Gene selection and classification in autism gene expression data

Autism spectrum disorders (ASD) are neurodevelopmental disorders that are currently diagnosed on the basis of abnormal stereotyped behaviour as well as observable deficits in communication and social functioning. Although a variety of candidate genes have been attributed to the disorder, no single g...

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Main Author:	Al-Jaf, Shilan Sameen Hameed
Format:	Thesis
Language:	English
Published:	2017
Subjects:	QA75 Electronic computers Computer science
Online Access:	http://eprints.utm.my/id/eprint/86999/1/ShilanSameenHameedMFC2017.pdf
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spelling	my-utm-ep.869992020-10-31T12:16:36Z Gene selection and classification in autism gene expression data 2017 Al-Jaf, Shilan Sameen Hameed QA75 Electronic computers. Computer science Autism spectrum disorders (ASD) are neurodevelopmental disorders that are currently diagnosed on the basis of abnormal stereotyped behaviour as well as observable deficits in communication and social functioning. Although a variety of candidate genes have been attributed to the disorder, no single gene is applicable to more than 1–2% of the general ASD population. Despite extensive efforts, definitive genes that contribute to autism susceptibility have yet to be identified. The major problems in dealing with the gene expression dataset of autism include the presence of limited number of samples and large noises due to errors of experimental measurements and natural variation. In this study, a systematic combination of three important filters, namely t-test (TT), Wilcoxon Rank Sum (WRS) and Feature Correlation (COR) are applied along with efficient wrapper algorithm based on geometric binary particle swarm optimization-support vector machine (GBPSO-SVM), aiming at selecting and classifying the most attributed genes of autism. A new approach based on the criterion of median ratio, mean ratio and variance deviations is also applied to reduce the initial dataset prior to its involvement. Results showed that the most discriminative genes that were identified in the first and last selection steps concluded the presence of a repetitive gene (CAPS2), which was assigned as the most ASD risk gene. The fused result of genes subset that were selected by the GBPSO-SVM algorithm increased the classification accuracy to about 92.10%, which is higher than those reported in literature for the same autism dataset. Noticeably, the application of ensemble using random forest (RF) showed better performance compared to that of previous studies. However, the ensemble approach based on the employment of SVM as an integrator of the fused genes from the output branches of GBPSO-SVM outperformed the RF integrator. The overall improvement was ascribed to the selection strategies that were taken to reduce the dataset and the utilization of efficient wrapper based GBPSO-SVM algorithm. 2017 Thesis http://eprints.utm.my/id/eprint/86999/ http://eprints.utm.my/id/eprint/86999/1/ShilanSameenHameedMFC2017.pdf application/pdf en public http://dms.library.utm.my:8080/vital/access/manager/Repository/vital:132618 masters Universiti Teknologi Malaysia, Faculty of Computing Faculty of Computing
institution	Universiti Teknologi Malaysia
collection	UTM Institutional Repository
language	English
topic	QA75 Electronic computers Computer science
spellingShingle	QA75 Electronic computers Computer science Al-Jaf, Shilan Sameen Hameed Gene selection and classification in autism gene expression data
description	Autism spectrum disorders (ASD) are neurodevelopmental disorders that are currently diagnosed on the basis of abnormal stereotyped behaviour as well as observable deficits in communication and social functioning. Although a variety of candidate genes have been attributed to the disorder, no single gene is applicable to more than 1–2% of the general ASD population. Despite extensive efforts, definitive genes that contribute to autism susceptibility have yet to be identified. The major problems in dealing with the gene expression dataset of autism include the presence of limited number of samples and large noises due to errors of experimental measurements and natural variation. In this study, a systematic combination of three important filters, namely t-test (TT), Wilcoxon Rank Sum (WRS) and Feature Correlation (COR) are applied along with efficient wrapper algorithm based on geometric binary particle swarm optimization-support vector machine (GBPSO-SVM), aiming at selecting and classifying the most attributed genes of autism. A new approach based on the criterion of median ratio, mean ratio and variance deviations is also applied to reduce the initial dataset prior to its involvement. Results showed that the most discriminative genes that were identified in the first and last selection steps concluded the presence of a repetitive gene (CAPS2), which was assigned as the most ASD risk gene. The fused result of genes subset that were selected by the GBPSO-SVM algorithm increased the classification accuracy to about 92.10%, which is higher than those reported in literature for the same autism dataset. Noticeably, the application of ensemble using random forest (RF) showed better performance compared to that of previous studies. However, the ensemble approach based on the employment of SVM as an integrator of the fused genes from the output branches of GBPSO-SVM outperformed the RF integrator. The overall improvement was ascribed to the selection strategies that were taken to reduce the dataset and the utilization of efficient wrapper based GBPSO-SVM algorithm.
format	Thesis
qualification_level	Master's degree
author	Al-Jaf, Shilan Sameen Hameed
author_facet	Al-Jaf, Shilan Sameen Hameed
author_sort	Al-Jaf, Shilan Sameen Hameed
title	Gene selection and classification in autism gene expression data
title_short	Gene selection and classification in autism gene expression data
title_full	Gene selection and classification in autism gene expression data
title_fullStr	Gene selection and classification in autism gene expression data
title_full_unstemmed	Gene selection and classification in autism gene expression data
title_sort	gene selection and classification in autism gene expression data
granting_institution	Universiti Teknologi Malaysia, Faculty of Computing
granting_department	Faculty of Computing
publishDate	2017
url	http://eprints.utm.my/id/eprint/86999/1/ShilanSameenHameedMFC2017.pdf
_version_	1747818519821549568

Gene selection and classification in autism gene expression data

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