Contact Info
Department of Applied Mathematics
University of Waterloo
Waterloo, Ontario
Canada N2L 3G1
Phone: 519-888-4567, ext. 32700
Fax: 519-746-4319
PDF files require Adobe Acrobat Reader
MC 5501
Caroline Colijn | Department of Mathematics, Simon Fraser University
Comparing trees and using them for prediction in pathogen sequence data
With the development of rapid, low-cost and readily available sequencing technologies, there is a need for quantitative methods to help interpret sequence datasets and relate them to the dynamics of biological systems. Trees (in the sense of graphs with no cycles) are a mainstay of how we represent and understand sequence data. I will introduce several flavours of trees with their motivating applications, and will describe new metrics -- true distance function -- on them. In particular we have a new metric derived from polynomials on (unlabelled) trees. In the second part of the talk I will focus on applying tree comparisons to the context of infectious disease: can we use trees to guess in advance which sub-populations of a circulating pathogen will succeed in the near future? I will use tree features and comparisons together with machine learning tools to make these predictions.
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Contact Info
Department of Applied Mathematics
University of Waterloo
Waterloo, Ontario
Canada N2L 3G1
Phone: 519-888-4567, ext. 32700
Fax: 519-746-4319
PDF files require Adobe Acrobat Reader
The University of Waterloo acknowledges that much of our work takes place on the traditional territory of the Neutral, Anishinaabeg and Haudenosaunee peoples. Our main campus is situated on the Haldimand Tract, the land granted to the Six Nations that includes six miles on each side of the Grand River. Our active work toward reconciliation takes place across our campuses through research, learning, teaching, and community building, and is co-ordinated within the Office of Indigenous Relations.