VictorJuiz/thesis huggingface dataset:
Geometry-Inspired Sampling Algorithms and Random Graphs

High-dimensional expansion, a generalization of graph expansion to higher-order edges, has recently garnered significant attention in the theoretical computer science community for the additional boost they give in applications like error-correction and approximate sampling. In this thesis, we explore two problems related to high-dimensional expansion, using tools from the geometry of polynomials as well as high-dimensional convex geometry./nFirst, we study approximate sampling from discrete distributions. The framework for sampling obtained from high-dimensional expansion provides both a natural set of random walks to use in MCMC algorithms, as well as a set of tools for their analysis. We show that the geometric properties (e.g. log-concavity) of a polynomial derived from the distribution allows us to speed up the implementations of these random walks./nNext, we study a random graph model called the ``random geometric graph,'' with an eventual goal of understanding its modeling capabilities as well as its high-dimensional expansion properties. Along the way, we prove new results about distinguishing the random geometric graph model from the Erdos-Renyi model, and develop a new geometric toolkit for analyzing these graphs.

Advisor: Rao, Satish
Resource-Constrained Sensing as a Shared Utility

Cloud computing revolutionized the ease with which we can build, deploy, and scale distributed computing services. These advances, however, have not extended to the physically distributed and resource-constrained computers deployed throughout the world to collect data, and their resource constraints have thus far confined them to function as inefficient, fixed-purpose data forwarders. Breaking these distributed sensors free of their resource-constraints by including them in a dynamic, programmable, distributed system will not only enable easier deployment and scaling of applications relying on their data, but it will also give us the ability to collect and process never-before-seen data and discover new ways sensing the world around us./nWe enable this vision in two parts. First we present a signpost-based platform which eases the building and deployment of sensors by providing the core services and hardware necessary for them to function. Next we explore the benefits of, and build a resource manager to form these resource-constrained sensors into a compute cluster akin to those found in the cloud. This enables multiple users to simultaneous program a cluster of sensors and quickly iterate on their programs through an application framework which abstracts away the details of scheduling and task distribution. By forming these sensors into a multiprogrammable cluster, we enable them to be accessed as a shared sensing utility rather than as a collection of individual nodes.

Advisor: Dutta, Prabal
Wawrzynek, John
The Dynamics and Components of Intracellular Lipid Inclusion Formation in Mycobacteria

Mycobacterium tuberculosis is an airborne bacterial pathogen responsible for the infectious disease tuberculosis. Tuberculosis is the second leading infectious killer after COVID-19 and was responsible for over 1.6 million deaths in 2021. Astoundingly, a quarter of the world is thought to have been infected by M. tuberculosis. If left untreated, TB has a high mortality rate of up to 50%. While a strict regime of antibiotics can treat the disease, the rise of multidrug resistant clinical M. tuberculosis strains threatens the world. Typically, a majority of the population can quell the disease into a latent TB infection (LTBI), although in 5-10% of cases, an infected individual is unable to prevent disease progression and the active bacteria can start their infection anew. These harrowing statistics demand the need to understand the biology of M. tuberculosis and the development of model systems to study the bacterium and its pathogenesis./nIntracellular lipid inclusions (ILI), receptacles of concentrated lipids, have long been perceived as hallmarks of non-replicating persistent bacteria found in LTBI. These organelles are thought to provide fuel for basal metabolic processes while the dormant bacteria withstand the immunological and chemical artillery launched by host immune cells. Understanding how and why ILI are formed would promote identification of tactical therapeutic targets against dormant bacilli and allow for sustained prevention and control of TB. Here, we provide surprising evidence that refutes this longstanding belief and suggests that ILI can be formed in actively replicating Mycobacterium marinum. We find this discovery is corroborated in several clinical M. tuberculosis strains and through next generation RNA sequencing we uncover some key differences in the transcriptional landscape of ILI producing and ILI barren bacteria, allowing us to decouple non-replicating persistence from ILI formation. Separately, we utilize an arrayed transposon mutagenesis library in M. marinum to identify four genes involved in the ILI formation pathway. M. marinum mutant strains with disruptions in these genes were used to study the role of ILI, allowing us to add mounting evidence to the importance of ILI in mycobacterial infection. Together, these findings suggest an alternative function of ILI in replicating M. marinum and M. tuberculosis, as well as provide novel models to study the purpose of ILI in M. tuberculosis pathogenesis.

