VictorJuiz/thesis huggingface dataset:
Approximate counting, phase transitions and geometry of polynomials

In classical statistical physics, a phase transition is understood by studying the geometry (the zero-set) of an associated polynomial (the partition function). In this thesis, we will show that one can exploit this notion of phase transitions algorithmically, and conversely exploit the analysis of algorithms to understand phase transitions./nAs applications, we give efficient deterministic approximation algorithms (FPTAS) for counting $q$-colorings, and for computing the partition function of the Ising model.

Advisor: Sinclair, Alistair
Trans-formations: Projects of Resignification in Tamil Nadu’s Transgender Rights Movement

As the term “transgender” rapidly gains traction worldwide— becoming, for many, key to accessing state recognition and medical access— it maps in irregular and ambivalent ways onto other legal and cultural frameworks. In India, the Supreme Court has treated the categories of “LGBT” and “transgender” rights in starkly different ways, criminalizing homosexuality while still upholding transgender rights (2013), and then radically reversing its stance in 2018. Rather than assert the singularity of the “local” against the homogenizing impact of the “global,” as some research has done, my dissertation examines the reach and implications of these debates in the South Indian state of Tamil Nadu by tracking “transgender imaginaries”: utopian visions that take the figure of the “transgender woman” as a point of departure to imagine how “changing sex” can allow subjects to speak powerful new kinds of radical “truth,” performatively inaugurating new ethical worlds. Transgender imaginaries imply competing “models of sex” (Plemons 2017): metapragmatic models held by social actors, of what constitutes “sex,” where it resides, how it is produced, how it is exposed, and what implications “sex” transformations have for the social body at large. I track how my interlocutors continually used the concept at different scales, indexing broad cultural anxieties, while paradoxically marking specific bodies./nChapter I examines how narratives about hijras—India’s iconic transgender community of ritual specialists—were interpreted in radically different ways in Chennai by journalists, human rights activists, doctors, public health officials and transgender-identified subjects, indexing anxieties about changing practices of kinship in Chennai, the neoliberalization of healthcare, and the incursion of “foreign” NGOs. Chapter II examines the figure of the thirunangai (meaning “Respectable Woman” in Tamil). “Thirunangai imaginaries” combine models of sex drawn from (a) the pro-Tamil, anti-caste ideologies of the Dravidian movement; (2) transnational models of sex change; and (3) pan-Indian “exposure models of sex” where sexed body parts, kinship affiliation, ascetic practice, and verbal license are imagined together to produce an ethical subject. Chapter III examines how the term koti— meaning an effeminate male— has circulated between the 1990s and the present in human rights documents, autobiographical stories, and jokes in Chennai, indexing the contingency and boundaries of what constitutes “maleness. Together these reveal the instability and ethical horizons of what “sex” is.

Advisor: Briggs, Charles L.
Cohen, Lawrence
Compiling Communication-Minimizing Query Plans

Because of the low arithmetic intensity of relational database operators, the performance of in-memory column stores ought to be bound by main-memory bandwidth, and in practice, highly-optimized operator implementations already achieve close to their peak theoretical performance. By itself, this would imply that hardware acceleration for analytics would be of limited utility, but I show that the emergence of full-query compilation presents new opportunities to reduce memory traffic and trade computation for communication, meaning that database-oriented processors may yet be worth designing./nMoreover, the communication costs of queries on a given processor and memory hierarchy are determined by factors below the level of abstraction expressed in traditional query plans, such as how operators are (or are not) fused together, how execution is parallelized and cache-blocked, and how intermediate results are arranged in memory. I present a Scala- embedded programming language called Ressort that exposes these machine-level aspects of query compilation, and which emits parallel C++/OpenMP code as its target to express a greater range of algorithmic variants for each query than would be easy to study by hand.

Advisor: Asanovic, Krste
System Design for Software Packet Processing

The role of software in computer networks has never been more crucial than today, with the advent of Internet-scale services and cloud computing. The trend toward software-based network dataplane—as in network function virtualization—requires software packet processing to meet challenging perfomance requirements, such as supporting exponentially increasing link bandwidth and microsecond-order latency. Many architectural aspects of existing software systems for packet processing, however, are decades old and ill-suited to/ntoday’s network I/O workloads./nIn this dissertation, we explore the design space of high-performance software packet processing systems in the context of two application domains, . First, we start by discussingthe limitations of BSD Socket, which is a de-facto standard in network I/O for server applications. We quantify its performance limitations and propose a clean-slate API, called MegaPipe, as an alternative to BSD Socket. In the second part of this dissertation, we switch our focus to in-network software systems for network functions, such as network switches and middleboxes. We present Berkeley Extensible Software Switch (BESS), a modular framework for building extensible network functions. BESS introduces various novel techniques to achieve high-performance software packet processing, without compromising on either programmability or flexibility.

