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Towards The Mathematical Intepretability Of Likelihood-Based Generative Models, Henry Li

Yale Graduate School of Arts and Sciences Dissertations

Probabilistic generative models have seen rapid adoption as algorithmic tools in a multitude of domains due to their unparalleled capacity to model and draw samples from complex high-dimensional data distributions in a wide range of modalities. At their core, these models are simply transformations that map a simple known distribution to an arbitrarily complex target distribution. As these algorithms essentially operate over measure spaces, they are inherently stochastic, and their implementational details allow their taxonomy as either explicit or implicit probabilistic models. Explicit models directly permit the evaluation of a likelihood function pθ(x), which is directly maximized with respect to …

Reading Into Things: Articulate Objects In North America, 1650-1820, Lily Higgins

Yale Graduate School of Arts and Sciences Dissertations

In the eighteenth century, it-narratives emerged as a new literary genre, elevating objects to the role of heroes and heroines. Investing fictional objects with the power to participate in human affairs, these stories offer insight into how the contemporaneous reading public grappled with the agency of objects in real life. Responding to questions about agency and subjectivity provoked within the early modern it-narrative, this dissertation considers how actual objects made and used within an ever-widening world of material goods were “speaking” to people in new ways, both exciting and disconcerting. Defining these “speaking” things as “articulate objects,” the research suggests …

Levitated Optomechanical Sensors For Fundamental Physics, Jiaxiang Wang

Yale Graduate School of Arts and Sciences Dissertations

This thesis focuses on utilizing more than 20 years of development of optomechanics to develop new measurement tools to solve open questions in fundamental physics. Optomechanical detectors offer a highly sensitive method for measuring weak forces. By optically trapping these systems in high vacuum, one can drastically reduce environmental noise and achieve exquisite control over the detector's center-of-mass motion, rotational degrees of freedom, and physical characteristics such as charge states. This level of isolation enables the detector's noise to reach the quantum measurement regime, where the dominant noise source is the measurement process itself. Such sensors are a powerful tool …

A Multi-Scale Perspective On Planet Formation, Konstantin Gerbig

Yale Graduate School of Arts and Sciences Dissertations

Planet formation is an inherently multi-scale process, spanning nine order of magnitude in spatial scale from micron-sized dust grains to planetary system. This thesis adopts a multi-scale perspective to investigate the physical mechanisms that drive this transformation, focusing on the coupled dynamics of dust and gas in protoplanetary disks, the formation of planetesimals, and the imprints of disk physics on orbital architectures in planet-hosting binary systems.

At the smallest scales, I present a new hydrodynamical instability that operates in dust-enhanced regions of protoplanetary disks if mass diffusion (or dust viscosity) declines sufficiently steeply with increasing dust density – conditions that …

Contingent Fees To Contain Bank Runs, Rafael Matta, Remo Oostdam, Enrico Perotti

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No abstract provided.

Online Appendix To "What Policy Combinations Worked?: The Effect Of Policy Packages On Bank Lending During Covid-19", Divya Kirti, Maria Soledad Martinez Peria, Prachi Mishra, Jan Strasky

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No abstract provided.

Sibling Rivalry In The Financial Safety Net: Governance Arrangements For Bank Resolution And Deposit Insurance (2025), Atilla Arda, Jan Nolte

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No abstract provided.

Investigating Tlr-Mediated Cytokine Synergy In Macrophages, Erick Salvador Rocha

Yale Graduate School of Arts and Sciences Dissertations

Cytokine dysregulation during microbial infections can dangerously increase the severity of associated diseases. Non-additive responses to simultaneous activation of toll-like receptor (TLR) signaling pathways are one potential contributor. Here we explored mechanisms underlying the TLR2/MyD88 and TLR3/TRIF-mediated responses in macrophages for canonical pro-inflammatory and antiviral targets including TNF, IL-6, IL-12p40, IFN-β and CXCL10. We found that all targets exhibited characteristic levels of synergistic cytokine activation that varied with TLR-ligand concentration and exposure time. These trends were conserved when the TLR3-ligand polyI:C (PIC) was combined with either of the TLR2-mediated pathogens S. aureus or L. pneumophila. Using pharmacological inhibitors, genetic …

Essays In Economics, Paul Schmidt-Engelbertz

Yale Graduate School of Arts and Sciences Dissertations

This dissertation consists of three essays in economics.