Advisor: Stanley, Sarah A
Orbitofrontal and Hippocampal Contributions to State Coding and Decision Making

To make informed decisions, one needs to understand the world in which those decisions are being made: the current task state. Both the orbitofrontal cortex (OFC) and the hippocampus (HPC) have been implicated in representing task state, but the nature of these representations, and what role each region plays, remains unclear. Recent work from our lab showed that HPC-driven neural oscillations in OFC are critical for value-guided decision making, and that value states in OFC oscillate during the deliberation process. We hypothesized that (1) both HPC and OFC robustly and flexibly represent task state while primates learn and make decisions, and (2) value state dynamics in OFC are shaped by theta oscillations originating from HPC./nWe simultaneously recorded large populations of neurons from OFC and HPC while two monkeys performed a probabilistic reversal learning task, where reward contingencies could be captured by two task states. Using population-level decoding, we found neural representations of task state in both OFC and HPC that remained stable within each trial but strengthened with learning as monkeys adapted to reversals. Subjects also appeared to use their understanding of task structure to anticipate reversals, evidenced by anticipatory neural representations of the upcoming task state. We then decoded representations of option values from OFC neurons recorded from two other monkeys performing a value-based decision-making task. Relating decoded state dynamics to theta-filtered LFP signals in OFC, we found that value states switched independent from theta cycles, suggesting that a mechanism other than HPC-driven theta oscillations shapes the dynamics of deliberation.

Advisor: Wallis, Joni
De-humanizing Care: An Ethnography of Mental Health Artificial Intelligence

What is it like to live in a world shaped by the axiom that there’s not enough care for all who need it—one in which artificially intelligent caregivers become, accordingly, not only thinkable, but necessary? This dissertation provides an ethnographic account of the turn to artificial intelligence in mental health care via a Silicon Valley startup (“The Startup”) that creates therapeutic chatbots. These bots offer on-demand, interactive emotional support to their human users through text (and in some instances, voice) messages. Though the story of AI in most medical applications is one of outpacing human ability while operating under direct (human) oversight, here the opposite is true: none of my interlocutors regard AI as superior in any way to a human therapist; and while my fieldsite’s team of psychologists monitor aspects of these exchanges, to oversee each interaction would nullify the very justifications that summoned these bots into health care—namely, their rapid scalability, low overhead costs, and 24/7 on-demand, discreet availability. Yet for all that AI isn’t a superior caregiver, it is nevertheless a caregiver— an identity that I explore by recognizing chatbots, startup workers, and end-users alike as ethnographic subjects. This dissertation examines the relationships that arise through and with AI care bots: I argue that the ontological ambiguity of human-bot bonds is not a threat to good care but the means of it; I examine the collaboration between AI and human care workers as one of colleagues who share a job requirement of being paradoxically expendable-yet-essential; and finally, I show how AI caregivers afford a glimpse of suicide prevention care unpaired from the ableism of “cure,” even as they reveal how surveillance and neglect in mental health care become mutually reinforcing. Across this dissertation, I aim to recenter disability in the theorization of human-technology relationships.

