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Topological Data Analysis of DNA sequence data in human gut microbiome Open Access

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Other title
Subject/Keyword
Persistence landscape
Topological data analysis
Persistent homology
Type of item
Thesis
Degree grantor
University of Alberta
Author or creator
Petrov, Pavel
Supervisor and department
Heo, Giseon (Mathematical and Statistical Sciences)
Examining committee member and department
Kong, Linglong (Mathematical and Statistical Sciences)
Cho, Eung (Mathematics)
Mizera, Ivan (Mathematical and Statistical Sciences)
Department
Department of Mathematical and Statistical Sciences
Specialization
Statistics
Date accepted
2014-09-12T11:30:05Z
Graduation date
2014-11
Degree
Master of Science
Degree level
Master's
Abstract
Persistent Homology broadly refers to tracking the topological features of a geometric object. This study aims to use persistent homology to explore the effect of Human Biotherapy on patients suffering from Clotridium Difficile Infection. The data is presented in the form of several distance matrices and these are analyzed applying summary statistics of persistent homology, namely barcodes, persistence diagrams and persistence landscapes. It is found that there is a difference in the area under the persistence landscapes before and after treatment in dimensions zero and one. These differences are explored using projection onto lower dimensions using isometric mapping. It is found that there are differences in the number of clusters in dimension zero and the number and length of loops in dimension one.
Language
English
DOI
doi:10.7939/R3XW4831V
Rights
Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission.
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