AIMC Topic: Selection, Genetic

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Smart breeding driven by big data, artificial intelligence, and integrated genomic-enviromic prediction.

Molecular plant
The first paradigm of plant breeding involves direct selection-based phenotypic observation, followed by predictive breeding using statistical models for quantitative traits constructed based on genetic experimental design and, more recently, by inco...

Robots as models of evolving systems.

Proceedings of the National Academy of Sciences of the United States of America
Experimental robobiological physics can bring insights into biological evolution. We present a development of hybrid analog/digital autonomous robots with mutable diploid dominant/recessive 6-byte genomes. The robots are capable of death, rebirth, an...

Disease variant prediction with deep generative models of evolutionary data.

Nature
Quantifying the pathogenicity of protein variants in human disease-related genes would have a marked effect on clinical decisions, yet the overwhelming majority (over 98%) of these variants still have unknown consequences. In principle, computational...

Using deep learning to identify recent positive selection in malaria parasite sequence data.

Malaria journal
BACKGROUND: Malaria, caused by Plasmodium parasites, is a major global public health problem. To assist an understanding of malaria pathogenesis, including drug resistance, there is a need for the timely detection of underlying genetic mutations and ...

On the Unfounded Enthusiasm for Soft Selective Sweeps III: The Supervised Machine Learning Algorithm That Isn't.

Genes
In the last 15 years or so, soft selective sweep mechanisms have been catapulted from a curiosity of little evolutionary importance to a ubiquitous mechanism claimed to explain most adaptive evolution and, in some cases, most evolution. This transfor...

A review of deep learning applications for genomic selection.

BMC genomics
BACKGROUND: Several conventional genomic Bayesian (or no Bayesian) prediction methods have been proposed including the standard additive genetic effect model for which the variance components are estimated with mixed model equations. In recent years,...

Design deep neural network architecture using a genetic algorithm for estimation of pile bearing capacity.

PloS one
Determination of pile bearing capacity is essential in pile foundation design. This study focused on the use of evolutionary algorithms to optimize Deep Learning Neural Network (DLNN) algorithm to predict the bearing capacity of driven pile. For this...

ImaGene: a convolutional neural network to quantify natural selection from genomic data.

BMC bioinformatics
BACKGROUND: The genetic bases of many complex phenotypes are still largely unknown, mostly due to the polygenic nature of the traits and the small effect of each associated mutation. An alternative approach to classic association studies to determini...

Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease.

Genome research
A central challenge in human genomics is to understand the cellular, evolutionary, and clinical significance of genetic variants. Here, we introduce a unified population-genetic and machine-learning model, called inear llele-pecific election nferenc ...

New Deep Learning Genomic-Based Prediction Model for Multiple Traits with Binary, Ordinal, and Continuous Phenotypes.

G3 (Bethesda, Md.)
Multiple-trait experiments with mixed phenotypes (binary, ordinal and continuous) are not rare in animal and plant breeding programs. However, there is a lack of statistical models that can exploit the correlation between traits with mixed phenotypes...