Advisor: Hayden, Cori
Nakamura, Karen
Graph Embeddings, Disentanglement, and Algorithm Maps

We tackle three disparate topics in this thesis - graph embeddings, disentanglement, and algorithm maps./nIn Chapters 2 and 3, we cover graph embeddings: methods which embed graph as vectors in a structure-preserving way. We start at the principle of superposition used by vector-symbolic architectures and derive the tensor product as the canonical binding operation along with a natural random code. Together, they form a novel embedding method, and we list some common graph operations our embeddings are capable of. We give a precise characterization of its statistical behavior, showing it achieves a packing upper bound. and go on to establish a link to adjacency matrices with applications toward their drastic compression. Then, we compare our method to other bind-and-sum methods and showcase a fundamental memory vs. capacity tradeoff./nIn Chapter t4, we cover disentanglement, the discovery of semantically meaningful latent factors. We assume that data lives on a low-dimensional manifold and define disentanglement in terms of local charts. Exploring the consequences of this definition, we find that commutativity of the latent factors is an equivalent condition for disentanglement. Under our framework, we also show that sufficiently rich generative models can always be disentangled, and we apply the commutativity condition to learning a dictionary of Lie group operators. We conclude with a discussion of how our definition relates to previous work, suggesting that it is no accident that commutativity - which has been used a computational or conceptual convenience - is so prevalent in these methods./nIn Chapter 5, we give some preliminary thoughts on the transfer of algorithms between different contexts. Our key insight is that, rather than focusing on the transfer of a single algorithm, it is more profitable to consider the conditions in which the states and actions of one setting can be mapped to those of another setting. This in turn induces a natural map of algorithms between contexts, and we give some basic consequences of these definitions.

Advisor: Hooker, Giles
Olshausen, Bruno A
The 20 Vertex Model and Related Domino Tilings

A configuration of the twenty vertex model is an orientation of each edge in a triangular lattice such that at each vertex the number of incoming and outgoing edges is equal. This is similar to the six vertex model, which takes place on a square lattice, that has long been of interest to combinatorialists for its connections to alternating sign matrices. Recently Di Francesco and Guitter uncovered interesting combinatorics for the twenty vertex model which previously was primarily studied by physicists. Di Francesco was also able to relate configurations of the twenty vertex model to domino tilings of a so-called Aztec triangle, and conjectured a product formula for enumerating these configurations. We examine the enumeration of these objects including several combinatorial bijections of the twenty vertex model. In particular we establish a relation from the aforementioned domino tilings to sequences of partitions, and then introduce a generalized Aztec triangle for which we obtain a generalization to Di Francesco's conjecture.

Advisor: Corteel, Sylvie
City-Building Practices in Riyadh, A Case of Master Planning from the Gulf

This research primarily investigates Riyadh’s 1972 master plan, designed by the Greek urbanist Doxiadis. The larger goal is forming a solid analysis of master-planning approaches in the Gulf region. The 1972 plan has been previously discussed in numerous research endeavors, but often it is treated as an isolated project, in ways that reveal only dimensions of “What?” What were its specific features? What were its productive impacts on Riyadh? And what undesirable consequences did it unintentionally have? However, the work in hand takes a different lens. It moves beyond the “What” to understand the “Why” or the “How.” Why was the plan developed in the way that was finally approved? How did it reach that shape? And why did it impact the city in the way it evidentially did? Those questions sit at the heart of this dissertation.Specifically, it aims to inspect the 1972 master plan as a product of negotiations between many influential players and the culmination of dynamics that were in place long before the work on the plan had even started, and which were significant in shaping its outcome. Rapid developments, occurring internally in Saudi Arabia and externally on the global stage, were instrumental in determining the plan’s final form. This dissertation concretely connects those relationships to the plan for the first time. The work’s main contribution is thus to analyze the range of factors surrounding the decision to construct the plan and show how they influenced the creation process. Throughout this research, many field visits and interviews were performed, archival material was recovered and examined, maps were evaluated, observations collected, and media analyzed. The research also depended on the collection of oral histories from a number of sources; some are original, others were never connected to this topic. What this research revealed is that contrary to the familiar narrative, the plan’s process was not linear or one-dimensional, nor did it unfold in a vacuum or emerge from a lab. Rather, it was arrived at following a complex, multilayered process, and unpacking those layers is essential to fully comprehending and judging it. Finally, the 1972 plan may be seen as representing a timely response to a city that urgently needed a vision for its future, one that absorbed the enormous challenges it faced and created a system for instilling order through a period of unprecedented urban population and territorial expansion.