The first essay, joint with Julia Selgrad and Samuel Slocum, is titled `The Impact of Geopolitical Tensions on International Investment and Asset Prices'. This paper examines the effects of geopolitical tensions on investment decisions and asset prices by studying the holdings of international mutual funds as well as the returns of the assets they hold. We show that increases in tensions between geopolitical adversaries lead to significant divestment between the two countries involved. In addition, the prices of assets that are divested from fall. Through studying mutual fund disclosures, we find that …

Worker And Consumer Choice In The Process Of Structural Transformation, Matthew Schwartzman

Yale Graduate School of Arts and Sciences Dissertations

Economic development encompasses more than just growth of average productivity and income per capita. Growth cannot occur without a broader process of structural transformation that reallocates economic activity across production units, sectors, and locations. This reallocation depends on workers’ choices of where and how to supply their labor and consumers’ choices of what to consume. The three chapters of my dissertation examine different forces that influence worker and consumer choices – such as labor market frictions, market access costs, uninsurable risk, and technological spillovers – and these choices’ implications for the aggregate path of the economy.

Services are the largest …

The Richness Of Perception: Dynamic Visual Representations From Static Images, Kimberly Wong

Yale Graduate School of Arts and Sciences Dissertations

What is the purpose of visual perception? The most common explanations suggest that “seeing” is for answering the question ‘What’s out there?’ — giving us information about the features and objects in the current local environment. This dissertation, in contrast, suggests a different approach: seeing is also for answering the question ‘What’s happening?’ — and the related questions ‘What just Happened?’ and ‘What’s about to happen?’. The critical difference is that while the more common answer seems implicitly static, these newer answers are intrinsically dynamic. This dissertation proposes that visual processing represents even certain static images …

Rigidity Of Kleinian Groups Via Dynamics On Higher Rank Spaces, Dongryul Kim

Yale Graduate School of Arts and Sciences Dissertations

his thesis is a summary of results obtained on papers; the first three are joint with Hee Oh.

Let Γ < PSL2(C) = Isom+(H3 ) be a Zariski dense Kleinian group whose ordinary set Ω = S 2 − Λ has at least two components. Let ρ : Γ → PSL2(C) be a Zariski dense discrete faithful representation with boundary map f : Λ → S 2 on the limit set.

In, Oh and I obtained a new rigidity theorem: if f is conformal on Λ, in the sense that f maps every circular slice of Λ into a circle, then f extends to a Möbius transformation g on S 2 and ρ is the conjugation by g. Moreover, unless ρ is a conjugation, the set Λf of conformal points of f in Λ, defined as the union of every circular slice C ∩ Λ with C a round circle such …

Hölderlin's Naturalism: Nature And Human Agency After Kant, Saurabh Saurendra Pal

Yale Graduate School of Arts and Sciences Dissertations

This dissertation focuses on Friedrich Hölderlin’s engagement with human self-relating to the natural world in the wake of Kantian rethinking of the human being as a normative subject. While it has often been noted that following the Pantheism controversy of the 1780s, a generation of poets and thinkers looked towards Spinozistic monism to overcome the dualisms and limitations of Kant’s Copernican revolution, the relevance of this development to moral concerns has received less consideration. This study proposes that the recurrent theme of “unification with nature” in Hölderlin’s literary and theoretical writings signifies a yearning for moral community¬—rather than metaphysical union—with …

Abolition In Color: Written And Oral Narratives Of Struggle In Black Latin America, Karina Alexandra Lopez

Yale Graduate School of Arts and Sciences Dissertations

This dissertation examines the different types of anti-slavery narratives written by people of Afro-descended writers in Cuba and Brazil at the end of the nineteenth century. During this time, literature acted as propaganda to further the spread of abolitionist ideas and ultimately end the abhorrent institution. While scholarship has tended to focus on the texts written by white abolitionists, this study places particular focus on the short stories and novels written by writers of color and points out the ways in which these texts not only contributed to swaying public opinion towards abolition, but also looked towards both the past …

