3,065 Works

Non-parametric Bayesian Inference with Application to System Biology

Yi Liu
The issue of interpretability for machine learning algorithms is vital to the natural science community. If the output of machine learning procedure is fully interpretable, natural scientists can directly brought conclusions from machine learning algorithms applied to their experimental data. In this thesis, I use Bayesian machine learning techniques to develop two new variable selection methods and present two new applications to the control of biological transcription. With respect to these applications, I introduce a...

The Comic Critique of Philosophy: Aristophanes, Plato, and the Bios Theōrētikos

Douglas David Williams
Attempts to trace the conceptual history of the bios theōrētikos have tended to begin with the Platonic-Aristotelian tradition, in which the bios theōrētikos emerges as an ideal among philosophers as they attempt to articulate and evaluate what it means to live a life dedicated to the pursuit of intellectual activity as an end in itself. In this study, I present a new account of the early history of the bios theōrētikos by interpreting this fourth-century...

Some Results in Proof Complexity and SAT-Solving

Shuo Pang
This thesis studies two NP-complete problems, {\it Clique} and {\it Boolean Satisfiability} (SAT), under the proof complexity view. For Clique, we study its average-case hardness. We show that with high probability over an Erd\"os-R\'enyi random graph $G$, the proof system under consideration has no short proof of the true statement ``$G$ contains no $k$-clique''. Here $k$ is a suitable parameter, and the shortness of proof is defined by natural complexity measures such as size, width,...

In-fridge Classical Controllers in Quantum Computing

Mohammad Reza Jokar
Today’s superconducting quantum computer prototypes rely on a classical controller at room temperature that controls the qubits inside the dilution refrigerator. This approach is simple and straightforward, however, it introduces significant scalability challenges: (1) quantum error correction techniques that are based on room temperature error decoding face exponential latency overhead due to the data backlog caused by the slow decoding process; (2) scalability is limited due to massive costs of generating and routing the microwave...

Direct Optical Lithography of Colloidal Inorganic Nanomaterials for Photonic and Optoelectronic Applications

Jia-Ahn Pan
This thesis focuses on the development of chemical approaches for direct optical patterning of colloidal nanomaterials. In Chapter 1, we introduce colloidal nanomaterials and their device applications. We then discuss the need for new methods to pattern nanomaterials which motivate the development of direct optical lithography of functional inorganic nanomaterials (DOLFIN). Chapter 2 discusses the establishment of a library of photosensitive ligands and additives for DOLFIN. We demonstrate the use of these photosensitizers to pattern...

How to Paint a Butterfly? Developmental Insights into Heliconius Embryology, Color Patterning, and Pigmentation

Erick Xavier Bayala Rodriguez
Butterfly coloration has motivated the curiosity of research across many biological disciplines. It has especially been relevant in trying to address the basis of phenotypic variation. Research in this area has mainly focused on uncovering the genetic basis of such color patterning schemes, leaving the precise developmental pathways linking genotype to phenotype shrouded in mystery. The gene aristaless, which plays a role in appendage patterning and extension, has been duplicated in Lepidoptera. One copy, aristaless1...

Unconventional Condensation Phenomena from Superconductors to Polaritons

Alex Edelman
Systems with strongly interacting constituents can acquire macroscopic coherence and develop collective excitations at new energy scales that would be difficult to foresee from the microscopic ingredients. Bose-Einstein condensation and superconductivity are two paradigmatic examples of this kind of emergence. In this thesis I consider how these phenomena change in the presence of a cavity, broadly construed as some kind of field that is capable of mediating long-range forces across the system. I focus specifically...

To Feel Like We Feel: Reading the Precious Banner Sūtra as Affective Regime

Adam Tyler Miller
The Precious Banner Sūtra (Skt. Mahāsaṃnipātaratnaketudhāraṇīsūtra, Ratnaketuparivarta; Tib. 'Dus pa chen po rin po che tog gi gzungs) has been known to scholarship for over a century, yet little attention has been paid to its riveting narrative of Māra’s failed yet incompletely quelled rebellion against the Buddha. Grounded in the history of religions and informed by affect theory, the sociology and history of emotions, and narratology, this dissertation argues that the Precious Banner contains what...

