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.

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.

Planar Topological Defects in Unconventional Superconductors

In this work, we consider the properties of planar topological defects in unconventional superconductors. Specifically, we calculate microscopically the interaction energy of domain walls separating degenerate ground states in a chiral p-wave fermionic superfluid. The interaction is mediated by the quasiparticles experiencing Andreev scattering at the domain walls. As a by-product, we derive a useful general expression for the free energy of an arbitrary nonuniform texture of the order parameter in terms of the quasiparticle scattering matrix. The thesis is structured as follows. We begin with a historical review of the theories of superconductivity (Sec. 1.1), which led the way to the celebrated Bardeen-Cooper- Schrieffer (BCS) theory (Sec. 1.3). Then we proceed to the treatment of superconductors with so-called "unconventional pairing" in Sec. 1.4, and in Sec. 1.5 we introduce the specific case of chiral p-wave superconductivity. After introducing in Sec. 2 the domain wall (DW) model that will be considered throughout the work, we derive the Bogoliubov-de Gennes (BdG) equations in Sec. 3.1, which determine the quasiparticle excitation spectrum for a nonuniform superconductor. In this work, we use the semiclassical (Andreev) approximation, and solve the Andreev equations (which are a particular case of the BdG equations) in Sec. 4 to determine the quasiparticle spectrum for both the single- and two-DW textures. The Andreev equations are derived in Sec. 3.2, and the formal properties of the Andreev scattering coefficients are discussed in the following subsection. In Sec. 5, we use the transfer matrix method to relate the interaction energy of the DWs to the scattering matrix of the Bogoliubov quasiparticles. This facilitates the derivation of an analytical expression for the interaction energy between the two DWs in Sec. 5.3. Finally, to illustrate the general applicability our method, we apply it in Sec. 6 to the interaction between phase solitons in a two-band s-wave superconductor.

L-Fuzzy Relations in Coq

Heyting categories, a variant of Dedekind categories, and Arrow categories provide a convenient framework for expressing and reasoning about fuzzy relations and programs based on those methods. In this thesis we present an implementation of Heyting and arrow categories suitable for reasoning and program execution using Coq, an interactive theorem prover based on Higher-Order Logic (HOL) with dependent types. This implementation can be used to specify and develop correct software based on L-fuzzy relations such as fuzzy controllers. We give an overview of lattices, L-fuzzy relations, category theory and dependent type theory before describing our implementation. In addition, we provide examples of program executions based on our framework.

An Abstract Algebraic Theory of L-Fuzzy Relations for Relational Databases

Classical relational databases lack proper ways to manage certain real-world situations including imprecise or uncertain data. Fuzzy databases overcome this limitation by allowing each entry in the table to be a fuzzy set where each element of the corresponding domain is assigned a membership degree from the real interval [0…1]. But this fuzzy mechanism becomes inappropriate in modelling scenarios where data might be incomparable. Therefore, we become interested in further generalization of fuzzy database into L-fuzzy database. In such a database, the characteristic function for a fuzzy set maps to an arbitrary complete Brouwerian lattice L. From the query language perspectives, the language of fuzzy database, FSQL extends the regular Structured Query Language (SQL) by adding fuzzy specific constructions. In addition to that, L-fuzzy query language LFSQL introduces appropriate linguistic operations to define and manipulate inexact data in an L-fuzzy database. This research mainly focuses on defining the semantics of LFSQL. However, it requires an abstract algebraic theory which can be used to prove all the properties of, and operations on, L-fuzzy relations. In our study, we show that the theory of arrow categories forms a suitable framework for that. Therefore, we define the semantics of LFSQL in the abstract notion of an arrow category. In addition, we implement the operations of L-fuzzy relations in Haskell and develop a parser that translates algebraic expressions into our implementation.

L-Fuzzy Structured Query Language

Lattice valued fuzziness is more general than crispness or fuzziness based on the unit interval. In this work, we present a query language for a lattice based fuzzy database. We define a Lattice Fuzzy Structured Query Language (LFSQL) taking its membership values from an arbitrary lattice L. LFSQL can handle, manage and represent crisp values, linear ordered membership degrees and also allows membership degrees from lattices with non-comparable values. This gives richer membership degrees, and hence makes LFSQL more flexible than FSQL or SQL. In order to handle vagueness or imprecise information, every entry into an L-fuzzy database is an L-fuzzy set instead of crisp values. All of this makes LFSQL an ideal query language to handle imprecise data where some factors are non-comparable. After defining the syntax of the language formally, we provide its semantics using L-fuzzy sets and relations. The semantics can be used in future work to investigate concepts such as functional dependencies. Last but not least, we present a parser for LFSQL implemented in Haskell.