Digital Commons Network^™

Resource-Aware Distributed Machine Learning: Unified Approaches For Private And Efficient On-Device Intelligence, Yeshwanth Venkatesha

Yale Graduate School of Arts and Sciences Dissertations

The widespread integration of Artificial Intelligence (AI) into everyday life is driving a paradigm shift towards deploying machine learning models on a massive, distributed ecosystem of edge devices. While this decentralization offers opportunities for data-driven applications, it introduces a fundamental trilemma: the concurrent pursuit of high performance, operational efficiency, and stringent data privacy. State-of-the-art AI models, particularly Large Language Models (LLMs), demand computational and memory resources that far exceed the capabilities of typical edge devices, creating significant bottlenecks in training and inference. Furthermore, the distributed nature of data gives rise to challenges of statistical heterogeneity and communication overhead, while the …

Multinomial Trees And Multinomial Percolation, Michele Tienni

Yale Graduate School of Arts and Sciences Dissertations

We study multinomial percolation, which is bond percolation on a family of graphs ("blow-up graphs") defined in terms of a fixed graph G. We compute connection thresholds in terms of distances on G. Moreover, if the percolation probability is inversely proportional to the blow-up multiplicity, there is a phase transition above which a giant component emerges. We show that many properties of the giant component can be computed using an analytic function with variables indexed by the vertices of G. Moreover, we find that the giant component gives rise to a natural field on G. As the blow-up multiplicity grows, …

Intestinal Mast Cell Control Of Behavioral And Oral Anaphylactic Responses, Nathaniel Dale Bachtel

Yale Graduate School of Arts and Sciences Dissertations

Organisms are challenged on a day-to-day basis with the decision of what, when and how much of a given food source to eat. These fundamental decisions require sensory mechanisms that evaluate the relative quantities of desired nutrients and harmful toxins present in each food source and integration of these factors with the current organismal state. In mammals, this sensing is accomplished by a diverse array of cells types, including epithelial cells, neurons, and immune cells which communicate the value of ingested food with the brain. Moreover, the immune system can store memory of past harm a given food source was …

Regulation Of Pre-Mrna Processing Through Nascent Rna Folding, Leonard Schaerfen

Yale Graduate School of Arts and Sciences Dissertations

RNA sequence determines the formation of intramolecular base pairs. Together with tertiary contacts, base pairs define every RNA's structure, or fold. The catalytic, regulatory, or coding potential of an RNA strongly depends on its folding pattern. Because base pairing occurs much faster than RNA synthesis (transcription) in cells, early structural states can govern RNA processing events and dictate the formation of functional conformations. These co-transcriptional structural states remained largely unknown. To address this gap, I developed CoSTseq, a chemical probing and enrichment method to measure nascent RNA base pairing upon exit from RNA polymerases (Pols) transcriptome-wide in living Saccharomyces cerevisiae …

Essays In Economic Theory, Carlo Maria Cusumano

Yale Graduate School of Arts and Sciences Dissertations

This doctoral thesis consists of three essays in microeconomic theory, each examining how different types of friction - political, informational, or contractual -  can affect strategic interactions and outcomes in important economic settings such as redistributive negotiations, product markets, and the workplace. The first essay (Chapter 2) investigates a redistributive negotiation where two parties seek to extract resources from a third party. While the third party lacks formal representation at the bargaining table, he can use costly protests to disrupt negotiations. The second essay (Chapter 3) analyzes a product market in which homogeneous-good firms compete for the unitary demand of …

A Peculiar Decoration: Production, Exchange, And Access To Usulután Pottery In The Late And Terminal Formative Southern Maya Region, Caitlin Reddington Davis

Yale Graduate School of Arts and Sciences Dissertations

Usulután is a pottery style featuring a bichromatic design in the form of parallel lines and blotches, often in yellow and orange colors. Although it is often associated with El Salvador, pottery in this style is commonly found across Southern Mesoamerica during the Formative period. During the Late and Terminal Formative periods (300 BCE - 200 CE) an intensive network of competitive city-states developed in the Southern Maya Region, including the Guatemalan Highlands, Pacific Slope, and Western El Salvador. Despite the abundance of Usulután pottery in the archaeological record of these cities, there has never been a study focused on …

Emotion Inferences: An Integrative And Dynamic Process, Srishti Goel

Yale Graduate School of Arts and Sciences Dissertations

Our understanding of what others around us feel, a process referred to as emotion inference, fundamentally shapes our behavior and social interactions. Early work largely focused on how people infer emotions from isolated, static, canonical facial expressions. Accumulating evidence and theoretical advancements suggest that emotion inference, instead, is a complex process that involves making meaning about a target’s experience by dynamically synthesizing information from multiple sources with existing knowledge. Yet, a comprehensive empirical account that captures this complexity is largely missing from the literature. In this dissertation, I propose and systematically test a research framework that addresses this complexity of …

