A Multi-Objective Genetic Algorithm with Side Effect Machines for Motif Discovery

Understanding the machinery of gene regulation to control gene expression has been one of the main focuses of bioinformaticians for years. We use a multi-objective genetic algorithm to evolve a specialized version of side effect machines for degenerate motif discovery. We compare some suggested objectives for the motifs they find, test different multi-objective scoring schemes and probabilistic models for the background sequence models and report our results on a synthetic dataset and some biological benchmarking suites. We conclude with a comparison of our algorithm with some widely used motif discovery algorithms in the literature and suggest future directions for research in this area.

Depopulating the Political Sidelines: CBC News Online Forum and Public Spheres in Canada

The subject of the Internet's potential to foster a public sphere has become a growing area of research in the social sciences in the last two decades. My research explores comments made by participants on the CBC News online politics forum during the May 2011 federal election in Canada. Based on conditions proposed by Jurgen Habermas in his concept of the public sphere and operationalized by Lincoln Dahlberg in his pioneering study of the Minnesota e-Democracy listserv, my thesis explores the potential for the CBC News online forum to foster a public sphere for Canadians. While examining the CBC News online forum against the criteria of the public sphere, I also interrogate Habermas' concept of a universal public sphere using the works of Nancy Fraser and other scholars, who argue for multiple public spheres.

Learning and Experiential Outcomes of Face-to-Face Versus Online Communications Courses

Higher education is rapidly trending toward the implementation of online (OL) courses and a blended facilitation style that incorporates both OL and face-to-face (FTF) classes. Though previous studies have explored the benefits and pitfalls of OL and blended learning formats from institutional, teacher, and student perspectives, scant research has examined learning outcomes for OL and FTF courses sharing identical content. This study used an explanatory mixed methods design—including pre- and post-test assessments, a questionnaire, and interviews—to explore similarities and differences in participant and teacher perceptions and outcomes (gain scores and final grades) of OL versus traditional FTF Communications courses, and to examine effects of students’ age and gender on learning preference and performance. Data collection occurred over a 4-month period and involved 183 student and 2 professor participants. The study used an SPSS program for data analysis and created a Microsoft Excel document to record themes derived from the questionnaire and interviews. Quantitative findings suggest there are no significant differences in gain scores, final grades, or other learning outcomes when comparing OL and FTF versions of identical Communications courses; however, qualitative findings indicate differences between facilitation styles based on student and professor perception. The study sheds light on student and faculty perceptions of facilitation styles and suggests areas for potential improvements in FTF- and OL-facilitated courses. The study ultimately recommends that students and faculty should have options when it comes to preferred delivery of course material.

A Continuum of Traversing Lines: Youth Political Participation in Gaia Online

This qualitative research project uses a Deleuzo-Guattarian theoretical framework to address the question: “How are the politically oriented social forums in Gaia Online experienced as a continuum of overlapping of lines, including molar lines, lines of flight, and molecular lines?” Although smooth lines of flight may occur in Gaia, there are always mechanisms that work to re-territorialize them as more striated molar operations. Conversely, while more striated molar lines may be evident in Gaia, there are also smooth lines of flight that attempt to deterritorialize them as smooth space. Founded in 2003, Gaia is a virtual community in which members use 3D avatars to socialize with others, create content, and play games. Deleuze and Guattari (1987) have defined space with three systems: on one end is state-oriented static space, on the other end is nomadic fluid space, and situated in the middle is molecular space which contains both smooth and striating elements. While state-oriented striated space is based on routines, rules, and specifications, nomadic smooth space is flexible, always changing, and full of possibility. Some of the smoother operations that are evident in Gaia include becoming other, decentred communications, desire as resistance, and lines of flight. Some of the more striated operations include social reproduction of gender norms/expectations, capitalist mechanisms, violence and intolerance linked to categories and binaries (racism/sexism/ageism), the regulation of desire, and the organisation of bodies.

An Ontario-Developed Online Special Education Teacher Course Model for China

This study investigated the effectiveness of an Ontario-developed online Special Education teacher training course as a model for in-service teacher professional development in China. The study employed a mixed method approach encompassing both a quantitative survey and a qualitative research component to gather perceptions of Chinese and Canadian teachers, educational administrators, and teacher-educators who have intensive experience with online education, Special Education, and teacher preparation programs both in China and Canada. The study revealed insufficient understanding of Special Education among the general Chinese population, underdevelopment of Special Education teacher preparation in China, and potential benefits of using a Canadian online teacher training course as a model for Special Education in China. Based on the literature review and the results of this study, it is concluded that online Canadian Special Education teacher in-service courses can set an example for Chinese Special Education teacher training. A caveat is that such courses would require localized modifications, support of educational authorities, and pilot testing.

Online Anonymity and the Kantian Publicity Principle: Can the Internet Solve the Paradox of Tyranny?

