Evolutionary synthesis of stochastic gene network models using feature-based search spaces

A feature-based fitness function is applied in a genetic programming system to synthesize stochastic gene regulatory network models whose behaviour is defined by a time course of protein expression levels. Typically, when targeting time series data, the fitness function is based on a sum-of-errors involving the values of the fluctuating signal. While this approach is successful in many instances, its performance can deteriorate in the presence of noise. This thesis explores a fitness measure determined from a set of statistical features characterizing the time series' sequence of values, rather than the actual values themselves. Through a series of experiments involving symbolic regression with added noise and gene regulatory network models based on the stochastic 'if-calculus, it is shown to successfully target oscillating and non-oscillating signals. This practical and versatile fitness function offers an alternate approach, worthy of consideration for use in algorithms that evaluate noisy or stochastic behaviour.

Bounds on edit metric codes with combinatorial DNA constraints

The design of a large and reliable DNA codeword library is a key problem in DNA based computing. DNA codes, namely sets of fixed length edit metric codewords over the alphabet {A, C, G, T}, satisfy certain combinatorial constraints with respect to biological and chemical restrictions of DNA strands. The primary constraints that we consider are the reverse--complement constraint and the fixed GC--content constraint, as well as the basic edit distance constraint between codewords. We focus on exploring the theory underlying DNA codes and discuss several approaches to searching for optimal DNA codes. We use Conway's lexicode algorithm and an exhaustive search algorithm to produce provably optimal DNA codes for codes with small parameter values. And a genetic algorithm is proposed to search for some sub--optimal DNA codes with relatively large parameter values, where we can consider their sizes as reasonable lower bounds of DNA codes. Furthermore, we provide tables of bounds on sizes of DNA codes with length from 1 to 9 and minimum distance from 1 to 9.

Finding the Open Spaces in Closed Systems: An Exploration of Critical Pedagogy with a Social Justice Directive in an Ontario Secondary School Classroom

This study examines the first experience of students, teachers, and an administrator in implementing a teacher-designed Leadership in Social Justice Program at a large urban Ontario secondary school. The program aimed to infuse a Freirean concept of critical pedagogical praxis (Freire, 1970/1993) in a grade 12 integrated educational experience with a social justice directive. Data were collected through two questionnaires and eight in-depth interviews. The data identified three areas of awareness that described ways in which student participants were impacted most profoundly (a) developing self-awareness, (b) understanding a new educational paradigm, and (c) finding a place in the world. The study found that the program was successful in highlighting the possibility for more meaningful education and engaged many students deeply; however, its success was limited by the lead teacher’s failure to fully grasp and implement tenets of Freirean critical pedagogy that involved the role of the teacher in pedagogical processes.

Queer Encounters: exploring experiences of (gender)queers in women's public washroom spaces

This thesis is based on 13 qualitative interviews conducted with 12 individuals whom I refer to as (gender)queers in Winnipeg, Manitoba, and St. Catharines, Ontario. Drawing on queer theory and the literature of sexuality and space, I explore how (gender)queers experience women's public washrooms as gendered and heterosexualized spaces. I examine the degree to which a simultaneous heterosexing and female gendering of women's public washrooms is linked to the marginalization and sometimes violent exclusion of (gender)queers within these particular spaces. I also discuss the ways in which (gender)queers may use a variety of strategies aimed at navigating heterosexualized and gendered public washrooms. Finally, I explore alternatives to conventional washrooms spaces, including the gender-neutral washrooms, multi-stall non-gendered public washrooms, and public washrooms in queer spaces.