Renewing Cells, Enduring Genes, And Metabolic Decline In Murine Liver Aging, John T. Gonzalez

Yale Graduate School of Arts and Sciences Dissertations

Aging is associated with physiological and molecular decline and a concurrent increase in dysfunction, chronic disease, and mortality. Despite the fact that aging is the greatest risk factor for many chronic diseases, fundamental aging research has historically lagged behind disease-specific research. This deterioration and it's repercussions has different manifestations in different organs. This dissertation focuses on dynamics of mouse aging with a focus on the liver. The liver's diverse functions are integral to many homeostatic processes, including maintaining metabolic balance, detoxifying harmful substances, supporting immune defense, and regulating blood and endocrine systems. Its impairment can lead to significant health issues. …

Site Optimization For A Dual Crisis: Co-Prioritizing Carbon And Biodiversity To Improve Conservation Impact In Indonesia, Saskia Braden

Library Map Prize

As the dual crises of climate change and biodiversity loss accelerate and human expansion reshapes the planet, calls to preserve Earth’s remaining wilderness have grown more urgent. However, in the race to protect as much as possible, as fast as possible, society risks missing what matters most. Not all conservation sites are equally valuable, and without strategic prioritization, limited resources may be squandered while critical ecosystems disappear. Few places illustrate this challenge as vividly as Indonesia: a rainforest nation that is home to some of the richest biodiversity and densest forest carbon stores on Earth but where conservation efforts are …

The Geometry Of Planetary Systems, Emma Marie Cain Louden

Yale Graduate School of Arts and Sciences Dissertations

The study of exoplanetary systems offers an observable window into the processes governing celestial bodies' formation, evolution, and current structure. Central to understanding these systems is their geometry, which encompasses the orientations, alignments, and spatial relationships among planets and their host stars. This dissertation investigates the pivotal role of planetary system geometry—particularly obliquities and orbital resonances—in illuminating the formation pathways and long-term evolutionary trends of both solar and exoplanetary systems.

This dissertation explores these themes through three comprehensive studies. Chapter 2 focuses on the role of tidal dissipation in shaping short-period exoplanets, examining whether the presence of obliquity-driven tidal interactions …

Controlling And Protecting Quantum Information In Superconducting Oscillators, Aniket Maiti

Yale Graduate School of Arts and Sciences Dissertations

Modern quantum experiments allow the precise manipulation and measurement of many-body quantum states, pushing quantum mechanics from a testable theory to a utilizable technology. The central promise of these experiments is to process quantum information for exponential advantages in computing, sensing, and communication. An interesting way to achieve such a processor is to manipulate quantum information stored in the continuous-variable (bosonic) phase space of electromagnetic radiation. Since photons in free space do not interact, such an approach necessarily requires the introduction of nonlinearity through strong light-matter couplings. However, since all matter is lossy, this inevitably introduces a trade-off between the …

Liquid-Liquid Phase Separation Of Cellular Prion Protein And Its Biological Implications, Yangyi Liu

Yale Graduate School of Arts and Sciences Dissertations

Liquid-liquid phase separation (LLPS) of macromolecules allows for a variety of cellular functions such as signal transduction and regulation of gene expression and is implicated in neurodegeneration. Cellular prion protein (PrPC) as the central player in prion and Alzheimer’s diseases has been previously discovered to undergo LLPS, while its molecular underpinnings and physiological functions remain unclear.

This thesis delves into the complexity of PrPC LLPS, characterizes its biophysical properties, and initiates a connection between PrPC LLPS and its physiological functions. In Chapter 2, site-specific interactions of PrPC that drive LLPS are identified, highlighting the importance of interactions between the N-terminal …

Framed Bundles, Abelianization, And The Ooguri-Vafa Space, Danny Nackan

Yale Graduate School of Arts and Sciences Dissertations

In this thesis we study the hyperkähler structure of a particular moduli space of Higgs bundles near the discriminant locus of the Hitchin fibration, which in this case consists of quadratic differentials with a double zero.

Gaiotto, Moore, and Neitzke predicted that the hyperkähler Ooguri-Vafa space Mov should provide a local model for Hitchin moduli spaces near the discriminant locus. To this end, Tulli identified Mov with a certain space of framed Higgs bundles with an irregular singularity.