Immanuel Kant’s publicity maxim states that other-regarding actions are wrong if their maxim is not compatible with their being made public. This has the effect of forbidding dissent or rebellion against tyranny, since rebels cannot make their intentions and plans public. However, new internet technologies offer public speech from behind the “shield” of anonymity, allowing dissent to be public but preventing reprisals from tyrants. This thesis examines not only this possibility, but the value of internet-based discursive spaces for politics, their viability as a mode for political communication, and their implications for Classical and Enlightenment approaches to politics and intellectual virtue. Anonymous internet communications favour logos-based reasoning and discourse, which, in the liberal-democratic tradition, is preferable to phronesis and its attendant elitism and chauvinism. These technologies can open new vistas for liberal-democratic politics.

New Contig Creation Algorithm for the de novo DNA Assembly Problem

DNA assembly is among the most fundamental and difficult problems in bioinformatics. Near optimal assembly solutions are available for bacterial and small genomes, however assembling large and complex genomes especially the human genome using Next-Generation-Sequencing (NGS) technologies is shown to be very difficult because of the highly repetitive and complex nature of the human genome, short read lengths, uneven data coverage and tools that are not specifically built for human genomes. Moreover, many algorithms are not even scalable to human genome datasets containing hundreds of millions of short reads. The DNA assembly problem is usually divided into several subproblems including DNA data error detection and correction, contig creation, scaffolding and contigs orientation; each can be seen as a distinct research area. This thesis specifically focuses on creating contigs from the short reads and combining them with outputs from other tools in order to obtain better results. Three different assemblers including SOAPdenovo [Li09], Velvet [ZB08] and Meraculous [CHS+11] are selected for comparative purposes in this thesis. Obtained results show that this thesis’ work produces comparable results to other assemblers and combining our contigs to outputs from other tools, produces the best results outperforming all other investigated assemblers.

Hidden Motives: An Analysis of Online ESL Teacher Hiring Practices in Japan and Hong Kong

Hidden Motives: An Analysis of Online English as a Second Language (ESL) Teacher Hiring Practices in Japan and Hong Kong is a qualitative research paper examines and compares two large-scale Asian English language teaching programs: Japan’s Japan Exchange and Teaching (JET) Programme (JET Programme, 2010) and Hong Kong’s Native-speaking English Teacher (NET) Scheme (NET Scheme, 2013). Both government sponsored programs recruit internationally and invite participants to work within each country’s public schools while living amongst local communities and both programs utilize their online presence to attract, inform, and recruit individuals. The purpose of this research is to investigate whether the JET and NET websites are transparent with their governmental motives aside from improving their students’ English language abilities. While JET and NET websites were interrogated, the research questions were regularly revisited to determine if the two sites made any underlying motives clear to the candidates. The research, supported by academic literature, exposed the JET Programme website to be a branch of the Japanese government’s soft power campaign, whereby JET teachers were hired firstly as potential advocates for Japan and Japanese culture rather than English teachers. Conversely, the NET Scheme appeared to be solely commissioned for English language improvement as reflected by their website. Findings from the research can provide insight to applicants to help them decide if they want to participant in these programs. Without clearly understanding the background that motivates these programs, participants may unknowingly be used to support the host government’s agendas.

A Study of Ordered Gene Problems Featuring DNA Error Correction and DNA Fragment Assembly with a Variety of Heuristics, Genetic Algorithm Variations, and Dynamic Representations

Ordered gene problems are a very common classification of optimization problems. Because of their popularity countless algorithms have been developed in an attempt to find high quality solutions to the problems. It is also common to see many different types of problems reduced to ordered gene style problems as there are many popular heuristics and metaheuristics for them due to their popularity. Multiple ordered gene problems are studied, namely, the travelling salesman problem, bin packing problem, and graph colouring problem. In addition, two bioinformatics problems not traditionally seen as ordered gene problems are studied: DNA error correction and DNA fragment assembly. These problems are studied with multiple variations and combinations of heuristics and metaheuristics with two distinct types or representations. The majority of the algorithms are built around the Recentering- Restarting Genetic Algorithm. The algorithm variations were successful on all problems studied, and particularly for the two bioinformatics problems. For DNA Error Correction multiple cases were found with 100% of the codes being corrected. The algorithm variations were also able to beat all other state-of-the-art DNA Fragment Assemblers on 13 out of 16 benchmark problem instances.

The Hidden Truths of Self-Presentation, Self-Disclosure, and Deception on Online Dating Profiles: A Call for Change

The way in which individuals seek romantic partners has changed considerably in the past decades, most notably through online dating sites (ODSs). Despite the possibility of misrepresentation amongst client users, such sites continue to grow in popularity because ODSs provide a large pool from which individuals can select and attract potential partners. While much research has been undertaken on ODSs, little empirical research has examined postsecondary students’ use of ODSs. Therefore, this study sought to investigate why postsecondary students have become involved with and how they present themselves on ODSs. The researcher surveyed 20 postsecondary students and conducted in-depth interviews with 2 participants who use ODSs. Although the limited sample prevented results from being generalized, quantitative and qualitative analyses suggest that participants became involved with ODSs for various purposes, such as seeking long-term relationships and/or marriage partners, or simply exploring or visiting ODSs out of curiosity. Findings indicate that ODS users’ physical appearance and/or “attractiveness” is considered the strongest predictor of relationship success. The study discusses how participants’ self-presentation affects outcomes of ODS usage, particularly when negative self-identification and presentation corresponding to factors such as individuals’ weight and age are taken into account.

