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
  • Graduation date
    Fall 2014
  • Type of Item
  • Degree
    Master of Science
  • DOI
  • 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.