Advisor: Ratnasamy, Sylvia
Distributed Sliding Mode Control for Nonlinear Consensus

This dissertation is concerned with the distributed control of nonlinear multi-agent consensus problems. The main objective of the consensus study is to design distributed algorithms that rely on only local interaction to achieve global group behavior. We propose a distributed sliding mode control (DSMC) framework for nonlinear heterogeneous multi-agent systems under different information exchange topologies. The DSMC constructs the topological sliding surface and reaching law via a so-called "topological structured function". The control law obtained by matching the topological sliding surface and topological reaching law is naturally distributed. Under this framework, topological diversity is explicitly incorporated. Also, the consensus problem is significantly simplified by mapping N interconnected higher-order dynamics into an N-th order sliding variable. The DSMC framework supports both leaderless consensus and consensus with a leader. For both cases, we show asymptotic stability when the topology contains a spanning tree, and further prove finite-time convergence under the undirected topologies. We also extend the DSMC framework to MIMO systems./nTo demonstrate the usage and show the effectiveness of DSMC, we discuss two major applications with simulation results. The first application is for heterogeneous platoon systems. The control objective is to regulate vehicles to travel at a common speed while maintaining desired inter-vehicle gaps. The information flow topology dictates the pattern of communication between vehicles in the platoon. The second application is for flocking of nonholonomic unicycle agents.

Advisor: Poolla, Kameshwar
Robust Control of the Sit-To-Stand Movement for Powered Lower Limb Orthoses

Safety in the execution of the sit-to-stand movement is a key feature for wide adoption of powered lower limb orthoses that assist the mobility of patients with complete paraplegia. This work provides techniques for planning the motion of these medical devices to yield biomechanically sound configurations, designing tracking controllers for the reference trajectories of the movements, evaluating the robustness of the controllers against parameter uncertainty, and assessing the ability of a proxy for the user to coordinate with the control input during rehabilitation and physical therapy sessions. Although our ideas can be applied to analyze any powered orthosis in the market, the featured numerical simulations consider a minimally actuated orthosis at the hips./nThe orthosis and its user are modeled as a three-link planar robot. The reference trajectories for the angular position of the links are defined from the desired behavior for the Center of Mass of the system, and the corresponding input trajectory is obtained using a computed torque method with control allocation. With the Jacobian linearization of the dynamics about the reference trajectories, a pool of finite time horizon LQR gains are designed assuming that there is control authority over the actuators of the orthosis, and the torque and forces that are applied by the user. Conducting reachability analysis, we define a performance metric for the robustness of the closed-loop system against parameter uncertainty, and choose the gain from the pool that optimizes it. Replacing the presumed controlled actions of the user with an Iterative Learning Control algorithm as a substitute for human experiments, we find that the algorithm obtains torque and forces that result in successful sit-to-stand movement, regardless of parameter uncertainty, and factors deliberately introduced to hinder learning. Thus we conclude that it is reasonable to expect that the superior cognitive skills of real users will enable them to synchronize with the controller of the hips through training. Further tests are performed to verify the robustness of the system in feedback with the LQR gain in the presence of measurement noise, and model uncertainty./nWe believe that our tests can set a good benchmark to systematically choose actuators for fitting a large variety of users, and develop a protocol for assessing the robustness of the sit-to-stand movement in clinical trials. This would then help to close the gap between these medical devices and standing wheelchairs, which still remain the most reliable mobility solution for patients with complete paraplegia.

Advisor: Packard, Andrew
On Systems and Algorithms for Distributed Machine Learning

The advent of algorithms capable of leveraging vast quantities of data and computational resources has led to the proliferation of systems and tools aimed to facilitate the development and usage of these algorithms. Hardware trends, including the end of Moore's Law and the maturation of cloud computing, have placed a premium on the development of scalable algorithms designed for parallel architectures. The combination of these factors has made distributed computing an integral part of machine learning in practice./nThis thesis examines the design of systems and algorithms to support machine learning in the distributed setting. The distributed computing landscape today consists of many domain-specific tools. We argue that these tools underestimate the generality of many modern machine learning applications and hence struggle to support them. We examine the requirements of a system capable of supporting modern machine learning workloads and present a general-purpose distributed system architecture for doing so. In addition, we examine several examples of specific distributed learning algorithms. We explore the theoretical properties of these algorithms and see how they can leverage such a system.