An Examination of the Development of Online Higher Education in Canada and China: Keeping Pace and Making Space

This study examined the similarities and differences that currently exist between Chinese and Canadian online higher education, and explored the economic, political, and sociocultural environments that have shaped online education in these two jurisdictions. Furthermore, this paper discussed the efficacy of, and potential for, future development of online learning in higher education in both Canada and China. The research employed a collective case study design to gather information and data on the development of online higher education. The analysis on Contact North in Canada and the One-Man University in China provide a comparative perspective on the development of 2 typical online higher educational institutions in these two countries. The study revealed that the development of online higher education is influenced by the economic, political, and sociocultural factors of environment. Contact North and the One-Man University share similarities in many aspects, but are characteristically different. The Contact North can set an example for establishing and operating a self-regulated MOOCs platform. The study also generated implications for both organizations.

Disease-Gene Association Using a Genetic Algorithm

Understanding the relationship between genetic diseases and the genes associated with them is an important problem regarding human health. The vast amount of data created from a large number of high-throughput experiments performed in the last few years has resulted in an unprecedented growth in computational methods to tackle the disease gene association problem. Nowadays, it is clear that a genetic disease is not a consequence of a defect in a single gene. Instead, the disease phenotype is a reflection of various genetic components interacting in a complex network. In fact, genetic diseases, like any other phenotype, occur as a result of various genes working in sync with each other in a single or several biological module(s). Using a genetic algorithm, our method tries to evolve communities containing the set of potential disease genes likely to be involved in a given genetic disease. Having a set of known disease genes, we first obtain a protein-protein interaction (PPI) network containing all the known disease genes. All the other genes inside the procured PPI network are then considered as candidate disease genes as they lie in the vicinity of the known disease genes in the network. Our method attempts to find communities of potential disease genes strongly working with one another and with the set of known disease genes. As a proof of concept, we tested our approach on 16 breast cancer genes and 15 Parkinson's Disease genes. We obtained comparable or better results than CIPHER, ENDEAVOUR and GPEC, three of the most reliable and frequently used disease-gene ranking frameworks.

Social Organization on the Web: How Sex workers Rights Organizations Engage in Activism and Advocacy Work Online

The purpose of this study was to examine how sex workers rights organizations use their websites as a site of activist and advocacy work and ask (i) how do various organizations conceptualize sex work on their websites, and to what extent do they incorporate an intersectional feminist perspective? (ii) what communication strategies are used by the four organizations to target audiences in the viewing public? (iii) what audiences do the four websites target? (iv) how do the four organizations discuss successes and challenges on their websites? (v) in what ways do sex worker right organizations use websites to further their goals? The websites of Maggie’s, POWER, and Stella attempt to embrace an intersectional feminist perspective of sex work, while PACE does not. The four organizations strategically use their websites to target audiences with diverse needs, specifically through advocacy efforts in educating the general public about the legitimacy of sexual labour. Additionally, to increase the use of the websites by sex workers, using social media platforms, such as Facebook and Twitter augment the untapped potential for creating action, mobilization, interaction, and dialogue on the websites.

Using PageRank Algorithm in Analyzing Dictionary Graphs and PageRank in Dynamic Graphs

In this thesis we are going to analyze the dictionary graphs and some other kinds of graphs using the PagerRank algorithm. We calculated the correlation between the degree and PageRank of all nodes for a graph obtained from Merriam-Webster dictionary, a French dictionary and WordNet hypernym and synonym dictionaries. Our conclusion was that PageRank can be a good tool to compare the quality of dictionaries. We studied some artificial social and random graphs. We found that when we omitted some random nodes from each of the graphs, we have not noticed any significant changes in the ranking of the nodes according to their PageRank. We also discovered that some social graphs selected for our study were less resistant to the changes of PageRank.

Community Detection in Multi-Layer Networks

In the scope of the current thesis we review and analyse networks that are formed by nodes with several attributes. We suppose that different layers of communities are embedded in such networks, besides each of the layers is connected with nodes' attributes. For example, examine one of a variety of online social networks: an user participates in a plurality of different groups/communities – schoolfellows, colleagues, clients, etc. We introduce a detection algorithm for the above-mentioned communities. Normally the result of the detection is the community supplemented just by the most dominant attribute, disregarding others. We propose an algorithm that bypasses dominant communities and detects communities which are formed by other nodes' attributes. We also review formation models of the attributed networks and present a Human Communication Network (HCN) model. We introduce a High School Texting Network (HSTN) and examine our methods for that network.