dataset designed for Self-Supervised Learning for Earth O bservation for the Landsat family of satellites (including 3 sensors and 2 product levels) and the largest Landsat dataset in history (5M image patches). Additionally, we modernize and re-release the L7 Irish and L8 Biome cloud detection datasets, and introduce the first ML benchmark datasets for Landsats 4-5 TM and Landsat 7 ETM+ SR. Finally, we pre-train the first foundation models for Landsat imagery using SSL4EO-L and evaluate their performance on multiple semantic segmentation tasks.