We extend this result by identifying the Ooguri-Vafa holomorphic symplectic form with a regularized version of the Atiyah-Bott form on …

Characterizing The Photochemistry And Photophysics Of Benzoylbenzoate And Formylbenzoate Anions Using Cryogenic Ion Spectroscopy, Olivia Caroline Moss

Yale Graduate School of Arts and Sciences Dissertations

Marine chromophoric dissolved organic matter (mCDOM) is a large and complex class of material predominantly found at the air-water interface in bodies of water. While it is known to generate radicals and unwanted byproducts, such as HONO· and ·OH, the mechanism of formation for these products currently is unknown. In this dissertation, a bottom-up approach is utilized to investigate possible reaction pathways by scaling down to small-molecule models of mCDOM. Namely, this dissertation investigates the photochemistry and photophysics of benzoylbenzoates (BBA¯). Analysis of the UV spectrum of the deprotonated species reveals two dominant processes upon photoexcitation of 4BBA¯, tag loss …

Planets Are Not Points: The Profound Effect Of Planetary Structure On Exoplanet System Architectures, Tiger Chen Lu

Yale Graduate School of Arts and Sciences Dissertations

The quantity and quality of astronomical data has advanced to the point in which truly detailed and nuanced theoretical models are necessary. In the field of exoplanetary dynamics, it has become increasingly clear that we must account for the effects of planetary structure when considering the dynamics of the system. In other words, Planets are not Points. This dissertation details my contributions to the field of exoplanet dynamics, split into three subcategories:

• Part I (Chapters 2 - 3): Numerical Methods & the N-Body Problem. These chapters discusses the numerical methods I have developed to study the analytically unsolvable N-Body …

Ole Rna Is A Component Of A Large Particle That Promotes Bacterial Growth Under Diverse Stresses, Seth Eugene Lyon

Yale Graduate School of Arts and Sciences Dissertations

Prior to the 1980s, RNA macromolecules were largely viewed as a transient carrier of the genetic code used for protein synthesis, with little chemical versatility beyond Watson-Crick-Franklin base-pairing. The discovery of catalytic RNAs in 1982, however, upended this view and established that RNA was a chemically capable biopolymer. Since then, several classes of RNA with functions independent from protein synthesis have been discovered in all domains of life. Excluding those that have functions relevant to protein translation, noncoding RNAs that are large (> 200 nt) and have a conserved, complex structure are rare in bacteria. However, as more bacteria were …

Computation And Estimation For Neural Networks Via Log-Concave Coupling, Curtis James Mcdonald

Yale Graduate School of Arts and Sciences Dissertations

In this work, we consider a Bayesian method to train single-hidden-layer neural networks with ℓ1 controlled weights by defining posterior distributions using different subsets of the training data, and combining posterior means to form our estimators. We consider both a joint Bayesian model for all parameters of the neural network at once, and a greedy Bayes model training the neurons one at a time based on the residuals of previous fits.

The log-likelihoods of the posterior distributions we define are multimodal and nonconcave, so sampling algorithms such as Markov Chain Monte Carlo (MCMC) will not be rapidly mixing to …

Quantum Computing In Discrete- And Continuous-Variable Architectures, Shraddha Singh

Yale Graduate School of Arts and Sciences Dissertations

This dissertation develops a theoretical framework for hybrid discrete-variable (DV) and continuous-variable (CV) quantum systems, focusing on control, state preparation, and error correction. Quantum computing holds the potential to surpass classical computation in tasks such as factorization, secure communication, and quantum simulation. Hybrid CV-DV systems offer a promising path by combining the stability and long coherence times of oscillators with the fast gate operations of qubits.

A central contribution of this work is the development of “non-abelian quantum signal processing” (NA-QSP), a generalization of quantum signal processing (QSP) [1] where the control parameters are non-commuting quantum operators, such as oscillator …

Examining Risk Factors, Screening, And Survival Of Early-Onset Colorectal Cancer In The United States, Sunny Siddique

Yale Graduate School of Arts and Sciences Dissertations

Background: In the United States (US), the incidence of early-onset colorectal cancer (EOCRC), defined as colorectal cancer (CRC) diagnosed among individuals < 50 years of age, has been increasing rapidly. Compared to late-onset CRC (i.e., CRC diagnosed among individuals aged 50 years and older), EOCRC is characterized by more aggressive pathology and distinct genetic profiles, indicating that the etiology of EOCRC may be different. There have been a limited number of studies examining the risk factors of EOCRC, and none have focused on early life risk factors, which could be particularly relevant to early-onset diseases. In May 2021, the US Preventive Services Task Force (USPSTF) reduced the recommended age of CRC screening from 50 years to 45 years, and the COVID-19 pandemic influenced the provision of preventive services across the country. These events could impact the patterns of screening for EOCRC, but no study has systematically assessed such impacts in a large sample of the US population. Furthermore, the role of ecological factors on survival disparities among individuals with EOCRC remains understudied, and prior studies evaluating these factors have not accounted for potential spatial correlation. These knowledge gaps warrant a set of epidemiological studies to clarify the risk factors, screening patterns, and prognostic factors of EOCRC.