Incompleteness Under Discussion

Yenan Sun
This dissertation re-examines a puzzling restriction on assertability of certain zero-marked sentences in the grammar of Mandarin Chinese, the so called incompleteness phenomenon (Kong 1994; He 1994; Tang and Lee 2000; Gu 2007; Tsai 2008; Guo 2015; Sybesma 2019; Tang 2022, among others). Unlike the majority of the existing analyses which attribute incompleteness to some context-free grammatical requirement, I establish the novel generalization that incompleteness is sensitive to the explicit or contextually implied Questions Under...

Caught by Surprise: Affect and Feminist Politics in the Art of Magali Lara

Maggie Borowitz
This dissertation explores the vibrant feminist art scene of 1970s and 80s Mexico City, centering upon the artistic practice of Magali Lara (b. Mexico City, 1956). I examine feminist practices during this period in conversation with broader understandings of what has constituted “political art” in twentieth-century Mexico, asking: What does a theory of political art that accounts for art’s affective power look like? And, how might the affective aspects of art allow for a type...

Towards the Study of Ultrafast Chiral Electronic Dynamics

Elizabeth M. Bain
This dissertation aims to provide new methods of interrogating the nature of electronicdynamics in chiral materials. The superiority of photosynthetic light harvesting over any man-made solar light harvesting devices motivates the study of how chirality affects light harvesting. A two-dimensional ultrafast chiral spectroscopy is designed and built. This new instrumentation has the capability to provide vital and unique insight into ‘handed’ electronic dynamics. The theory behind the cancellation of achiral background is described. Great care...

Music’s Visual Waves: Popular Music Technology and Audiovisual Aesthetics

Amy Elizabeth Skjerseth
This dissertation explores how technological innovations influenced music and visual culture over four decades, from 1960s transistor radios to 1990s Auto-Tune. Portable music technologies in the postwar era inspired American and British filmmakers and pop stars to give pop songs increasingly mobile and visual meanings. In the 1960s and ’70s, American avant-garde filmmakers transformed pop songs’ often patriarchal and heteronormative subject matter with moving images that championed women’s and sexual liberation. And when music videos...

Coherent Configurations: Motion, Spectral Properties, Robustness

Bohdan Kivva
The principal theme of this thesis is the interplay between symmetry and regularity in discrete structures. The most general class of structures we consider are coherent configurations, certain highly regular colorings of complete graphs. This class includes such diverse structures as the orbital configurations of permutation groups and association schemes originating from the design of experiments in statistics. Metric schemes, a subclass of association schemes, are derived from distance-regular graphs. Johnson, Hamming, and Grassman schemes...

Philology as a Way of Knowing: Classical Philology in the Reformed German Universities, 1730–1830

Kristine Palmieri
This is the first comprehensive history of the philology seminar as an institutional, intellectual, pedagogical, and scientific space. It also breaks new ground by studying the history of philology from a history of science perspective. “Philology as a Way of Knowing” demonstrates how and why classical philology became the preeminent science at German universities in the period 1730–1830 by telling two interrelated stories. On one hand, it reveals how the transformation of philological methods and...

Effects of Climate Change on Interactions between a Forest Pest and Its Natural Enemies

Jiawei Liu
Climate change can often lead to severe but complicated effects on ecosystems. Previous studies of the effects of climate change on ecosystems have often focused on single species, thereby neglecting species interactions and underlying mechanisms. To comprehensively understand how climate change influences ecosystems, interactions among multiple species should be considered. Here we provide an example of why species interactions are important for understanding and predicting the effects of climate change on a forest pest species,...

What Are You Waiting For? Factors That Influence Patient Decisions and Experiences

Annabelle Roberts
In my dissertation research, I explore the psychology of patience. Patience has primarily been studied as a choice. When people are patient, they are willing to wait to receive a better outcome later instead of a worse outcome sooner. The decision to wait predicts better outcomes in a variety of domains, from health to financial decision-making. However, there are many situations where people are not given a choice about whether to wait. In these situations,...

Interpretable Data Science: Applications and Theory in Climate Science and Public Health

Abby Stevens
New statistical and machine learning methods have led to important advances in image and natural language processing, genetics, digital advertising, and other fields where there is an abundance of high-quality digital data and strong market incentives for automating tasks. This thesis intentionally focuses on areas such as climate science and public health, as they have suffered in this space without the same scale of training data and private investment. Part 1 of this thesis focuses...

