Global Genotype by Environment Prediction Competition Reveals That Diverse Modeling Strategies Can Deliver Satisfactory Maize Yield Estimates

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 20, 2024

Abstract Predicting phenotypes from a combination of genetic and environmental factors is grand challenge modern biology. Slight improvements in this area have the potential to save lives, improve food fuel security, permit better care planet, create other positive outcomes. In 2022 2023 first open-to-the-public Genomes Fields (G2F) initiative Genotype by Environment (GxE) prediction competition was held using large dataset including genomic variation, phenotype weather measurements field management notes, gathered project over nine years. The attracted registrants around world with representation academic, government, industry, non-profit institutions as well unaffiliated. These participants came diverse disciplines include plant science, animal breeding, statistics, computational biology others. Some had no formal genetics or plant-related training, some were just beginning their graduate education. teams applied varied methods strategies, providing wealth modeling knowledge based on common dataset. winner’s strategy involved two models combining machine learning traditional breeding tools: one model emphasized environment features extracted Random Forest, Ridge Regression Least-squares, focused genetics. Other high-performing teams’ included quantitative genetics, classical learning/deep learning, mechanistic models, ensembles. used, such genetics; weather; data, also diverse, demonstrating that single far superior all others within context competition.

Language: Английский

Global Genotype by Environment Prediction Competition Reveals That Diverse Modeling Strategies Can Deliver Satisfactory Maize Yield Estimates

Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 22, 2024

Abstract Predicting phenotypes from a combination of genetic and environmental factors is grand challenge modern biology. Slight improvements in this area have the potential to save lives, improve food fuel security, permit better care planet, create other positive outcomes. In 2022 2023, first open-to-the-public Genomes Fields initiative Genotype by Environment prediction competition was held using large dataset including genomic variation, phenotype weather measurements, field management notes gathered project over 9 years. The attracted registrants around world with representation academic, government, industry, nonprofit institutions as well unaffiliated. These participants came diverse disciplines, plant science, animal breeding, statistics, computational biology, others. Some had no formal genetics or plant-related training, some were just beginning their graduate education. teams applied varied methods strategies, providing wealth modeling knowledge based on common dataset. winner's strategy involved 2 models combining machine learning traditional breeding tools: 1 model emphasized environment features extracted random forest, ridge regression, least squares, focused genetics. Other high-performing teams’ included quantitative genetics, learning/deep learning, mechanistic models, ensembles. used, such weather, data, also diverse, demonstrating that single far superior all others within context competition.

Language: Английский

tensorEVD: A Fast Algorithm to Factorize High-Dimensional Tensor Product Matrices

Published: Nov. 14, 2023

Language: Английский