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Gene Frequency

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Scalable CNN-based classification of selective sweeps using derived allele frequencies.

Bioinformatics (Oxford, England)
MOTIVATION: Selective sweeps can successfully be distinguished from neutral genetic data using summary statistics and likelihood-based methods that analyze single nucleotide polymorphisms (SNPs). However, these methods are sensitive to confounding fa...

Computationally Efficient Demographic History Inference from Allele Frequencies with Supervised Machine Learning.

Molecular biology and evolution
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...

Exploitation of surrogate variables in random forests for unbiased analysis of mutual impact and importance of features.

Bioinformatics (Oxford, England)
MOTIVATION: Random forest is a popular machine learning approach for the analysis of high-dimensional data because it is flexible and provides variable importance measures for the selection of relevant features. However, the complex relationships bet...

Autosomal deletion/insertion polymorphisms for global stratification analyses and ancestry origin inferences of different continental populations by machine learning methods.

Electrophoresis
A lot of population data of 30 deletion/insertion polymorphisms (DIPs) of the Investigator DIPplex kit in different continental populations have been reported. Here, we assessed genetic distributions of these 30 DIPs in different continental populati...

Detecting adaptive introgression in human evolution using convolutional neural networks.

eLife
Studies in a variety of species have shown evidence for positively selected variants introduced into a population via introgression from another, distantly related population-a process known as adaptive introgression. However, there are few explicit ...

Machine learning-based identification and characterization of 15 novel pathogenic SUOX missense mutations.

Molecular genetics and metabolism
Isolated sulfite oxidase deficiency (ISOD) is a rare hereditary metabolic disease caused by absence of functional sulfite oxidase (SO) due to mutations of the SUOX gene. SO oxidizes toxic sulfite and sulfite accumulation is associated with neurologic...

Improving genomic prediction accuracy for meat tenderness in Nellore cattle using artificial neural networks.

Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie
The goal of this study was to compare the predictive performance of artificial neural networks (ANNs) with Bayesian ridge regression, Bayesian Lasso, Bayes A, Bayes B and Bayes Cπ in estimating genomic breeding values for meat tenderness in Nellore c...

Predicting Amyloid-β Levels in Amnestic Mild Cognitive Impairment Using Machine Learning Techniques.

Journal of Alzheimer's disease : JAD
BACKGROUND: Amyloid-β positivity (Aβ+) based on PET imaging is part of the enrollment criteria for many of the clinical trials of Alzheimer's disease (AD), particularly in trials for amyloid-targeted therapy. Predicting Aβ positivity prior to PET ima...