Methods: We conducted three innovative research studies to understand EOCRC etiology, screening, and survival using a range of study designs and analytical methods. In the first study, we included 1,221 cases diagnosed with EOCRC at the age of 0-39 years during 1988-2021 and 61,050 controls without cancer matched on year of birth from the California Linkage Study of Early-Onset Cancers, which is a nested case-control study within the California birth cohort. Odds ratios (OR) and 95% confidence intervals (CI) …

On The Analysis Of Average Hyperbolicity And Its Applications, Joon-Hyeok Yim

Yale Graduate School of Arts and Sciences Dissertations

This thesis bridges the ideas of hyperbolic geometry and geometric group theory with practical applications in graph theory and machine learning. A metric space (X, d) is said to be Gromov δ-hyperbolic if, for any points x, y, z, w ∈ X, the inequality d(x, y) + d(z, w) ≤ max(d(x, z) + d(y, w), d(x, w) + d(y, z)) + 2δ holds. This definition generalizes key properties of …

Men Take Care Of Each Other”: Evaluation Of A Community-Based Model For Pre-Exposure Prophylaxis Services Among Male Bar Patrons In Rural South Africa, Phoebe Chen

Yale Medicine Thesis Digital Library

Low engagement with HIV services persists among young men with harmful alcohol use in South Africa. We previously piloted a rural community-based HIV service delivery model to engage this key population. In the initial study, male nurses visited alcohol-serving venues to provide HIV testing and pre-exposure prophylaxis (PrEP) services. From November 1 to December 30, 2021, we conducted interviews with 17 of 34 male pilot participants to evaluate program barriers, facilitators, and suggestions. All Interviewees were satisfied with HIV testing and PrEP services. Participants overcame testing avoidance through peer influence and enhanced privacy. Barriers for PrEP initiation were stigma (PrEP …

The Development Of A Novel Large Language Model Method For Identification Of Incarceration History Via The Electronic Health Record And Evaluation Of Care Processes In The Emergency Department Setting, Thomas Huang

Yale Medicine Thesis Digital Library

Objective: Incarceration is a significant social driver of health and patients with a history of incarceration face systemic healthcare disparities, higher morbidity, mortality, and racialized health inequities. Incarceration status is largely invisible due to poor electronic health record (EHR) capture. In this thesis, we aim to develop, train, and validate a novel natural language processing technique to more effectively identify incarceration status in the EHR and apply this method in the emergency department setting to demonstrate proof of concept and elucidate care process disparities.Methods: The study population consisted of adult patients (≥ 18 y.o.) who presented to the emergency department …

Patient-Level Factors And Social Determinants Of Clinical Outcomes In Spine Oncology, Sumaiya Sayeed

Yale Medicine Thesis Digital Library

Background: Boney tumors of the spine pose a high morbidity among patients, requiring an extensive multidisciplinary treatment regimen, including surgical resection, chemotherapy, and radiation. Spinal metastases make up the majority of spinal boney tumors, while primary osseous tumors of the spine are much rarer. Due to the heterogeneity of tumor types, differences in presentation, and diversity of the patient population, treatment recommendations vary by individual, thus resulting in disparities in patient mortality and presenting a large burden on the healthcare system. Patient health status, including malnutrition, comorbidity burden, and frailty, as well as socioeconomic factors, such as race, have shown …

The Effect Of The Ketogenic Diet On The Circadian Rhythmicity Of Glymphatic Function In Mice, Tanner Metcalfe

Yale Medicine Thesis Digital Library

The glymphatic system is a network of perivascular spaces that coordinates removal of waste products from brain parenchyma. It is known that the glymphatic system is under control of the circadian rhythm, however little is known about factors that influence this control. Data has shown that the expression of specific circadian rhythm genes is altered when exposed to the ketogenic diet. In this experiment, we show that the day-night rhythmicity of glymphatic function is extinguished in mice exposed to the ketogenic diet through the up-regulation of influx of cerebrospinal fluid to brain parenchyma and the reduction in cervical lymph node …

Clinical Predictors Of Fluid-Responsive Acute Kidney Injury, Cindy Khanh Nguyen

Yale Medicine Thesis Digital Library

CLINICAL PREDICTORS OF FLUID-RESPONSIVE ACUTE KIDNEY INJURY

Cindy Khanh Nguyen, Abinet M. Aklilu, Yu Yamamoto, Bashar A. Kadhim, Claudia Coronel-Moreno, Francis P. Wilson. Section of Nephrology, Department of Internal Medicine, Yale University, School of Medicine, New Haven, CT.

