Topological Data Analysis of DNA sequence data in human gut microbiome

• Author / Creator

  Petrov, Pavel

• 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.

• Subjects / Keywords

  • Topological data analysis
  • Persistent homology
  • Persistence landscape

• Graduation date

  Fall 2014

• Type of Item

  Thesis

• Degree

  Master of Science

• DOI

  https://doi.org/10.7939/R3XW4831V

• License

  This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for non-commercial purposes. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.