The Cotzumalhuapa Obsidian System: Economy Of Procurement, Production, And Provisioning In A Classic Mesoamerican Polity, David Rafael Mccormick Alcorta

Yale Graduate School of Arts and Sciences Dissertations

This dissertation expands scholarly modeling of pre-contact economic organization in Mesoamerica through an in-depth examination of obsidian systems of Cotzumalhuapa, an important polity during the Late-Terminal Classic (650-950 CE) in Escuintla, Guatemala. The exchange of obsidian into the region from several sources was critical because other types of tool-grade stone were locally unavailable. Overtime, sophisticated systems developed to mine, transform, and move obsidian in a variety of forms across the landscape. Technological changes in manufacturing processes led to universal adoption of prismatic blades and fomented the importance of lithic artisans specializing in core-blade reduction. Access to obsidian to produce tools …

Decoding Heterogeneity In Human Aging: Omic Biomarkers Of Age-Related Disorders, Yaroslav Markov

Yale Graduate School of Arts and Sciences Dissertations

Biological aging unfolds along multiple heterogeneous trajectories shaped by both acquired molecular drift and inherited genetic variation. This dissertation investigates two complementary axes of aging heterogeneity: (1) stochastic, individually acquired epigenomic deviations; and (2) genotype-defined risk exemplified by the APOEε4 allele, the strongest genetic determinant of late-onset Alzheimer’s disease (AD).

1) Stochastic Epigenetic Mutation Detection

We developed SEMdetectR, a robust R-based pipeline for identifying and quantifying stochastic epigenetic mutations (SEMs) -- rare, outlier CpG methylation events that accumulate idiosyncratically with age. Using technical replicates from three independent cohorts, we uncovered previous methodological flaws undermining SEM reliability and trained a machine …

Precision Bootstrap Studies Of Fermions And Stress Tensors In Conformal Field Theories, Matthew Stephen Mitchell

Yale Graduate School of Arts and Sciences Dissertations

Conformal field theories (CFTs) describe a wide variety of scale-invariant phenomena. As CFTs are tightly constrained by symmetry, unitarity, and self-consistency, it is possible to compute rigorous bounds on their observables by translating these constraints into a semidefinite programming problem. This approach, known as the numerical conformal bootstrap, has been used to great success in recent years, and has produced the tightest bounds to-date on the critical exponents of 3d Ising and O(N) models. In this work, we conduct bootstrap studies of spinning operators in several CFTs.

First, we present a numerical bootstrap analysis of the critical 3d Gross–Neveu–Yukawa models, …

Biomedical Privacy And Security: Histology Image Vulnerabilities And Blockchain Solutions, Eric Ni

Yale Graduate School of Arts and Sciences Dissertations

Biomedical research increasingly relies on vast datasets, such as genomic sequences, electronic health records, and histology images, to advance scientific knowledge and clinical applications. However, the sensitive nature of biomedical data poses significant privacy risks, particularly with emerging capabilities of artificial intelligence and machine learning technologies. This dissertation addresses two central challenges in biomedical data privacy and security: quantifying privacy risks associated with histology images and developing innovative blockchain-based methods to ensure secure data storage and sharing.

The first part of this work investigates the vulnerability of histology images—commonly perceived as safe for public sharing—to privacy breaches. Utilizing advanced computational …

Discovery Of Plant Secondary Metabolism Through Computational And Synthetic Biology Technologies, Shenqi Wang

Yale Graduate School of Arts and Sciences Dissertations

Plants have evolved to produce a myriad of secondary metabolites, which have been a rich source of small molecules with numerous applications in modern medicine. However, many therapeutic small molecules still rely on plant sources for their production and confront various challenges such as low purification efficiency, slow growth of plants, and the scarcity of species. Advances in synthetic biology have created alternative opportunities to overcome these challenges by producing valuable plant natural products through heterologous expression of the biosynthetic pathways in microorganisms. However, the biosynthetic pathways of many plant natural products remain poorly understood due to inaccurate gene annotations …

Essays On Gender In Macroeconomics, Lindsey Uniat

Yale Graduate School of Arts and Sciences Dissertations

My dissertation examines interactions between recent macroeconomic trends in the labor market, including technological change and structural transformation, and changes in female labor supply.