Specific Aims: We aimed to explore and identify common clinical variables that may be helpful in selecting patients who will benefit from volume challenge when the fluid-responsiveness of AKI is unclear.

Methods: Our study is a retrospective secondary analysis of a clinical trial that prospectively enrolled adult patients at Yale-New Haven Hospital with AKI defined by the 2012 Kidney Disease: Improving Global …

Adopting America’S Future Citizens: The Children’S Bureau And The Plight Of East Asian War Orphans, 1950-1969, Caroline Chen

Harvey M. Applebaum ’59 Award

This essay considers the role of the Children’s Bureau in the transnational adoptions of East Asian war orphans from 1950-1969. World War II and other Cold War conflicts left hundreds of thousands of children in Japan, Hong Kong, and Korea orphaned and displaced. This essay argues that the Children’s Bureau played an important role in the transnational adoptions of East Asian war orphans. The Bureau was the only federal agency involved in these adoptions explicitly devoted to child welfare. Cold War geopolitics imbued the Bureau’s approach. Through transnational adoptions, the agency simultaneously responded to Cold War pressures to help children …

The Mirror Of Scripture: Historical Memory, Translation, And The Bible In Early Modernity, 1450-1660, Colin Glen Hoch

Yale Graduate School of Arts and Sciences Dissertations

Contributing to the latest thematic trends in early modern studies, this dissertation project maintains that contested historical memory, or the competing ways that European Christians envisioned themselves as part of an ancient and authoritative biblical tradition, constituted the creative engine at the heart of shaping the early modern Bible (c.1450- 1660). In an era when successful claims to custom and antiquity conferred the highest legitimacy, historical memory was a critical source of identity and authority, even if, as recent theorists of early modern memory assert, memory itself meant something different in the period. The Bible in myriad forms served as …

Molecular Mechanism Of Vibrio Cholerae Biofilm Adhesion, Xin Huang

Yale Graduate School of Arts and Sciences Dissertations

Bacterial biofilms are surface-attached communities of bacterial cells enclosed in an extracellular matrix formed on environmental surfaces and host tissues. Biofilm formation represents a common strategy in facilitating host colonization and infection by human pathogens, and the polymeric matrix provides a mechanism for drug and host immune resistance by acting as a barrier around biofilm-dwelling cells. Bacteria often express multiple adhesive proteins (adhesins), but it is often unclear whether adhesins have specialized or redundant roles. Here, we combine mutagenesis, biochemistry, single-cell imaging, and bioinformatics to show how Vibrio cholerae, the causal agent of pandemic cholera, uses two biofilm-specific adhesins …

Disruption Of The Rhogef Trio In Neurodevelopmental Disorders Leads To Impairments In Multiple Domains Of Function, Amanda Jeng

Yale Graduate School of Arts and Sciences Dissertations

Neurodevelopmental disorders (NDDs) affect the normal development and function of the brain, and include disorders such as autism spectrum disorder, intellectual disability, schizophrenia, bipolar disorder, and epilepsy. While these are diagnostically distinct disorders, NDDs share considerable comorbidities and present with overlapping symptoms. In addition, the risk genes for NDDs overlap significantly, further suggesting shared underlying pathology of these disorders. Mutations in the gene TRIO are enriched in individuals with neurodevelopmental disorders. TRIO encodes a large multidomain protein with two guanine nucleotide exchange factor domains for the Rho family of small GTPases and a putative kinase domain, as well as multiple …

Unveiling Planetary Processes With The Solar System And Exoplanets, William Garrison Levine

Yale Graduate School of Arts and Sciences Dissertations

Both solar system and exoplanet science study the same class of objects to advance our knowledge of fundamental planetary processes. Our solar system provides a detailed view of a single planetary system in one epoch. In contrast, exoplanets offer sparser data from thousands of diverse systems in various evolutionary states. Holistic research on planetary objects must draw from both complementary sources. After introducing this mindset in Chapter 1, Chapters 2-4, each highlight a case study with this philosophy.

Chapters 2 & 3 draw on an emergent pathway to connect the solar system and exoplanets: interstellar small bodies. The discovery of …