(Re)Making the View: The Shifting Imaginary of West Lake, from the 13th to the 19th Century

Yunfei Shao
Examining the images of West Lake from the thirteenth to the nineteenth century in China, this dissertation focuses on the representation of the place as a topographic, historic, and cultural site. Following two lines of inquiry, this dissertation explores the boundaries and efficacies of site-specific paintings while probing the long-perceived Song (960–1279) lineage of West Lake paintings. This dissertation considers paintings of West Lake as images constructed from vision, experience, memory, and history. These images...

Deep Generative Models: Design, Improvements and Applications

Qing Yan
Deep generative models (DGM) combine the deep neural networks with generative models to learn the underlying generation mechanism of the data of interest. This has emerged as a important approach to extracting knowledge from data in machine learning and artificial intelligence. However, there are many challenges to learning and applying DGMs in different domains despite their promising potential. Therefore, this thesis focuses on understanding, improving, and applying different deep generative models. First, we introduce the...

Legal and Extralegal Factors Affecting Sentencing: The Domestic Nature, Judicial Transparency, and Types of Counsel

Yali Peng
The purpose of this dissertation is to examine three factors that can influence sentencing: the domestic nature of the crime, the type of attorney, and the level of judicial transparency. Normatively, the part on the domestic nature examines how it should be approached. In contrast to other sentencing factors, such as criminal histories for which jurisdictions adopt a uniform approach, each jurisdiction treats the domestic factor differently. The domestic nature may serve both as a...

Corporate Debt Standardization and the Rise of Electronic Bond Trading

Artur Bezerra De Carvalho
I study the impact of standardization on secondary corporate bond markets as the industry adopts electronic trading systems. I show that covenants can reduce debt rollover costs by mitigating agency problems. However, when trading in the more liquid electronic markets is restricted to standardized securities, firms must weigh the benefits of offering credit protection against e-trading’s lower transaction costs. I investigate firms’ choices of leverage and debt type when creditors are not fully informed about...

Reduced Density Matrix Methods for the Resolution of Electron Correlation and Their Applications to Bimetallic Complexes

Jan-Niklas Boyn
The most fundamental struggle of modern electronic structure theory is the accurate description of electron correlation, which is commonly divided into its dynamic and multireference or strong parts. The former is readily captured with various modern electronic structure methods at polynomial computational cost, while the latter exhibits exponential scaling in traditional wave function based theories. For the precise and tractable computation of molecular electronic properties and processes it is essential to develop methods that capture...

Development and Kinetic Analysis of Emerging Positron Emission Tomography Radiotracer Vandium-48-labeled Vanadyl Acetylacetonate

Brittany Broder
Vanadyl acetylacetonate (VO(acac)2) has shown promise as a magnetic resonance imaging (MRI) agent due to its high selectivity for cancer cells, which could facilitate differentiation of carcinogenesis stages progressing from inflammation to malignant tumor. This is especially vital for types of cancer where inflammation is a recognized component or precursor for tumorigenesis, such as colorectal cancer (CRC) [32]. The novel positron emission tomography (PET) radiotracer vanadium-48-labeled-VO(acac)2 (48VO(acac)2) is a positron-emitting, long-lived (t1/2 = 16 days)...

Modulating RhoA Effectors Induces Transitions to Oscillatory and More Wavelike RhoA Dynamics in Caenorhabditis elegans Zygotes

Baixue Yao
The biological world is full of patterns, from macroscopic patterns such as leaf veins to microscopic patterns that underlie processes such as cell polarization and migration. The implementation of such biological functions requires spatiotemporal control of cellular activities. A key challenge in biology is to understand the mechanisms of pattern formation. Mathematical theories on biological pattern formation were first introduced in the 1950s. Since then mathematical biologists have been trying to explain biological patterns with...

Disclosing Labor Demand

Gurpal Singh Sran
I study disclosure choices in job postings and the trade-off between two channels: detailed postings inform and attract optimal job applicants (i.e., a labor market channel) but could also inform competitors in labor and product markets (i.e., a proprietary costs channel). First, I provide evidence consistent with a proprietary costs channel: private firms and redacting firms are less specific in their postings, and postings are more often anonymous in industries with high levels of trade...

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