In Chapter 1, I investigate the role of factors affecting female labor supply, such as social norms and discrimination, in the decline of routine jobs in the U.S. since the 1970’s. While typically attributed to changes in labor demand, the decline in routine employment has been larger for women than men, reflecting a shift of female employment out of routine clerical jobs and into non-routine professions. This paper presents a quantitative analysis of the impact of …

Challenges In Modern Machine Learning: Generalization And Responsible Use, Grigoris Velegkas

Yale Graduate School of Arts and Sciences Dissertations

Modern machine learning (ML) systems operate in settings where classical theoretical analysis, which relies on worst-case bounds, often fails to provide meaningful guarantees. Neural networks and large language models are trained with significantly more parameters than training data, yet they generalize well in practice—contrary to theoretical results. Additionally, ML algorithms are increasingly deployed in high-stakes applications, raising concerns about replicability and, more broadly, their responsible use. This thesis makes progress on two fundamental challenges in modern ML: (i) developing generalization guarantees beyond worst-case analysis, and (ii) designing algorithms with provable replicability guarantees.

In the first part of the thesis, we …

Structural And Functional Analysis Of Translation Inhibition By Betacoronavirus Non-Structural Protein 1, Michael Brandon Vetick

Yale Graduate School of Arts and Sciences Dissertations

humans: SARS-CoV, SARS-CoV-2, and MERS-CoV. Key to their viral lifecycle is Non-structural protein 1 (Nsp1), an essential pathogenicity factor that potently restricts the cell’s antiviral response. Despite poor protein sequence conservation of Nsp1 between evolutionarily distant β-CoVs, these proteins have proven to be highly conserved both functionally and structurally. Nsp1 functions by inhibiting host gene expression through contacts made with two mRNA ribonucleoprotein (mRNP) complexes: the initiating ribosome and the Nxf1/Nxt1 mRNA nuclear export complex. It is believed that two Nsp1 functions occur on the ribosome: Nsp1 is able to coordinate cleavage of the host mRNA and Nsp1 is able …

Navigating The Neighborhood: Community, Identity, And Gentrification In Crown Heights, Brooklyn, Kayla Karyl Thomas

Yale Graduate School of Arts and Sciences Dissertations

Crown Heights, Brooklyn, New York. This dissertation is a multi-method community study focusing on 21st century gentrification, concurrent socio-political changes, and their relationship to the ways residents understand and negotiate routine interpersonal relationships. The empirical core of the dissertation consists of three distinct yet interrelated papers on the social landscape of the contemporary Crown Heights neighborhood. These papers detail a range of approaches that residents adopt to better understand their own experiences of discrimination, gentrification, and efforts at reconstructing community and responding to change. Complemented by a chapter on the history of a single ‘representative’ Crown Heights apartment building, its …

Majority Dynamics On Random Graphs With Almost Balanced Initial Settings: The Power Of Few, Hoang Bao Linh Tran

Yale Graduate School of Arts and Sciences Dissertations

A community of n people participate in a parliamentary election with two major parties. Every person initially supports one side, and with each day, changes their opinion to match the majority among their friends. This process, commonly known as Majority Dynamics in literature, and similar processes, have been studied in many different contexts, including Statistical Physics, Computer Science, Economics and Ecology, as discussed in the influential survey by Mossel and Tamuz (2014).

