Simon Fraser University Undergraduate Collection

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This collection contains undergraduate honours theses and certain other selected undergraduate works by SFU undergraduate students.

Learning efficiency in the Inverse Ising Problem

Author: 
Peer reviewed: 
No, item is not peer reviewed.
Date created: 
2018-04
Abstract: 

In recent years, the amount of data available on biological systems such as genetic regulatory networks and neural networks has increased exponentially, thanks to improvements in experimental methods such as drop-seq [1], which enables biologists to simultaneously analyze RNA expression in thousands of cells. To keep pace with the available data, modern machine learning requires efficient methods for using this data to develop predictive models about the natural world. Using a canonical statistical physics example, the Inverse Ising problem, we ask how physical factors such as temperature affect the learning efficiency. In a network governed by a Hamiltonian with spin-spin interactions, we construct a linear system of equations based on equilibrium observations of spin states, and use linear algebra to solve for the underlying spin-spin couplings. We show that there exists an optimal temperature Topt for which learning is most efficient. Furthermore, we discuss several physical correlates for the scaling of Topt with network size for a simple uniform-coupling network and discuss the extension to more general distributions of couplings. The Fisher information, which depends strongly on the variance of the spin-spin alignment, is shown to predict this scaling most accurately.

Document type: 
Thesis
File(s): 
Supervisor(s): 
David Sivak
Department: 
Science: Department of Physics
Thesis type: 
Honours Bachelor of Science

Optimal Control of Cellular States

Author: 
Peer reviewed: 
No, item is not peer reviewed.
Date created: 
2017-04
Abstract: 

Recent experimental advancements have allowed for the precise spatial and temporal control of chemical potentials between proteins in the vicinity of one another through optogenetic techniques [3]. This new technique allows for the investigation of cell signalling. Cells communicate by sending chemical signals to induce changes in chemical potentials which then leads to a change of cellular state. In this thesis we apply non-equilibrium theory [6] to model the response of cells to changes in chemical potential, then, by assuming cells want to minimize wasted energy we derive the optimal protocol for cells to change their cellular state through changes in chemical potential. We provide the theoretical framework to derive this optimal protocol for three separate two state chemical reactions: a discrete open system attached to a bath of proteins, a discrete closed system where the total number of proteins is fixed and a continuous closed system where we consider both the spatial and temporal dependence. Although the theory developed is applicable to these reactions for any transition rates, we assume a specific form which closely resembles cell signalling. The resistance to changes in chemical potential is shown to increase exponentially with chemical potential for an open system, to increase exponentially then decay slowly with chemical potential for a closed system and decreases as 1/r where r is the distance from the change. From this we find the optimal protocol and compare the excess work required to change the cellular state using the optimal and naive (constant velocity) protocols. For an open system the optimal protocol is much better than the naive if the chemical potential is varied across a large distance. For a closed system we find similar behaviour for smaller chemical potentials but the improvement then peaks and decreases slowly for very large distances. The spatial dependence of the continuous system has the added effect of decreasing the improvement and smoothing out the peak. We show that our results are consistent with one another in the limiting cases. From this we conclude that cells which require changes in chemical potential within the peak region to change their cellular state will gain the largest benefit from the optimal protocols derived. The optimal protocol has a simple logarithmic form in time µ(t) = ln(ct + b), with c and b constants, for the open system, for the closed and continuous systems it has a more complex shape. Proof of concept of directly simulating the system for comparison is shown, and issues with simulation are discussed.

Document type: 
Thesis
File(s): 
Supervisor(s): 
David Sivak
Department: 
Science: Department of Physics
Thesis type: 
Honours Bachelor of Science

Optimal Regulation of Circadian Clock

Author: 
Peer reviewed: 
No, item is not peer reviewed.
Date created: 
2018-07
Abstract: 

A circadian clock (sometimes called a circadian oscillator or rhythm) oscillates roughly once every 24 hours, enabling us to organize our physical and mental activities at the time that is most optimal. The Nobel Prize in physiology or medicine in 2017 was awarded to the scientists who discovered the molecular mechanisms controlling the circadian clock.[1] In this thesis, we study the circadian clock in a physical and mathematical setting. The modified Kuramoto model which describes the synchronization between coupled oscillators is chosen as the equation of motion to study the circadian clock of living organisms. More specifically, we picture our physical system as two individual oscillators, one the solar-cycle oscillator and the other an internal-clock oscillator of a living organism. As in the real world, there is always random noise that prevents living organisms from having perfect knowledge of the outside world. Noise can either come from the environmental background or uncertainty in the internal processing of the organism. The deterministic and stochastic versions of the modified Kuramoto model are separately analyzed. The cost analysis based on the phase synchronization between the two oscillators in both deterministic and stochastic environments can reflect the optimization problem of an organism’s circadian clock. Our approach of analyzing the circadian clock can provide us an insight to regulate the operation of a circadian clock within a noisy environment and with internal noise.

