Mathematics (Faculty of)
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exKidneyBERT: A Language Model for Kidney Transplant Pathology Reports and the Crucial Role of Extended Vocabularies
(University of Waterloo, 20220930)Background: Pathology reports contain key information about the patient’s diagno sis as well as important gross and microscopic findings. These informationrich clinical reports offer an invaluable resource for clinical ... 
Modelling Allostery using a Computational Analysis of SideChain Interactions
(University of Waterloo, 20220930)Allostery refers to the regulation of protein activity arising from an effector molecule, such as a ligand, binding to a protein. The exact mechanisms that take place in allosteric regulation are still a source of debate ... 
A Las Vegas Algorithm for the Ordered Majority Problem
(University of Waterloo, 20220929)In this thesis, we study the majority problem using ordered comparisons under the Las Vegas randomized algorithm model. The majority problem asks whether a given set of n elements, each with some colour, has a colour which ... 
Studying and Leveraging API Usage Patterns
(University of Waterloo, 20220929)Software projects make use of libraries extensively. Libraries have intended API surfaces—sets of exposed library interfaces that library developers expect clients to use. However, in practice, clients only use small ... 
Consensus Problems in Hybrid MultiAgent Systems
(University of Waterloo, 20220928)A multiagent system (MAS) is a dynamic system that consists of a group of interacting agents distributed over a network. In the past decades, the study of distributed coordination of multiagent systems has been widely ... 
Designing a Unity Plugin to Predict Expected Affect in Games Using Biophilia
(University of Waterloo, 20220928)Video games can generate different emotional states and affective reactions, but it can sometimes be difficult for a game’s visual designer to predict the emotional response a player might experience when designing a game ... 
Dash+: Extending Alloy with Replicated Processes for Modelling Transition Systems
(University of Waterloo, 20220927)Modelling systems abstractly shows great promise to uncover bugs early in system development. The formal language Alloy provides the means of writing constraints abstractly but lacks explicit constructs for describing ... 
On the power of interleaved lowdepth quantum and classical circuits
(University of Waterloo, 20220926)Lowdepth quantum circuits are a wellsuited model for nearterm quantum devices, given short coherence times and noisy gate operations, making it pivotal to examine their computational power. It was already known as early ... 
Examination of Parametric Subharmonic Instability of K₁ Internal Tides Generated by Tidal Flow over a Ridge
(University of Waterloo, 20220926)Internal gravity waves are thought to be a predominant source of mixing in the Earth's oceans. Here, we explore the interplay between two phenomena experienced by internal gravity waves  parametric subharmonic instability ... 
Edgedisjoint Linkages in Infinite Graphs
(University of Waterloo, 20220926)The main subject of this thesis is the infinite graph version of the weak linkage conjecture by Thomassen [24]. We first prove results about the structure of the lifting graph; Theorems 2.2.8, 2.2.24, and 2.3.1. As an ... 
Connectivity Properties of the Flip Graph After Forbidding Triangulation Edges
(University of Waterloo, 20220923)The flip graph for a set $P$ of points in the plane has a vertex for every triangulation of $P$, and an edge when two triangulations differ by one flip that replaces one triangulation edge by another. The flip graph is ... 
Clique minors in dense matroids
(University of Waterloo, 20220923)The objective of this thesis is to bound the number of points a $U_{2,\ell+2}$ and $M(K_{k+1})$minorfree matroid has. We first prove that a sufficiently large matroid will contain a structure called a tower. We then use ... 
Theoretical Description of the Forces on a Point Charge Moving Parallel to a Supported Twodimensional Material
(University of Waterloo, 20220922)A charged particle, moving at a certain distance and parallel to a target, experiences a stopping force that slows it down and an image force that deflects it towards the target's surface. In this work, we aimed to describe ... 
Turning Open Government Data Portals into Interactive Databases
(University of Waterloo, 20220921)The launch of open governmental data portals (OGDPs), such as data.gov, data.gov.in, and open.canada.ca, have popularized the open data movement of the last decade, which now includes numerous other portals from other ... 
Transversal Problems In Sparse Graphs
(University of Waterloo, 20220920)Graph transversals are a classical branch of graph algorithms. In such a problem, one seeks a minimumweight subset of nodes in a nodeweighted graph $G$ which intersects all copies of subgraphs~$F$ from a fixed family ... 
A Counterexample to a Conjecture About TrianleFree Induced Subgraphs of Graphs with Large Chromatic Number
(Elsevier ScienceDirect, 202301)We prove that for every n, there is a graph G with χ(G) ≥ n and ω(G) ≤ 3 such that every induced subgraph H of G with ω(H) ≤ 2 satisfies χ(H) ≤ 4.This disproves a wellknown conjecture. Our construction is a digraph with ... 
Induced Subgraphs and Tree Decompositions III. ThreePathConfigurations and Logarithmic Treewidth.
(Advances in Combinatorics, 20220909)A theta is a graph consisting of two nonadjacent vertices and three internally disjoint paths between them, each of length at least two. For a family H of graphs, we say a graph G is Hfree if no induced subgraph of G is ... 
Empirical Game Theoretic Models for Autonomous Driving: Methods and Applications
(University of Waterloo, 20220916)In recent years, there has been enormous public interest in autonomous vehicles (AV), with more than 80 billion dollars invested in selfdriving car technology. However, for the foreseeable future, selfdriving cars will ... 
KGPipeline: An Automated Knowledge Graph Generation Framework
(University of Waterloo, 20220916)Knowledge Graphs (KGs) have many applications, specifically in information retrieval and question answering. Community projects are conducted for building largescale KGs with crowdsourcing, but building KGs with this ... 
POEM: PatternOriented Explanations of CNN Models
(University of Waterloo, 20220916)While Convolutional Neural Networks (CNN) achieve stateoftheart predictive performance in applications such as computer vision, their predictions are difficult to explain, similar to other types of deep learning models. ...