VictorJuiz/thesis huggingface dataset:
Connected Quadratic Programs for Autonomy

This dissertation describes the work I have done on the subject of computing equilibrium solutions of connected quadratic programs (QPs), particularly for the connected programs arising in the context of autonomous system design. Reasoning about the interaction between multiple mathematical programs enables the analysis and solution to a wealth of problems inaccessible by standard optimization formulations./nOne of the most commonly arising examples of connected optimization problems is the bilevel program, comprised of an outer-level and inner-level program. The outer-level problem is subject to a constraint that a subset of decision variables solve the inner-level problem. Another class of connected optimization problems are those of Nash equilibrium problems, in which optimization problems are solved simultaneously./nBeyond these and some other simple organizations of problem, general interactions among optimization problems are not well studied, despite the potential for modeling many interesting real-world problems. Presumably this is because with generalization in problem organization comes increased complexity, both from an analysis and computation perspective./nTo address this, it is claimed in this work that it is possible to compute equilibrium solutions to a broad range of connected optimization problems, assuming those problems take the form of convex quadratic programs. This claim is based off a result that equilibrium solutions to a collection of QPs with piecewise linear constraints can be represented as a piecewise linear mapping. Recursive application of this result leads to the results for generally nested equilibrium problems. Theoretical results and computational approaches for this class of problem are developed. The efficacy of the presented methodologies is demonstrated on various problems faced by autonomous vehicles.

Advisor: Tomlin, Claire
Investigating Relationships Between Semantic Representations in the Human Brain

Humans are constantly taking in information from a multitude of dissimilar sources to integrate and update their existing mental representations, but the series of computations that underlie this process are still largely unknown. We do know that these complex processes recruit multiple brain networks that interface with each other, but the precise roles that these networks play can change depending on task demands, and the full extent of this is only partially understood. This research presented in this dissertation focuses on furthering this knowledge specifically in the domain of semantic representation in humans./nIn this dissertation, I first summarize the existing literature on semantic representations in the human brain. In addition to this, I describe how careful computational modeling methods alongside naturalistic experimental conditions allow us to answer very precise questions about representations in the human brain. I then present two functional magnetic resonance imaging (fMRI) experiments that explore new avenues of research in semantic representation and further show the strength of these methods. The first of these experiments illustrates that the visual and linguistic semantic networks of the brain are more precisely aligned than had previously been hypothesized. This pattern would not have been discovered using most typical fMRI analysis methods. In the second experiment, I analyze how linguistic semantic representations update after learning and memorization. Specifically, after participants have spent many hours memorizing songs, we can see that their semantic representations of the content of the song lyrics can shift dramatically./nTogether, these two experiments show the importance of studying semantic representations not only in a single modality or setting. Without looking at the relationships between different types of representations or how representations are updated with learning and experience, we will never have a full picture of how the brain is functioning in complex, naturalistic environments.

Advisor: Gallant, Jack
Land Power: Real Estate and the US Military in South Korea

Land has been essential to American military power in Korea from 1945 into the present day. The dissertation charts the evolution of American “land power” in South Korea, focusing on the transition from direct military dispossessions during the Korean War to a US military real estate system that became increasingly enmeshed in South Korea’s land development system in the post-war decades. Today, American land power in South Korea consists not only of the US military’s ability to project force from a point in space, but also of land valued as a commodity in a way that serves the ongoing US military presence in the country. In the early 2000s, military lands accumulated during the Korean War through mass civilian dispossession began to function as assets in the US-South Korea burden-sharing system. Even with a reduction of the total number of US bases in South Korea, alliance burdens have been increasingly shifted onto South Korea and onto localities. The South Korean state has treated most released US military lands as an asset used to fund the US-South Korea alliance, essentially forcing local communities to either repurchase their own lands back from the state, or to lure investors and developers to do so by passing deregulatory measures. Further, political devolution and neoliberalization created conditions in which the politics of (de)militarization were almost entirely subsumed by a new pro-growth and pro-deregulation politics of development in many places. The dissertation argues in favor of a multi-scalar anti-dispossession critique of US militarism that considers (de)militarization as a process that extends beyond the walls of any military base and into a landscape of uneven local development.