Document type: 
Thesis
File(s): 
Supervisor(s): 
David Sivak
Department: 
Science: Department of Physics
Thesis type: 
Honours Bachelor of Science

Energy and Information Transduction In Strongly-Coupled Systems

Peer reviewed: 
No, item is not peer reviewed.
Date created: 
2019-04
Abstract: 

Molecular machines are stochastic systems that interconvert different forms of energy, such as chemical potential energy and mechanical energy. These machines are generally comprised of many subunits that each perform a specific function. We develop a novel model that captures some of the important behaviours of rotary stochastic coupled systems. This model contains an explicit reference to the degree of coupling between subunits and allows for the investigation of energy transduction as a function of coupling strength. Evolving the system using Fokker-Planck dynamics, we find that the efficiency of this energy transduction is tightly correlated with coupling strength. In addition, recent developments in theoretical studies have established links between information theory and stochastic thermodynamics. Prompted by these developments, we investigate the information-theoretic quantities of nostalgia and learning rate. We find that, in this model, these quantities lose their link to the thermodynamics of the system, as here we consider the case of symmetric coupling between subsystems whereas these quantities were originally derived for asymmetric coupling.

Document type: 
Thesis
File(s): 
Supervisor(s): 
David A. Sivak
Department: 
Science: Department of Physics
Thesis type: 
Honours Bachelor of Science

WL Honours Thesis Myth and Modernity: Orphic Traces in Thomas Mann’s Magic Mountain

Author: 
Peer reviewed: 
No, item is not peer reviewed.
Date created: 
2018-12-20
Abstract: 

This paper is a study of the influence and reception of the mythological tropes of descent and return as seen in Thomas Mann’s 1924 novel, The Magic Mountain and, more broadly, within the context of the early twentieth-century modernity. Making reference to Friedrich Nietzsche, Walter Strauss, and Modris Eksteins, it draws connections between Castorp’s desire-driven journey of descent and Germany’s own inwards turn. Moreover, by analyzing the traces of the Orphic myth noticeable in the novel and examining the importance of Orpheus myth to modernist sensibilities, this paper argues that despite the promise of unity the novel appears to signal, Castorp’s inability to retain his vision reveals Mann’s novel as a satirical commentary not only on the individual’s fragmentation but, significantly, on the cultural atomization of early twentieth century Germany.

Document type: 
Graduating extended essay / Research project
File(s): 
Supervisor(s): 
Mark Deggan
Department: 
World Literature

Deep Learning for Satellite Image Analysis

Author: 
Peer reviewed: 
No, item is not peer reviewed.
Date created: 
2017-12-18
Abstract: 

Deep learning architectures have the potential of saving the world from losing football fieldsized forest areas each second. These architectures possess large learning capacities when compared to conventional machine learning architectures, and thus are trained on sizable data-sets to efficiently extract both coarse and fine features from various image scenes. As a result, they can provide crucial information that is needed to manage the deforestation process and its consequences on the environment and ecosystem more effectively. This thesis outlines the two deep learning based systems designed for satellite image analysis. The first system analyzed satellite images of the Amazon, and the goal was to interpret the image content by providing a set of labels that best describe it. The highest performing architecture was able to achieve a score of 92.886% while a combination of several high performance, yet uncorrelated, architectures increased the overall score to 93.070%. This result is only 0.248% lower than what current state of the art algorithms achieved on the same task. The second system was designed to detect the presence of clouds in Landsat 8 images by analyzing small chips within each large image. This system produced cloud masks, which were then compared to the corresponding ground truth cloud masks obtained from the provided images. The predicted cloud masks were able to achieve an average score of 92.931%, which is very high for the given accuracy measure.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Ivan V. Bajić
Department: 
Applied Sciences: School of Engineering Science
Thesis type: 
Honours Bachelor of Applied Science

Exploring the Molecular Properties of Collagen Type IV with Atomic Force Microscopy

Author: 
Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2018-04-13
Abstract: 

