Deep Learning for genomic data analysis
Autor(a) principal: | |
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Data de Publicação: | 2017 |
Tipo de documento: | Dissertação |
Idioma: | por |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | https://repositorio-aberto.up.pt/handle/10216/106492 |
Resumo: | Since the Human Genome Project, the availability of genomic data has largely increased. In the last years, genome sequencing technologies and techniques have been improving at a fast rate, resulting in a cheaper and faster genome sequencing. Such amount of data enables both more complex analysis and advances in research. However, a sequencing process quite often produces a huge amount of data that is highly complex. A considerable computational power and efficient algorithms are mandatory in order to extract useful information and perform it in reasonable time, which can represent a constraint on the extraction and comprehension of such information.In this work, we focus on the biological aspects of RNA-Seq and its analysis using traditional Machine Learning and Deep learning methods. We divided our study into two branches. First, we built and compared the accuracy of classifiers that were able distinguish the RNA-seq samples of thyroid cancer patients from samples of healthy persons. Secondly, we have investigated the possibility of building comprehensible descriptions for the differences in the RNA-Seq data by using Denoising Autoencoders and Stacked Denoising Autoencoders as base classifiers and then devising post-processing techniques to extract comprehensible and biologically meaningful descriptions out of the constructed models. |
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Deep Learning for genomic data analysisEngenharia electrotécnica, electrónica e informáticaElectrical engineering, Electronic engineering, Information engineeringSince the Human Genome Project, the availability of genomic data has largely increased. In the last years, genome sequencing technologies and techniques have been improving at a fast rate, resulting in a cheaper and faster genome sequencing. Such amount of data enables both more complex analysis and advances in research. However, a sequencing process quite often produces a huge amount of data that is highly complex. A considerable computational power and efficient algorithms are mandatory in order to extract useful information and perform it in reasonable time, which can represent a constraint on the extraction and comprehension of such information.In this work, we focus on the biological aspects of RNA-Seq and its analysis using traditional Machine Learning and Deep learning methods. We divided our study into two branches. First, we built and compared the accuracy of classifiers that were able distinguish the RNA-seq samples of thyroid cancer patients from samples of healthy persons. Secondly, we have investigated the possibility of building comprehensible descriptions for the differences in the RNA-Seq data by using Denoising Autoencoders and Stacked Denoising Autoencoders as base classifiers and then devising post-processing techniques to extract comprehensible and biologically meaningful descriptions out of the constructed models.2017-07-142017-07-14T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesisapplication/pdfhttps://repositorio-aberto.up.pt/handle/10216/106492TID:201804042porVítor Filipe Oliveira Teixeirainfo:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-11-29T13:08:00Zoai:repositorio-aberto.up.pt:10216/106492Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T23:34:11.119597Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Deep Learning for genomic data analysis |
title |
Deep Learning for genomic data analysis |
spellingShingle |
Deep Learning for genomic data analysis Vítor Filipe Oliveira Teixeira Engenharia electrotécnica, electrónica e informática Electrical engineering, Electronic engineering, Information engineering |
title_short |
Deep Learning for genomic data analysis |
title_full |
Deep Learning for genomic data analysis |
title_fullStr |
Deep Learning for genomic data analysis |
title_full_unstemmed |
Deep Learning for genomic data analysis |
title_sort |
Deep Learning for genomic data analysis |
author |
Vítor Filipe Oliveira Teixeira |
author_facet |
Vítor Filipe Oliveira Teixeira |
author_role |
author |
dc.contributor.author.fl_str_mv |
Vítor Filipe Oliveira Teixeira |
dc.subject.por.fl_str_mv |
Engenharia electrotécnica, electrónica e informática Electrical engineering, Electronic engineering, Information engineering |
topic |
Engenharia electrotécnica, electrónica e informática Electrical engineering, Electronic engineering, Information engineering |
description |
Since the Human Genome Project, the availability of genomic data has largely increased. In the last years, genome sequencing technologies and techniques have been improving at a fast rate, resulting in a cheaper and faster genome sequencing. Such amount of data enables both more complex analysis and advances in research. However, a sequencing process quite often produces a huge amount of data that is highly complex. A considerable computational power and efficient algorithms are mandatory in order to extract useful information and perform it in reasonable time, which can represent a constraint on the extraction and comprehension of such information.In this work, we focus on the biological aspects of RNA-Seq and its analysis using traditional Machine Learning and Deep learning methods. We divided our study into two branches. First, we built and compared the accuracy of classifiers that were able distinguish the RNA-seq samples of thyroid cancer patients from samples of healthy persons. Secondly, we have investigated the possibility of building comprehensible descriptions for the differences in the RNA-Seq data by using Denoising Autoencoders and Stacked Denoising Autoencoders as base classifiers and then devising post-processing techniques to extract comprehensible and biologically meaningful descriptions out of the constructed models. |
publishDate |
2017 |
dc.date.none.fl_str_mv |
2017-07-14 2017-07-14T00:00:00Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/masterThesis |
format |
masterThesis |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
https://repositorio-aberto.up.pt/handle/10216/106492 TID:201804042 |
url |
https://repositorio-aberto.up.pt/handle/10216/106492 |
identifier_str_mv |
TID:201804042 |
dc.language.iso.fl_str_mv |
por |
language |
por |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
instname_str |
Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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1799135653449957376 |