Advisor: Watts, Michael J
Synthetic Design of Vehicles for Macromolecule Delivery

The following dissertation presents work done towards the development of delivery strategies for proteins and nucleic acids to mammalian cells, as well as targeted imaging materials to bacteria. Delivery of large molecules such as proteins, nucleic acids, and large synthetic molecules remains a major bottleneck in the field of drug delivery, and despite an abundance of research into the topic, the delivery of intracellular proteins has still not seen clinical significance. To address this, we sought to develop new delivery vehicles in an endeavor to address current challenges in drug delivery./nChapter 1 discusses the development of acid-sensitive surfactants for the delivery of nucleic acids. This class of molecules, termed caged surfactants, consists of a membrane disruptive surfactant that has been masked with two PEG chains through an acetal linker. This prevents it from entering the membrane in its intact state; however, after acetal hydrolysis in the acidic endosomal compartment, release of free surfactant causes endosomal release of any co-delivered cargo. The simultaneous delivery of caged surfactant with nucleic acid was achieved using two strategies: (i) inclusion of two primary amines on the caged surfactant to allow complexation through electrostatic interactions, and (ii) inclusion of the RNA-binding dye thiazole orange (TO) to allow tight binding through intercalation. In this study we show that amine-containing caged surfactant (PCS) and TO-containing caged surfactant (TCS) increase the delivery of mRNA and siRNA, respectively./nChapter 2 discusses the development of delivery vehicles for the delivery of proteins to mammalian cells. The chapter consists of two separate studies. The first study utilized a fluorescent acid-sensitive membrane disruptor (FEDS) as an adjuvant to Lipofectamine-based delivery of CRISPR-Cas9. FEDS successfully increased the delivery efficacy of Cas9 to HEK cells. In addition, due to its fluorescent properties the cells with Cas9-triggered gene editing could be sorted through a fluorescence cell sorter. The second study describes the development of a polyethylene glycol-Eosin Y block copolymer (PEG-pEosin) for protein delivery. The Eosin Y moieties bind a wide range of proteins, and PEG-pEosin can therefore be used as a general protein delivery tool. Using PEG-pEosin we successfully delivered Cre recombinase to Ai9 cells through a PEG-pEosin/Cre/Listeriolysin O complex, wherein the Lysteriolysin O serves as an endosomal disruptive component./nChapter 3 presents a maltohexaose-indocyanine green conjugate for the detection of infective endocarditis. Maltohexaose (MH) is a sugar that is specifically taken up by bacteria, and it is relatively tolerant of modifications to its reducing end. The FDA-approved dye indocyanine green (ICG) was conjugated to MH to yield a low toxicity, high wavelength probe that was shown to accumulate in bacterial vegetations in an endocarditis rat model.

Advisor: Murthy, Niren
Francis, Matthew B
Formalizing and Testing Computational Cognitive Models of Social Collaboration

The greatest human achievements are never completed alone. However, social interaction is complex and successful collaboration even more so. Tremendous amounts of information and processing are involved in predicting, interpreting, and working with others. These calculations are implicit, deeply embedded in the human psyche and not easily accessible for analysis or improvement. Knowing what algorithms the mind is solving when collaborating with others would be invaluable, both for our own knowledge and improvement of social collaboration between people, and to reconstruct these algorithms in systems outside ourselves. People increasingly interact with artificial intelligence systems, and developing models of social interaction could enable these systems to seamlessly assist us. This premise motivates my work: that by understanding the algorithms behind social collaboration, we can improve interactions between people, and between people and machines./nIn this dissertation, I formalize and test computational models of collaboration, focusing on three problem areas. First, I investigate how people collaborate in recalling information. Though one might expect memory to be a solitary venture, researchers have long studied the differences in how people recall information in groups compared to alone, though only for small group sizes. Luhmann and Rajaram (2015) hypothesized mechanisms of large-scale recall using an agent-based model. I test the predictions of this model with an empirical experiment recruiting thousands of participants. Second, I investigate another key component of collaboration: people’s intuitive judgments of how shared resources should be allocated among people with different preferences. I collect empirical data from participants under a number of decision conditions, then use an inverse reinforcement learning model to determine what underlying mathematical fairness principles characterize people’s choices. Third, I investigate how people infer others’ preferences, a key component of collaboration. My coauthors and I present a rational model for inferring preferences from response times, using a Drift Diffusion Model to characterize how preferences influence response time and Bayesian inference to invert this relationship. We then compare the model’s predictions to collected empirical data. These three case studies comprise novel models of social interaction, tested with behavioral experiments, aimed at improving human and technological collaboration.

Advisor: Griffiths, Thomas L.
Connections: Corruption, Conscription, and Counterrevolution in Egypt after Mubarak

This dissertation examines the Egyptian counterrevolution of 2013 through an ethnographic account of young men living in a rural Nile Delta province associated with state power and corruption. Building on two years of ethnographic fieldwork, it considers the moral dilemmas of corruption through forms of giving and kinship, paying particular attention to the ways that love produced through affinal kinship justifies making exceptions to the law. Through a historical investigation of the origins of the Egyptian nation-state, this research posits the formative role of the conscription of the Egyptian peasantry during the reign of Mohammed Ali Basha, arguing that the politics of the counterrevolution can be traced back to this constitutive moment. Through the conscription of the peasantry en masse, Ali Basha also instituted the family as the sovereign exception to the law and laid the conditions for the army to emerge as the primary institution for the expression of popular will.