Collagen type IV is a network-forming collagen that provides support and anchorage to cells. Its basic structural unit is a 410 nm long and 1.5 nm in diameter triple helix, with natural discontinuities in the triple-helical defining Gly-X-Y sequence. The C-terminal globular domain (NC1) in a collagen IV molecule plays an important role in forming networks, and has recently been reported to be structurally triggered by chloride ions to form hexamers outside the cell. How this hexamer assembles in vitro remains unknown. Here, I aim to use atomic force microscopy (AFM) to investigate the molecular basis of collagen type IV network assembly by studying the effects of different solvent conditions on the stability of the NC1 domain. Studying the dissociation of this hexametric domain can shed light onto how it assembles in solution and under what ionic conditions. The flexibility of the collagen type IV molecule is also investigated by performing statistical analysis of AFM-imaged chains and estimating persistence length, a mechanical property that quantifies the flexibility of a polymer. Here, I investigate the effects of triple helix interruptions on the flexibility of the molecule, by comparing collagen type IV to other fibrillar collagens that are continuously triple-helical. In addition, I determine a position-dependent flexibility profile of the molecule showcasing the effects of over-lapping interruptions, from a α1(IV)]2–α2(IV) mouse collagen type IV, on the persistence length.

Document type: 
Thesis
File(s): 

Inventing the “Virgo Angla”: Power, Patronage, and Self-Representation in the Poetry of Elizabeth Jane Weston

Author: 
Peer reviewed: 
No, item is not peer reviewed.
Date created: 
2018-04-23
Abstract: 

An individual’s self-presentation can leverage their place in the economy of social power: so suggest the patronage letters of Elizabeth Jane Weston (1582-1612), a young Neo-Latin poet in the court of Holy Roman Emperor Rudolf II. This paper examines how Weston adopted the persona of “Virgo Angla” (“The British Maiden”) and used conventionalized rhetorical techniques to navigate the power dynamics of patronage in the Neo-Latin Republic of Letters. Close readings of Weston’s letters explore how her self portrayal was a critical ingredient in her appeals to patronage: Weston portrayed herself in terms that emphasized her youth and gender, which she deployed in strategic modesty tropes and doubled discourses throughout her oeuvre. Ultimately, these close readings examine how Weston used her literary self-presentation to successfully play the patronage game, underscoring the notion that personal branding has currency in social power dynamics.

Document type: 
Graduating extended essay / Research project
File(s): 
Supervisor(s): 
Melek Ortabasi

De-sketching

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2018-06-22
Abstract: 

Many software applications exist for plotting graphs of mathematical functions, yet there are none (to our knowledge) that perform the inverse operation - estimating mathematical expressions from graphs. Since plotting graphs (especially by hand) is often referred to as "sketching," we refer to the inverse operation as "de-sketching." As the number of mathematical expressions that approximate a given curve can be quite large, in this demo we restrict our attention to polynomials, and present a deep model that performs de-sketching by finding the best second-degree polynomial to fit the curve in the input image. Currently, our trained model is able to provide reasonably accurate estimates of polynomial coefficients for both synthetically-generated and hand-drawn curves.

Document type: 
Conference presentation
File(s): 

Expanding the Moroccan Storytelling Circle: Adaptations of Indigenous Moroccan Orality from Paul Bowles’ Five Eyes to Betsy Bolton’s Maghrebi Voices

Author: 
Peer reviewed: 
No, item is not peer reviewed.
Abstract: 

This essay examines the traces of indigenous Moroccan oral storytelling in various collections of translated work. By focusing on the variations of form across these collections, and highlighting the commonalities between these stories, this essay argues that traces of the oral tradition found in translations from Morocco are evidence to the survival of its storytelling roots, and that these adaptations create an opportunity for the growth of new spaces in the tradition. A key example is Paul Bowles’ Five Eyes, a 1979 text adapted from the oral stories of illiterate Moroccans. Being both a set of performances adapted into writing, as well as a set of collaborative translations, Five Eyes moves between genres. This essay considers such movement through a background of cultural mediation, utilizing Homi Bhabha’s concept of “third space”. It also offers the analysis of a consistent literary style across texts originating in orality as well as in written form, by using Joseph Frank’s now-classic framework of spatiality and temporality in narrative structure. Using Five Eyes to build a perspective towards the process of literary adaptations from oral traditions, this essay enters more recent Moroccan collections. Such narratives include Mohamed Said Raihani’s “The Moroccan Dream” – a collection of contemporary written translations by Moroccan authors. This essay then enters the discussion of the halqa storytelling tradition in Morocco through Richard Hamilton’s The Last Storytellers, to provide a comparison in style between legitimated and illiterate indigenous storytellers. These stories, though having diverged from a common heritage, show similar styles, structures and grammatical cues that originate in oral performance. Betsy Bolton’s website, Maghrebi Voices, provides a contemporary endpoint, juxtaposing components that occur in each previous example, including recorded oral stories, written narratives, commentary and translated works, on an online platform.

Document type: 
Graduating extended essay / Research project
File(s): 
Supervisor(s): 
Mark Deggan