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ACCURATE DETECTION OF SELECTIVE SWEEPS WITH TRANSFER LEARNING

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Date Issued:
2021
Abstract/Description:
Positive natural selection leaves detectable, distinctive patterns in the genome in the form of a selective sweep. Identifying areas of the genome that have undergone selective sweeps is an area of high interest as it enables understanding of species and population evolution. Previous work has accomplished this by evaluating patterns within summary statistics computed across the genome and through application of machine learning techniques to raw population genomic data. When using raw population genomic data, convolutional neural networks have most recently been employed as they can handle large input arrays and maintain correlations among elements. Yet, such models often require massive amounts of training data and can be computationally expensive to train for a given problem. Instead, transfer learning has recently been used in the image analysis literature to improve machine learning models by learning the important features of images from large unrelated datasets beforehand, and then refining these models through subsequent application on smaller and more relevant datasets. We combine transfer learning with convolutional neural networks to improve classification of selective sweeps from raw population genomic data. We show that the combination of transfer learning with convolutional neural networks allows for accurate classification of selective sweeps.
Title: ACCURATE DETECTION OF SELECTIVE SWEEPS WITH TRANSFER LEARNING.
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Name(s): Sigler, Priya, author
DeGiorgio, Michael , Thesis advisor
Florida Atlantic University, Degree grantor
Department of Computer and Electrical Engineering and Computer Science
College of Engineering and Computer Science
Type of Resource: text
Genre: Electronic Thesis Or Dissertation
Date Created: 2021
Date Issued: 2021
Publisher: Florida Atlantic University
Place of Publication: Boca Raton, Fla.
Physical Form: application/pdf
Extent: 78 p.
Language(s): English
Abstract/Description: Positive natural selection leaves detectable, distinctive patterns in the genome in the form of a selective sweep. Identifying areas of the genome that have undergone selective sweeps is an area of high interest as it enables understanding of species and population evolution. Previous work has accomplished this by evaluating patterns within summary statistics computed across the genome and through application of machine learning techniques to raw population genomic data. When using raw population genomic data, convolutional neural networks have most recently been employed as they can handle large input arrays and maintain correlations among elements. Yet, such models often require massive amounts of training data and can be computationally expensive to train for a given problem. Instead, transfer learning has recently been used in the image analysis literature to improve machine learning models by learning the important features of images from large unrelated datasets beforehand, and then refining these models through subsequent application on smaller and more relevant datasets. We combine transfer learning with convolutional neural networks to improve classification of selective sweeps from raw population genomic data. We show that the combination of transfer learning with convolutional neural networks allows for accurate classification of selective sweeps.
Identifier: FA00013785 (IID)
Degree granted: Thesis (M.S.)--Florida Atlantic University, 2021.
Collection: FAU Electronic Theses and Dissertations Collection
Note(s): Includes bibliography.
Subject(s): Transfer learning (Machine learning)
Neural networks (Computer science)
Natural selection
Genomes
Persistent Link to This Record: http://purl.flvc.org/fau/fd/FA00013785
Use and Reproduction: Copyright © is held by the author with permission granted to Florida Atlantic University to digitize, archive and distribute this item for non-profit research and educational purposes. Any reuse of this item in excess of fair use or other copyright exemptions requires permission of the copyright holder.
Use and Reproduction: http://rightsstatements.org/vocab/InC/1.0/
Host Institution: FAU
Is Part of Series: Florida Atlantic University Digital Library Collections.