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Detecting adaptive introgression in human evolution using convolutional neural networks.

ABSTRACT: 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 frameworks for jointly modelling introgression and positive selection, in order to detect these variants using genomic sequence data. Here, we develop an approach based on convolutional neural networks (CNNs). CNNs do not require the specification of an analytical model of allele frequency dynamics and have outperformed alternative methods for classification and parameter estimation tasks in various areas of population genetics. Thus, they are potentially well suited to the identification of adaptive introgression. Using simulations, we trained CNNs on genotype matrices derived from genomes sampled from the donor population, the recipient population and a related non-introgressed population, in order to distinguish regions of the genome evolving under adaptive introgression from those evolving neutrally or experiencing selective sweeps. Our CNN architecture exhibits 95% accuracy on simulated data, even when the genomes are unphased, and accuracy decreases only moderately in the presence of heterosis. As a proof of concept, we applied our trained CNNs to human genomic datasets-both phased and unphased-to detect candidates for adaptive introgression that shaped our evolutionary history.

SUBMITTER: Gower G

PROVIDER: S-EPMC8192126 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundWorkplace bullying has been measured in many studies to investigate its effects on mental health issues. However, none have used web-based computerized adaptive testing (CAT) with bully classifications and convolutional neural networks (CNN) for reporting the extent of individual bullying in the workplace.ObjectiveThis study aims to build a model using CNN to develop an app for automatic detection and classification of nurse bullying-levels, incorporated with online Rasch computerized adaptive testing, to help assess nurse bullying at an earlier stage.MethodsWe recruited 960 nurses working in a Taiwan Ch-Mei hospital group to fill out the 22-item Negative Acts Questionnaire-Revised (NAQ-R) in August 2012. The k-mean and the CNN were used as unsupervised and supervised learnings, respectively, for: (1) dividing nurses into three classes (n=918, 29, and 13 with suspicious mild, moderate, and severe extent of being bullied, respectively); and (2) building a bully prediction model to estimate 69 different parameters. Finally, data were separated into training and testing sets in a proportion of 70:30, where the former was used to predict the latter. We calculated the sensitivity, specificity, and receiver operating characteristic curve (area under the curve [AUC]), along with the accuracy across studies for comparison. An app predicting the respondent bullying-level was developed, involving the model's 69 estimated parameters and the online Rasch CAT module as a website assessment.ResultsWe observed that: (1) the 22-item model yields higher accuracy rates for three categories, with an accuracy of 94% for the total 960 cases, and accuracies of 99% (AUC 0.99; 95% CI 0.99-1.00) and 83% (AUC 0.94; 95% CI 0.82-0.99) for the lower and upper groups (cutoff points at 49 and 66 points) based on the 947 cases and 42 cases, respectively; and (2) the 700-case training set, with 95% accuracy, predicts the 260-case testing set reaching an accuracy of 97. Thus, a NAQ-R app for nurses that predicts bullying-level was successfully developed and demonstrated in this study.ConclusionsThe 22-item CNN model, combined with the Rasch online CAT, is recommended for improving the accuracy of the nurse NAQ-R assessment. An app developed for helping nurses self-assess workplace bullying at an early stage is required for application in the future.

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Detecting adaptive introgression in human evolution using convolutional neural networks.

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