Advisor: Bosselmann, Peter
Queer Idiosyncrasies: Description and Deviance in the Novels of Zola and Huysmans

Queer Idiosyncrasies: Description and Deviance in the Novels of Zola and Huysmans proposes to complicate literary-historical narratives about the relationship between French naturalism and decadence using analytical approaches informed by sex and gender studies and queer theory. In particular, it examines the ways in which these writers’ penchant for literary description and cultural moralism leads to new and surprising expressions of non-normative genders and sexualities that are at odds with their aesthetic projects. Their novels are revealed as intertexts—responding and adapting to one another—whose forms, styles, and themes are mutually shaped over the course of their authorial careers./nThe first chapter consists of a comparative study of Zola’s La curée and Huysmans’s Marthe, histoire d’une fille. Here, I contend that La curée’s heterotopic style manifests early naturalism’s anxieties concerning the conjugal deviance and androgyny of modern France, and that Marthe’s poetics of placelessness prefigures decadent tropes even in Huysmans’s naturalist phase. In the following chapter, I argue that Zola’s anti-clerical novel La faute de l’abbé Mouret, in attempting to write a scientifically informed version of Genesis, unwittingly models a radical type of gender parity based on friendship. I then frame Huysmans’s En rade as a decadent parody of La faute in which sterility and auto-eroticism are inextricably bound up with decadent autoreferentiality. Chapter three turns to Huysmans and Zola’s late works—Là-bas and Paris respectively—to show how their individual polemics against modernity and modernism offer visions of liberated womanhood and subversive homosexuality. Finally, in the short coda that follows, I perform close readings of a third author’s work, La Marquise de Sade by Rachilde, to affirm both the possibilities and the limits of my own methodology, and to recast Rachilde’s relationship to naturalism and decadence.

Advisor: Sanyal, Debarati
Introspective Theories and Geminal Categories

In provability logic, a key principle is Löb's theorem, stating that if the provability of P provably entails P, then P itself is provable (in modal logic notation, □ P ⊢ P has as a consequence ⊢ P). This was first discovered in the follow-up work on Gödel's incompleteness theorems, with Gödel's results viewable as following from Löb's theorem. Later, it was also seen that the same formal pattern of Löb's theorem described certain fixed point constructions studied under the name of "guarded recursion"./nThe aim of these notes is to draw attention to a certain simple class of category-theoretic structures which serve as an abstract environment for deriving Löb's theorem and such fixed point constructions, allowing for a vastly generalized and unified understanding of the scope of applicability of such constructions. These are the structures we call "introspective theories"./nThis very minimal categorical definition nontrivially entails Löb's theorem and guarded recursion at both the term and type level. We also demonstrate how this abstraction offers a clean unification of the interpretation of the Gödel-Löb incompleteness theorems in traditional logic or via arithmetic universes a la Joyal, along with the interpretation by Birkedal et al of guarded recursion in presheaves over well-founded orders, along with the distinct classical interpretation of the GL modal logic in well-founded transitive Kripke frames./nWe also explore free instances of our structure, which turn out to admit a tractable explicit description. The free introspective theory is what we call "the theory of geminal categories", and we explore also some further illuminating relationships between the concepts of introspective theories and geminal categories.

Advisor: Scanlon, Thomas
Pretrained Representations for Embodied AI

The world is messy and imperfect, unstructured and complex, and nonetheless we must still accomplish the basic behaviors necessary for survival. It is for this purpose, ecologically relevant behavior, that vision evolved 500-600 million years ago./nThis thesis is about how learn representations of the visual world that are useful for the types of behaviors we might want an embodied AI system to do. In the first part of this thesis, we systematically study how bottlenecking visual inputs through different pretrained representations affects the ability of a robot to learn different atomic navigation skills (Chapter 2) and manipulation skills (Chapter 3) through trial-and-error. The main finding is that the appropriate pretrained representation greatly improves the sample efficiency for skill acquisition, and greatly improves the generalization of the learned skill. In the second part of the thesis, we use the lessons learned in order to improve the accuracy of the representations in a larger variety of contexts (indoors, outdoors, tabletop settings, and so on). In Chapter 4 we do this through adding cross-prediction consistency objectives. In Chapter 5 we do this by leveraging vast amounts of 3D data available on the internet and from a robot's prior experience./nThe methods are primarily developed for the purpose of vision and action, but many of the ideas are general and could work for other sensory modalities and behaviors.

