AIMC Topic: Models, Genetic

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Multi-task genomic prediction using gated residual variable selection neural networks.

BMC bioinformatics Jul 7, 2025
BACKGROUND: The recent development of high-throughput sequencing techniques provide massive data that can be used in genome-wide prediction (GWP). Although GWP is effective on its own, the incorporation of traditional polygenic pedigree information i...
Neural Networks, Computer Animals Models, Genetic Bayes Theorem Pedigree Swine Mice Genomics
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Breeding perspectives on tackling trait genome-to-phenome (G2P) dimensionality using ensemble-based genomic prediction.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik Jul 4, 2025
Trait Genome-to-Phenome (G2P) dimensionality and "breeding context" combine to influence the realised prediction skill of different whole genome prediction (WGP) methods. Theory and empirical evidence both suggest there is likely to be "No Free Lunch...
Plant Breeding Genome, Plant Quantitative Trait Loci Machine Learning Artificial Intelligence Algorithms Genomics Phenotype Models, Genetic Crops, Agricultural
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Generative prediction of causal gene sets responsible for complex traits.

Proceedings of the National Academy of Sciences of the United States of America Jun 12, 2025
The relationship between genotype and phenotype remains an outstanding question for organism-level traits because these traits are generally . The challenge arises from complex traits being determined by a combination of multiple genes (or loci), whi...
Models, Genetic Quantitative Trait Loci Multifactorial Inheritance Genome-Wide Association Study Genotype Humans Machine Learning Phenotype Gene Expression Profiling Transcriptome
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Toward a general framework for AI-enabled prediction in crop improvement.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik Jun 12, 2025
A theoretical framework for AI and ensembled prediction for crop improvement is introduced and demonstrated using the logistic map. Symbolic/sub-symbolic AI-based prediction can increase predictive skill with increase in system complexity. The curse ...
Bayes Theorem Crops, Agricultural Plant Breeding Phenotype Models, Genetic Artificial Intelligence
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Generative AI for predictive breeding: hopes and caveats.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik Jun 11, 2025
Among the broad area of artificial intelligence (AI), generative AI algorithms have emerged as a revolutionary technology able to produce highly realistic 'synthetic' data, akin to standard simulation but with fewer contraints. The main focus of gene...
Algorithms Phenotype Computer Simulation Genotype Models, Genetic Artificial Intelligence Plant Breeding
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Assessing simulation-based supervised machine learning for demographic parameter inference from genomic data.

Heredity Jun 6, 2025
The ever-increasing availability of high-throughput DNA sequences and the development of numerous computational methods have led to considerable advances in our understanding of the evolutionary and demographic history of populations. Several demogra...
Algorithms Computer Simulation Genomics Humans Neural Networks, Computer Machine Learning Supervised Machine Learning Genetics, Population Models, Genetic Bayes Theorem
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Performance of deep-learning-based approaches to improve polygenic scores.

Nature communications Jun 2, 2025
Polygenic scores, which estimate an individual's genetic propensity for a disease or trait, have the potential to become part of genomic healthcare. Neural-network based deep-learning has emerged as a method of intense interest to model complex, nonl...
Humans Neural Networks, Computer Gene-Environment Interaction Phenotype Multifactorial Inheritance Linear Models Linkage Disequilibrium Polymorphism, Single Nucleotide Deep Learning Models, Genetic Genome-Wide Association Study United Kingdom Genetic Predisposition to Disease
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Statistical algorithms for the analysis of deleterious genetic mutations.

Bio Systems Apr 30, 2025
We present algorithms for model selection and parameter estimation concerning deleterious genetic mutations. Three models are considered: single gene mutation, double cross-effect mutations or no genetic cause. Each of these models include unknown pa...
Breast Neoplasms Models, Genetic Models, Statistical Ovarian Neoplasms Mutation Humans Algorithms Computer Simulation Female
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Sweet pepper yield modeling via deep learning and selection of superior genotypes using GBLUP and MGIDI.

Scientific reports Apr 27, 2025
Intelligent knowledge about Capsicum annuum L. germplasm could lead to effective management of germplasm. Here, 29 accessions of sweet pepper were investigated in two separate randomized complete block design with three replications in the field cond...
Capsicum Genotype Neural Networks, Computer Plant Breeding Models, Genetic Deep Learning Fruit
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EBMGP: a deep learning model for genomic prediction based on Elastic Net feature selection and bidirectional encoder representations from transformer's embedding and multi-head attention pooling.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik Apr 19, 2025
Enhancing early selection through genomic estimated breeding values is pivotal for reducing generation intervals and accelerating breeding programs. Recently, deep learning (DL) approaches have gained prominence in genomic prediction (GP). Here, we i...
Models, Genetic Deep Learning Plant Breeding Genomics Polymorphism, Single Nucleotide
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