Advisor: Jordan, Michael I
The Role of Lipid Droplets in Cellular Energy Homeostasis and Interorganelle Communication

Lipid droplets (LDs) are ubiquitous organelles that play a critical role in lipid homeostasis by regulating the storage and mobilization of fatty acids. When nutrient supplies are limited, the fatty acids stored in LDs are transferred to the mitochondria for the generation of energy. As starvation persists however, autophagy is triggered to degrade and recycle damaged organelles. Autophagy releases FAs into the cytosol to replenishing LDs with new FAs, increasing LD abundance. Interestingly, the autophagy-dependent LDs cluster in close proximity to mitochondria, forming membrane contact sites (MCSs). MCSs are areas of close apposition between the membranes of two organelles mediated by tethering forces that arise from protein-protein interaction. However, the identity of a LD-mitochondrial tethering complex and the functional importance of the LD-mitochondrial contacts in FA transfer and energy homeostasis are unknown./nIn chapter one, we observed an increase in LD abundance during prolonged nutrient deprivation. Starvation-induced LDs are not required for fatty acid delivery to mitochondria, but instead LDs sequester fatty acids that are released during autophagy to prevent lipotoxic dysregulation of mitochondrial function. In chapter two, we established an inducible heterodimer tethering system to temporally and spatially regulate LD-mitochondrial contact to study the functional importance of the interorganelle contact. Finally, in chapter three we employed proximity-labeling proteomics to identify protein tethers that mediate the close positioning of LDs and mitochondria. Together, our studies advance our understanding of organelle communication in the maintenance of lipid and energy homeostasis.

Advisor: Olzmann, James A.
Fluctuation Analysis of Order Positions Under General Cancellations

In a modern financial market, limit order books are usually managed under the price- time priority rule (i.e. orders are ranked by price and then time/position). Empirical studies of limit order books show that the major component of the order flow occurs in the best bid/ask queue [1], and the order’s positional value can be of the same order of magnitude as the bid-ask spread [9]. As a consequence, analyzing the order positions in the best bid/ask queue plays an important role in the field of algorithmic trading./nIn this dissertation, we analyze the fluctuation of scaled order positions around their limits in the best bid queue under the general assumption for cancellations, which allows us to generalize the existing result [4, Theorem 15] to include more realistic situations. We first derive the stochastic differential equation that the fluctuation satisfies. Then we prove that the fluctuation is a Gaussian process with mean zero. Furthermore, we show that it has the mean-reverting property, where the mean-reverting level is the same as the fluctuation of scaled best bid queue length multiplied by the order positions relative to the best bid queue length and the mean-reverting speed is proportional to the rate of change of cancellations in the best bid queue.

Advisor: Evans, Steven Neil
Novel lipid metabolism pathways at the host-pathogen interface of Mycobacterium tuberculosis infections

The bacterial pathogen Mycobacterium tuberculosis has been a major contributor to mortality throughout human history and is uniquely difficult to treat with available antibiotics. M. tuberculosis is currently recognized as the leading cause of death due to a single infectious agent in humans worldwide, killing between 1.5 and 2 million people every year. While disease burden is largely concentrated in poor communities without access to healthcare and pharmaceuticals, a recent rise in multi-drug resistant strains threatens all of us. This looming public health crisis heightens the need for new therapies to be developed. It also highlights the need to better understand bacterial lifestyles and molecular dynamics of host-pathogen interaction./nM. tuberculosis lives inside the phagosome of host macrophages, a hostile compartment deadly to most phagocytosed microbes. Even sequestered inside the phagosome, M. tuberculosis has evolved mechanisms to manipulate the host and developed the ability to acquire factors required for survival and replication. My research has focused on the fundamental yet perplexing questions of what carbon sources M. tuberculosis accesses and survives upon during infection, and conversely how host cells alter their lipid metabolism in response to infection. Previously, M. tuberculosis was thought to manipulate macrophages to form lipid droplets as a readily available store of carbon to support bacterial growth. However, my work demonstrated that macrophages produce lipid droplets in support of host immune responses, as part of a novel signaling pathway involving IFN-γ, HIF-1α, and HIG2. I also found that bacteria are incapable of acquiring lipids from macrophage lipid droplets and that instead bacteria acquire lipids from an unknown source intracellularly. These findings inspired screens in an arrayed transposon library to identify prokaryotic genes important for lipid import and survival during infection. I present the discovery of three novel genes required for import of fatty acids and formation of prokaryotic lipid droplets during infection. Separately, I present a new randomly barcoded transposon library that will enable high-throughput selection assays to define gene fitness and function.