Advisor: Hirschkind, Charles
Conductive Materials for Additive Manufacturing: Towards Multi-Functional, Multi-Material 3D Printed Systems

Additive manufacturing or three-dimensional (3D) printing has been popularized in applications, including automotive, aerospace, medical, architectural, consumer products, and electronics. Despite interest in using 3D printing for microdevice fabrication, limitations in resolution, surface roughness, support material removal, dimensional fidelity, and material diversity have limited the scope of applications. 3D printing techniques are generally limited to a single class of material due to incompatible processing requirements between multiple types of materials, which limits the electrical functionality, mechanical properties or other functionalities of one or more materials. This dissertation presents methods combining mechanically and electronically functional materials, resulting in a new class of multi-functional, multi-material 3D printed systems to address the limitations of current single-material 3D printing systems./nFor commercial 3D printing systems that utilize proprietary materials, where the surface chemistry is relatively unknown, there are few viable options to construct electrical materials. In the first part of this dissertation, the commercially available, intrinsically conductive polymer PEDOT:PSS has been modified to chemically adhere to MultiJet 3D printing materials, where their exact compositions are unknown. A study into the addition of silane to enhance adhesion of PEDOT:PSS chains to a polymer surface is conducted and the conductivity of the PEDOT:PSS film is further enhanced by the introduction of other additives into the polymer mixture. A three-dimensional lattice structure is printed and coated with this polymer mixture to generate a 3D electrode structure. As a demonstration example, a prototype sensor capable of determining changes in ethanol content in water has been tested via changes in conductivity with a measured detection limit of ~0.19 %v/v./nThe second part of this dissertation proposes a method for fully-3D printed multi-material structures using stereolithography 3D printing. A mixture of Ni particles and commercially available 3D printing resin is created to realize an electrically functional material that can be printed using a benchtop stereolithography 3D printer. A printing protocol is developed to enable the generation of multi-material structures with a single 3D printer and the conductivity of the Ni-resin composite part is measured to be ~150 S/cm. With the ability to print multi-functional, multi-material systems, a microfluidic capacitive sensing device is proposed to demonstrate the potential application of this printing technique.

Advisor: Lin, Liwei
Automated Measurements of Gas Exchange in Wetlands

Wetlands are the largest natural producer of methane, a potent greenhouse gas. One way in which dissolved methane can be emitted from wetlands is via hydrodynamic transport. This transport pathway includes stirring and bulk motion in the water column as well as diffusion near the air-water interface. It is driven by sources of near-surface turbulence, such as natural convection (e.g. temperature-driven stirring) and forced convection (e.g. wind shear, precipitation, honami). Relative to other methane transport pathways in wetlands, hydrodynamic transport has been understudied and its contributions to total methane flux have been underestimated./nWe developed a low-cost, autonomous, and programmable underwater camera to measure water velocity in wetlands. We used this camera in a model wetland to correlate gas exchange across the air-water interface to water-side velocity statistics. Our results found a positive quadratic relationship with a non-zero intercept between the standard deviation of vertical velocity and the normalized gas transfer velocity (k600). This camera was then deployed in Burns Bog outside of Metropolitan Vancouver, British Columbia, Canada in order to estimate the site's methane flux due to hydrodynamic transport. Using water-side velocity statistics to calculate k600, we found that hydrodynamic transport was responsible for approximately 17.2% of total methane flux in Burns Bog; this percentage varied very little throughout the day. Finally, we compare a heat-flux-based method for estimating k600 against our water-velocity-based approach. We found that the heat-flux-based method had consistently lower estimates for k600 and gas flux relative to the water-velocity-based approach. This was because the heat flux data only captured stirring due to natural convection whereas the water-velocity-based approach included both natural and forced convection.

Advisor: Variano, Evan
Designing New Scripts: Exploring the Everyday Practices of Blackness Among AfroPuerto Rican Mothers in California

The purpose of this dissertation was to explore how AfroPuerto Rican mothers engage in Blackness as a sociocultural-historical practice. An analysis of ethnographic data, including participant-observations and life history interviews with six AfroPuerto Rican women in California, were the means used to describe the teaching and learning (or teaching/learning) practices within AfroPuerto Rican multigenerational communities that focus on Blackness as an ancestral, cooperative, and activist practice. This study documents how the participating AfroPuerto Rican women’s enactments of blackness-as-practice reflected communal, proleptic understandings of blackness within AfroPuerto Rican communities. Through the use of Black and AfroLatinx feminist lenses and sociocultural understandings of human activity, I suggest how researchers andpractitioners can learn from AfroPurto Rican mother-designers to design educational environments for the teaching of blackness-as-practice.