Tran and Vu (2019) considered the process on a Erdös-Rényi G(n, p) random graph and discovered the "Power of Few" phenomenon: Starting from a …

Psychosocial Correlates Of Hiv Prevention, Care, And Well-Being Among Older Women Aging With Hiv, Thi Vu

Yale Graduate School of Arts and Sciences Dissertations

Background: Approximately 54% of the nearly 1.1 million people living with diagnosed HIV in the United States are aged 50 and older. From 2015 to 2019, diagnoses among women ages 55 years and older increased by 7% while diagnoses among other age groups decreased. In 2019, women made up 19% of all HIV diagnoses. Despite advances in HIV science and education, there is still a dearth of research focused on the growing population of older women with HIV. Durvasula’s Contextualized Model for HIV/AIDS Care and Prevention for Older Women highlights that older women with HIV face different barriers to care, …

Essays On Microeconomic Theory, Stephan Wolfgang Waizmann

Yale Graduate School of Arts and Sciences Dissertations

This dissertation consists of three papers on microeconomic theory.

The first paper studies repeated zero-sum games with incomplete information. In contrast to the canonical setting of Aumann and Maschler (1995), the paper assumes that the uninformed player is a sequence of short–lived players. When monitoring of past actions is perfect, Aumann and Maschler’s (1995) “Cav u”-result extends. When monitoring is imperfect, the payoff of the informed player can be strictly higher when facing a sequence of short–lived players than in the canonical setting, depending on parameters. The paper provides a partial characterization of equilibrium payoffs when monitoring is imperfect. …

Fabrication And Characterization Of Chalcogenide And Oxide Thin Films, Shuhang Pan

Yale Graduate School of Arts and Sciences Dissertations

This dissertation explores the fabrication, structural characterization, and quantum transport properties of chalcogenide and oxide thin films. High-quality SnTe films were synthesized via molecular beam epitaxy (MBE), demonstrating tunable topological surface states through nanoscale patterning. Magnetoconductivity measurements revealed weak antilocalization (WAL) effects across continuous and patterned films, with coherence lengths governed by boundary scattering in hole-patterned geometries. Advanced focused ion beam (FIB) protocols enabled atomic-resolution transmission electron microscopy (TEM) of monolayer ZrO2 on silicon, defect distribution in off-stoichiometric CaWO4 films and orientation analysis in YVO4 thin films. Josephson junctions fabricated on superconducting Nd1−xEuxNiO2 thin films exhibited …

In Vitro Characterization And Evolution Of Sylvatic And Endemic Dengue-4 Viruses, Andrew Peric

Yale Graduate School of Arts and Sciences Dissertations

Dengue virus is the world’s preeminent arthropod-borne virus that infects hundreds of millions of people each year, and circulates in four distinct serotypes named 1, 2, 3, and 4. Dengue virus cycles between mosquito and human hosts in a transmission cycle called the endemic cycle, which is responsible for the majority of recorded dengue infections worldwide. However, dengue also exists in a second transmission cycle called the sylvatic cycle, which mirrors the endemic cycle with wildlife, including non-human primates, replacing humans in this transmission cycle. Phylogenetic analyses support the hypothesis that spillover events from the sylvatic cycle into human populations …

West From West Point: The U.S. Military Academy And The Romantic Frontier, Ryan Shaw

Yale Graduate School of Arts and Sciences Dissertations

This dissertation examines the influence of Romanticism on the culture and curriculum of the United States Military Academy in the early nineteenth century, and demonstrates how it shaped the behavior of U.S. Army officers on the far western frontier. While historians have long associated Romanticism with the frontier experience, it has traditionally been framed as an output, rather than an input. This study identifies West Point as an unexpected but significant source of Romantic ideals.

The history of the Academy is presented uniquely here as a contest between three competing visions: A republican ideal of a modest military …

Machine Learning And Cheminformatics Methods For Retrosynthetic Planning, Yu Shee

Yale Graduate School of Arts and Sciences Dissertations

Designing efficient synthetic routes automatically remains a central challenge in chemistry. This thesis presents machine learning and algorithmic strategies for retrosynthetic planning that aim to improve both efficiency and practical usability over previous approaches.

We first introduce the site-specific template (SST) generation framework (Chapter 2), which leverages transformer-based models for template generation and reaction center labeling to enable targeted single-step disconnections. We then develop DirectMultiStep (DMS) (Chapter 3), a multistep-first model that generates complete synthetic routes directly from product molecules, avoiding recursive search and achieving strong performance on benchmark datasets. In parallel, we propose FragmentRetro (Chapter 4), an efficient, stock-aware, …