Advisor: Stanley, Sarah
Investigating the Mechanisms of Neural Stem Cell Mechanotransduction: The Roles of Angiomotin and Hyperglycemia

Neural stem cells (NSCs) are remarkable mediators of structural plasticity in the adult mammalian brain and play important roles in physiological and pathophysiological neurobiology. Ongoing research has uncovered that mechanical cues can potently regulate NSC behavior. For example, soft substrates promote the neuronal differentiation of NSCs by suppressing cytoskeletal contractility and perturbation of the same pathway influences neurogenesis in vivo. However, the mechanisms that link cytoskeletal signaling to transcriptional regulation and govern stiffness-dependent NSC fate commitment are not fully understood. Additionally, studies have shown that dysfunction of hippocampal NSCs may underlie the cognitive deficits linked to diabetes. This may be due to the dysregulation of cellular energetics, which is tightly regulated in stem cells and influences cytoskeletal dynamics. Therefore, the effect of hyperglycemia on NSC mechanotransductive signaling warrants further study./nIn this dissertation, we show that angiomotin (AMOT) is critical for mechanotransduction in NSCs. Loss of AMOT inhibited neurogenesis on soft substrates while also severing the functional tie between reduced myosin contractility and increased neurogenesis. We found that AMOT is critically regulated by its phosphorylation and localization and promotes neurogenesis by inhibiting yes-associated protein (YAP) and upregulating -catenin activity. Additionally, we found that hyperglycemia suppresses NSC growth in culture and that NSC mechanosensitive differentiation can be regulated by glucose concentration. Specifically, activation of 5’adenosine monophosphate-activated protein kinase (AMPK) either by lowering the glucose concentration or metformin treatment rescued neurogenesis on stiff substrates while high glucose or compound C (AMPK inhibitor) treatment suppressed neurogenesis. Therefore, hyperglycemia may have a direct influence on how NSCs sense and respond to their physical microenvironment through an AMPK-dependent mechanism./nThese findings significantly add to our understanding of how NSCs sense, integrate, and respond to biophysical inputs and how those pathways are influenced by glucose dysregulation. Further elucidation of these mechanisms has the power to inform how NSCs are regulated in health and disease while also advancing how these cells are utilized in regenerative medicine approaches in the nervous system.

Advisor: Kumar, Sanjay
Schaffer, David V
ARTELIA GREEN’S & OLIVIA WILLIAMS’ LEGACY: A STUDY ON THE PEDAGOGICAL PRACTICES THAT IMPROVE HEALTH FOR BLACK CHILDREN

This dissertation examines the relationship between caring teaching practices and greater health outcomes for black children. Public health theory suggests that Black youth generally experienced greater levels of adversity compared to non-black youth (Schilling et al., 2007; Marie, 2016). Exposure to these frequent and/or sustained stressors without the buffering care of a supportive adult can change children’s brains and bodies, including disrupting learning, behavior, immune systems, and even the way DNA is read and transcribed. My research examines the efficacy of critical classroom pedagogy (Duncan-Andrade & Morrell, 2008) and social design-based research (Gutierrez, 2016) as a framework to address and attenuate the impacts of toxic stressors that black youth embody./nThis study honors research principles grounded in care (Angelou, 1979; Noddings, 1988; Duncan-Andrade, 2006), to generate grounded theory for social transformation. This dissertation anchors data (field notes, classroom video, in-depth interviews) in order to integrate the fields of education and public health to produce ecologically valid findings that: 1) highlight and reproduce that types of teaching practices and conditions that mediate healthier children and 2) reframe our understandings of the possibilities of education.

Advisor: Perlstein, Daniel
Entanglement and Geometry

There is now strong evidence of a deep connection between entanglement in quantum gravity and the geometry of spacetime. In this dissertation, we study multiple facets of this connection. We start by quantifying the entanglement of a scalar quantum field theory as a function of the curvature of its background. We then shift our focus to the AdS/CFT duality, and we prove multiple logical relationships between geometric statements in AdS and entropic statements in the CFT. Many of these proofs work in the presence of quantum corrections, and we prove under which geometric conditions entanglement wedge nesting continues to imply the quantum null energy condition (QNEC) when the CFT is on an arbitrary curved background. We also demonstrate that the non-gravitational limit of the quantum focusing conjecture implies the QNEC, given the same geometric conditions. Next, we prove the connection between the boundary of the future of a surface and the null geodesics originating orthogonally from that surface. This theorem is important for proving that the area of holographic screens increases monotonically. Finally, we derive the holographic prescription for computing Renyi entropies of a CFT with the formalism of quantum error-correction. In the process, we provide evidence that the quantum gravity degrees of freedom related to the AdS geometry are maximally-mixed.

Advisor: Bousso, Raphael