Advisor: Guiterrez, Kris D
Automated, FPGA-Based Hardware Emulation of Dynamic Frequency Scaling

The simultaneous growth of new applications and death of transistor scaling trends is driving an explosion in custom silicon projects spanning all domains of computing. However, the enormous non-recurring engineering (NRE) cost of designing a modern system-on-a-chip (SoC) remains a major barrier to the wider adoption of custom silicon. Of concern to this dissertation is the lack of a good full-system simulation technology, a key driver of pre-silicon verification and validation costs. While field-programmable gate arrays (FPGAs) can be fast and relatively inexpensive hosts for simulation, mapping SoC clocking structures onto an FPGA such that they are represented accurately and deterministically is challenging. For this reason and others, many SoC designers turn to expensive hardware emulation platforms and their proprietary compilers. To radically reduce the cost of doing fast and accurate full-system simulation, the ADEPT Lab designed FireSim: an open-source, FPGA-based hardware emulation framework hosted in the public cloud./nIn this dissertation, we begin by introducing FireSim’s compiler infrastructure, called Golden Gate, which is capable of performing general multi-cycle resource optimizations in order to fit large SoCs on a single FPGA. Here we extend Golden Gate to present non-invasive, optimization-compatible schemes for simulating SoC clocking structures. First, we describe a simple approach for simulating systems with multiple fixed-frequency clocks. We then generalize this to support a general class of clock and reset structures, which can be composed to simulate dynamic frequency scaling, using an approach based on prior work in conservative parallel discrete-event simulation. The resulting work differs from prior academic FPGA-based projects in that it supports a much larger space of input designs, is easier to deploy to other FPGAs, and, like any good simulator, is deterministic---all while supporting simulation rates fast enough to productively boot operating systems and run real applications.

Advisor: Asanovic, Krste
Bachrach, Jonathan R
New Approaches to Old Questions in Intellectual Property

This dissertation presents three empirical studies of the American intellectual property system./nIn the first chapter, my coauthors and I explore the extent to which copyright’s incentive function is aligned with the economic realities of the commercial music industry. Using a novel panel dataset of music sales and streams, we find that that most commercial music—even blockbuster releases—has an extremely short commercial “half-life.”/nIn the second, I investigate the predictability of patent litigation, the outcome of which is typically thought to be difficult to forecast. Using a computational model of the text of asserted patent claims and other characteristics of the patent and litigation, I find that decisions about patent validity are more predictable than previously recognized./nFinally, I replicate several leading descriptive studies of patent litigation, and find that their substantive conclusions are sensitive to coding choices and the period over which the sample is drawn.

Advisor: McCrary, Justin
Rubinfeld, Daniel
Economies of the Sacred: St. Ursula's Reliquaries and the Making of the Market

In 1106, as Cologne was expanding its city walls, a group of masons discovered the purported mass grave of St. Ursula and the 11,000 Virgins. Under the supervision of neighboring religious houses, the martyrs’ bodies were excavated and exported on what we might call a commercial scale. At least 1,800 skulls were distributed among Cologne’s twelve parish churches, and countless others were translated as ecclesiastical gifts across the archdiocese. By the fourteenth century, as the Rhineland became increasingly urbanized, the relics began figuring in the local economy. Some went into the hands of secular elites and others moved along Hanseatic trade routes. Churches that had long possessed relics of the 11,000 Virgins commissioned new types of sumptuous containers atypical of traditional treasury arts. Rather than being made from precious metals and stones, they were fashioned by local craft industries and secular laborers. Wooden busts were produced in the Rhineland, painted boxes were made in Cologne, and silk veils were sewn and embroidered for skull relics in the Low Countries. Ursula and her companions came to be patrons of economic activity and products of it./nThis dissertation explores the ways in which relics, defined as priceless according to canon law, became intertwined with the market. On the one hand, this is a study of mercantile culture affecting understandings of sacred objects and their value: the commoditization of religion, as it were. On the other hand, it puts pressure on such a secularization narrative and considers the persistent role of holy patrimony in conceptualizations of urbanism. Relics’ and reliquaries’ proximity to the market raised vital questions about the ethics of sacred and secular city life and its administration. How could the sacred be valued, and who had the power to decide? Did mercantilism stem from commercialism or saintly patronage? Who should manage marketplaces: temporal or religious powers?

Advisor: Fricke, Beate
Honig, Elizabeth