AIMC Topic: Genetics, Population

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Inference and Analysis of Population Structure Using Genetic Data and Network Theory.

Genetics Feb 17, 2016
Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance-based app...
Algorithms Models, Genetic Cluster Analysis Genetics, Population Humans Neural Networks, Computer
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Hierarchical boosting: a machine-learning framework to detect and classify hard selective sweeps in human populations.

Bioinformatics (Oxford, England) Aug 26, 2015
MOTIVATION: Detecting positive selection in genomic regions is a recurrent topic in natural population genetic studies. However, there is little consistency among the regions detected in several genome-wide scans using different tests and/or populati...
Demography Genetics, Population Humans Polymorphism, Genetic Selection, Genetic Machine Learning Genomics
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Artificial neural networks reveal efficiency in genetic value prediction.

Genetics and molecular research : GMR Jun 18, 2015
The objective of this study was to evaluate the efficiency of artificial neural networks (ANNs) for predicting genetic value in experiments carried out in randomized blocks. Sixteen scenarios were simulated with different values of heritability (10, ...
Inheritance Patterns Animals Genotype Selection, Genetic Computer Simulation Plants Neural Networks, Computer Genetics, Population Breeding Reproducibility of Results Phenotype
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Deep learning insights into distinct patterns of polygenic adaptation across human populations.

Nucleic acids research Dec 11, 2024
Response to spatiotemporal variation in selection gradients resulted in signatures of polygenic adaptation in human genomes. We introduce RAISING, a two-stage deep learning framework that optimizes neural network architecture through hyperparameter t...
Genomics Models, Genetic Phylogeny Deep Learning Adaptation, Physiological Multifactorial Inheritance Genetics, Population Genome, Human Selection, Genetic Humans Neural Networks, Computer
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Tree Sequences as a General-Purpose Tool for Population Genetic Inference.

Molecular biology and evolution Nov 1, 2024
As population genetic data increase in size, new methods have been developed to store genetic information in efficient ways, such as tree sequences. These data structures are computationally and storage efficient but are not interchangeable with exis...
Neural Networks, Computer Phylogeny Genetics, Population
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Using Runs of Homozygosity and Machine Learning to Disentangle Sources of Inbreeding and Infer Self-Fertilization Rates.

Genome biology and evolution Jul 3, 2024
Runs of homozygosity (ROHs) are indicative of elevated homozygosity and inbreeding due to mating of closely related individuals. Self-fertilization can be a major source of inbreeding which elevates genome-wide homozygosity and thus should also creat...
Animals Models, Genetic Homozygote Machine Learning Self-Fertilization Genetics, Population Inbreeding
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Computationally Efficient Demographic History Inference from Allele Frequencies with Supervised Machine Learning.

Molecular biology and evolution May 3, 2024
Inferring past demographic history of natural populations from genomic data is of central concern in many studies across research fields. Previously, our group had developed dadi, a widely used demographic history inference method based on the allele...
Supervised Machine Learning Gene Frequency Neural Networks, Computer Models, Genetic Genetics, Population Humans
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Interpreting generative adversarial networks to infer natural selection from genetic data.

Genetics Apr 3, 2024
Understanding natural selection and other forms of non-neutrality is a major focus for the use of machine learning in population genetics. Existing methods rely on computationally intensive simulated training data. Unlike efficient neutral coalescent...
Genomics Selection, Genetic Genetics, Population Neural Networks, Computer Machine Learning Humans
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Deep Learning in Population Genetics.

Genome biology and evolution Feb 3, 2023
Population genetics is transitioning into a data-driven discipline thanks to the availability of large-scale genomic data and the need to study increasingly complex evolutionary scenarios. With likelihood and Bayesian approaches becoming either intra...
Genetics, Population Neural Networks, Computer Deep Learning Bayes Theorem Algorithms
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dnadna: a deep learning framework for population genetics inference.

Bioinformatics (Oxford, England) Jan 1, 2023
MOTIVATION: We present dnadna, a flexible python-based software for deep learning inference in population genetics. It is task-agnostic and aims at facilitating the development, reproducibility, dissemination and re-usability of neural networks desig...
Genetics, Population Reproducibility of Results Neural Networks, Computer Deep Learning Software
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