Advisor: Malik, Jitendra
Zamir, Amir
The Hepatic Integrated Stress Response Suppresses the Somatotroph Axis to Control Liver Damage in Nonalcoholic Fatty Liver Disease

Nonalcoholic Fatty Liver Disease (NAFLD) is a progressive liver disease that can lead to liver cirrhosis and hepatocellular carcinoma, eventually resulting in death. The disease is prevalent worldwide, affecting around a quarter of the population, and is associated with risk factors such as obesity and type 2 diabetes. Currently, no standard treatment exists for NAFLD, which is characterized by excessive hepatic lipid accumulation leading to ER and mitochondrial stress, impaired insulin signaling, and inflammatory response. These events form a vicious cycle and exacerbate the progression of NAFLD. Sirtuin 7 (SIRT7), an NAD+-dependent deacetylase, is a nutrient sensor that alleviates ER stress and mitochondrial protein folding stress and prevents fatty liver. The insulin/IGF-1 signaling is the first nutrient-sensing pathway reported to regulate longevity in model organisms. Inhibiting the Insulin/IGF-1 signaling extends the lifespan of mice and worms. Paradoxically, low circulating IGF-1 is linked to hepatic steatosis and severe liver fibrosis in NAFLD. It remains unclear whether the somatotroph axis, which controls the insulin/IGF-1 signaling pathway, plays a role in liver damage during the progression of NAFLD./nThis dissertation aimed to explore the underlying mechanisms of NAFLD and develop a novel therapeutic strategy to combat this progressive liver disease. Chapter 1 provided a comprehensive review of the current state of nutrient-sensing pathways and oxidative stress response. We also discussed the therapeutic opportunities to prevent aging- or disease-driven tissue dysfunction by targeting the nutrient-sensing pathways. In Chapter 2, we investigated the role of the somatotroph axis in NAFLD and identified a novel regulatory pathway involving hepatic ER stress and ATF3, which suppresses the somatotroph axis in hepatocytes and leads to decreased cell proliferation and ER stress- induced cell death. Our findings in genetic and diet-induced NAFLD mouse models suggest that the suppressed somatotroph axis prevents apoptosis and inflammation but decreases hepatocyte proliferation and exacerbates fibrosis in the livers. Finally, we demonstrated that pharmacological activation of SIRT7 via NAD+ boosting reduces hepatic ER stress, rescues the suppressed somatotroph axis, and ameliorates NAFLD pathogenesis, offering a promising new therapeutic approach for treating this disease.

Advisor: Firestone, Gary
Compactness theorems on hyperkähler 4-manifolds

Hyperkähler manifolds are one of the simplest examples of Einstein manifolds. They are Ricci-flat Riemannian manifolds with special holonomy. In dimension 4, hyperkähler 4-manifolds can be purely described by a triple of symplectic 2-forms that satisfy the pointwise orthonormal condition with respect to the wedge product./nIn this dissertation, we proved the compactness of a set of hyperkähler 4-manifolds with boundary under Cheeger-Gromov topology, where we assume only geometric control on the boundary and topological conditions. We showed that our proof can be extended to Einstein 4-manifolds with boundary by assuming only additional topological conditions./nFurthermore, we discuss the period map for K3 surfaces in a differential geometric setting. We gave a simple proof for the surjectivity of the period map, without invoking Yau's theorem on the Calabi conjecture or any algebraic geometry. The key is to show that when a sequence of hyperkähler metrics has bounded period in some sense, then the sequence has a convergent subsequence under Cheeger-Gromov topology.

Advisor: Sun, Song