{"id":{"repo_id":"uwo","oai_identifier":"oai:uwo.scholaris.ca:20.500.14721/30175"},"canonical_url":"https://search.dev.ndltd.org/etd/uwo/oai:uwo.scholaris.ca:20.500.14721/30175","repository":{"repo_id":"uwo","name":"Western University","base_url":"https://uwo.scholaris.ca/server/oai/request"},"display":{"title":"Optimal clustering techniques for metagenomic sequencing data","abstract":"Metagenomic sequencing techniques have made it possible to determine the composition of bacterial microbiota of the human body. Clustering algorithms have been used to search for core microbiota types in the vagina, but results have been inconsistent, possibly due to methodological differences. We performed an extensive comparison of six commonly-used clustering algorithms and four distance metrics, using clinical data from 777 vaginal samples across 5 studies, and 36,000 synthetic datasets based on these clinical data. We found that centroid-based clustering algorithms (K-means and Partitioning around Medoids), with Euclidean or Manhattan distance metrics, performed well. They were best at correctly clustering and determining the number of clusters in synthetic datasets and were also top performers for predicting vaginal pH and bacterial vaginosis by clustering clinical data. Hierarchical clustering algorithms, particularly neighbour joining and average linkage, performed less well, failing unequivocally on many datasets.","abstract_html":"Metagenomic sequencing techniques have made it possible to determine the composition of bacterial microbiota of the human body. Clustering algorithms have been used to search for core microbiota types in the vagina, but results have been inconsistent, possibly due to methodological differences. We performed an extensive comparison of six commonly-used clustering algorithms and four distance metrics, using clinical data from 777 vaginal samples across 5 studies, and 36,000 synthetic datasets based on these clinical data. We found that centroid-based clustering algorithms (K-means and Partitioning around Medoids), with Euclidean or Manhattan distance metrics, performed well. They were best at correctly clustering and determining the number of clusters in synthetic datasets and were also top performers for predicting vaginal pH and bacterial vaginosis by clustering clinical data. Hierarchical clustering algorithms, particularly neighbour joining and average linkage, performed less well, failing unequivocally on many datasets.","abstract_has_math":false,"creators":["Cameron, Erik T"],"institution":"The University of Western Ontario","degree_name":"M Sc","degree_level":null,"degree_discipline":"Applied Mathematics","degree_department":null,"school":null,"contributors":[],"advisors":["L. M. Wahl"],"committee_chairs":[],"committee_members":[],"year":2012,"date_issued":"2012-08-02","date_published":"2012-08-02","updated_at":"2026-07-27T21:55:59Z","subjects":["vaginal microbiota","bacterial vaginosis","metagenomics","cluster analysis","distance metric"],"languages":["en_ca"],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/20.500.14721/30175","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["L. M. 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In citing or referring to this thesis, use the DOI or handle from this page instead. Sample citation: Author name, \"Thesis title.\" (Year). Western University Open Repository. https://doi.org/10.71858/123456."]},{"key":"dc:description.abstract","label":"Abstract","values":["Metagenomic sequencing techniques have made it possible to determine the composition of bacterial microbiota of the human body. Clustering algorithms have been used to search for core microbiota types in the vagina, but results have been inconsistent, possibly due to methodological differences. We performed an extensive comparison of six commonly-used clustering algorithms and four distance metrics, using clinical data from 777 vaginal samples across 5 studies, and 36,000 synthetic datasets based on these clinical data. We found that centroid-based clustering algorithms (K-means and Partitioning around Medoids), with Euclidean or Manhattan distance metrics, performed well. They were best at correctly clustering and determining the number of clusters in synthetic datasets and were also top performers for predicting vaginal pH and bacterial vaginosis by clustering clinical data. Hierarchical clustering algorithms, particularly neighbour joining and average linkage, performed less well, failing unequivocally on many datasets."]},{"key":"dc:title","label":"Title","values":["Optimal clustering techniques for metagenomic sequencing data"]}]}],"canonical_facts":{"dc:contributor.advisor":["L. M. Wahl"],"dc:creator":["Cameron, Erik T"],"dc:date.accessioned":["2025-07-10T18:37:39Z"],"dc:date.available":["2025-07-10T18:37:39Z"],"dc:date.issued":["2012-08-02"],"dc:description":["The thesis cover page in the PDF document includes references to Western University’s previous institutional repository platform, known as Scholarship@Western, and links to that platform (beginning with ir.lib.uwo.ca). In citing or referring to this thesis, use the DOI or handle from this page instead. Sample citation: Author name, \"Thesis title.\" (Year). Western University Open Repository. https://doi.org/10.71858/123456."],"dc:description.abstract":["Metagenomic sequencing techniques have made it possible to determine the composition of bacterial microbiota of the human body. Clustering algorithms have been used to search for core microbiota types in the vagina, but results have been inconsistent, possibly due to methodological differences. We performed an extensive comparison of six commonly-used clustering algorithms and four distance metrics, using clinical data from 777 vaginal samples across 5 studies, and 36,000 synthetic datasets based on these clinical data. We found that centroid-based clustering algorithms (K-means and Partitioning around Medoids), with Euclidean or Manhattan distance metrics, performed well. They were best at correctly clustering and determining the number of clusters in synthetic datasets and were also top performers for predicting vaginal pH and bacterial vaginosis by clustering clinical data. Hierarchical clustering algorithms, particularly neighbour joining and average linkage, performed less well, failing unequivocally on many datasets."],"dc:identifier.uri":["https://hdl.handle.net/20.500.14721/30175"],"dc:language.iso":["en_ca"],"dc:publisher":["The University of Western Ontario"],"dc:subject":["vaginal microbiota","bacterial vaginosis","metagenomics","cluster analysis","distance metric"],"dc:title":["Optimal clustering techniques for metagenomic sequencing data"],"dc:type":["thesis"],"thesis:degree_discipline":["Applied Mathematics"],"thesis:degree_name":["M Sc"]},"updated_at":"2026-07-27T21:55:59Z"}