VictorJuiz/thesis huggingface dataset:
Simplification algorithms for large virtual worlds [electronic resource]

Metaverses are virtual worlds where users create the entire world: all objects, their models and behavior, are user-generated. Rich, large-scale metaverses have been imagined in the realm of fiction for decades. Such worlds, however, present significant technical challenges due to the limitations of network and graphics resources. Since the world is user-generated, the content has to be stored in a shared, networked resource such as the cloud. Since they contain hundreds of thousands of 3D objects, it is too expensive for a graphics card to render them at interactive frame rates. Finally, due to their dynamic, user-generated nature, we cannot rely on hand-crafted or pre-computed levels of detail. Combined, these factors necessitate a dynamic and automatic approach to aggregate and simplify 3D content. This dissertation describes a simplification pipeline for displaying large metaverses. The basic approach is to group objects into simplified aggregates, and then display a small subset of objects and aggregates that complete the view of the world. Building on this approach, the key contributions are a set of algorithms that optimize this approach for low download and rendering cost. These algorithms are based on the insight that metaverses generally possess a high degree of spatial coherence: similar and even identical objects are often placed closely together. Using a technique called instancing, such a group of identical objects can be efficiently represented as one object and a set of transformations to create its duplicates. The dissertation describes three main algorithms. First, it presents an algorithm to group visually similar objects into aggregates, reducing the download cost of virtual worlds by up to 25%. Second, it presents a technique to deduplicate highly similar objects within each aggregate, which further increases instancing and reduces download cost. Third, it proposes a new instance-aware algorithm for simplifying these aggregates' models. On highly instanced models, this algorithm results in simplified versions that are orders of magnitude smaller compared to existing simplification algorithms. Compared to existing techniques, these algorithms decrease the network transfer cost of displaying large metaverses by up to 80%. Furthermore, they reduce the rendering cost of displaying the metaverses by up to 23%. Combined with texture atlasing, an implementation detail crucial for rendering performance, this makes it possible to display these metaverses at interactive frame rates. Finally, we validate our results using a large, distributed metaverse rendered at interactive frame rates over a wide area network.

Advisor: Levis Philip primary advisor. Thesis advisor
Freedman Michael J.
Hanrahan P. M. (Patrick Matthew) advisor. Thesis advisor
Simulating the interaction between wind turbines and the atmosphere using a blade element momentum model coupled to a full 3D atmospheric model [electronic resource]

With the rapid growth of wind power as an alternative source of energy, it is important to determine how large wind farms will affect weather and climate. The interaction between turbines and the atmosphere plays a role in wind farm siting, as well as determining the best layout for optimum power production. To this end, a wind turbine parameterization based on the Blade Element Momentum (BEM) method is developed to be placed into a 3D atmospheric model. The BEM model is implemented and tested against three different turbines to verify that it is a good model to use for this purpose. Before integration into the atmospheric model, the basic theory behind the BEM is used to estimate the energy lost from the lowest 1 km of the atmosphere due to large deployments of wind energy. This energy loss is found to be quite small. Even with wind power assumed to replace all fossil fuel energy sources, the loss over the entire lowest 1 km of the atmosphere ranged from 0.006- 0.008%. It is expected, however, that the turbine-atmosphere interaction will be more pronounced in the local scale. To study these small-scale effects, the BEM parameterization is then integrated into GATOR-GCMOM, a global to urban scale atmospheric model. The parameterization calculates the forces applied by the turbine blades to the flow going through the rotor and this is added to GATOR-GCMOM as body forces in the momentum equations. The coupled model is used to simulate the feedback of turbines on different meteorological variables given realistic weather conditions provided by GATOR-GCMOM. The simulations have four nested grids, going from a global domain down to an urban scale domain, located over Oklahoma City. They are initialized with meteorological conditions from NCEP files. Results from two times of day are presented, 6 AM and 12 PM, to show the effect of atmospheric stability. Turbine effects are more defined in the early morning hours, when the atmosphere is stable. In general, wind speeds decrease at hub height and increase near the surface. Turbulent kinetic energy increases at hub height and decreases near the surface. Surface heat fluxes mostly increase in the wake. During the early morning hours, greater mixing in the wake brings warmer air aloft down to the ground and cooler air from the ground up to the hub region. The opposite happens during the day, when cooler air from above is mixed down to the ground and warm air from below is mixed upward. The incorporation of actively changing weather highlights the importance of atmospheric stability, as well as soil and surface properties, in the study of turbine-atmosphere interactions. It also yields unexpected power production patterns as the small scale circulations affect the winds upstream of each turbine.

Keywords: Civil and Environmental Engineering.
Advisor: Jacobson Mark Z. (Mark Zachary) primary advisor. Thesis advisor
Fringer Oliver B. (Oliver Bartlett) advisor. Thesis advisor
Street Robert
Simulation methods for non-stationary queues and value function computation [electronic resource]

The first part of the dissertation is concerned with the challenges that arise in the planning of stochastic simulations of systems in which time-of-day effects, day-of-week effects, or seasonal effects are present. In such simulations, one would like to avoid simulating the system over the entire time horizon of interest, say [0, t]. Since such non-stationary models frequently exhibit a "loss of memory", it is often possible to accurately compute system performance measures by generating paths only over [s, t], provided that s is chosen properly. We propound using reflected Brownian motion (RBM) with time-dependent drift and volatility as a guide to choose s in the setting of such simulations. We develop the first exact simulation method for reflected Brownian motion (RBM) with time-dependent drift and volatility. The running time of generating exact samples of non-stationary RBM at any time t is uniformly bounded. These exact samples can be used for planning simulations of non-stationary complex queueing systems. The second part of the dissertation addresses the estimation, via simulation, of value functions in the context of expected infinite horizon discounted rewards for Markov chains. Estimating such value functions plays an important role in approximate dynamic programming and applied probability in general. One approach is to build an approximation to the value function by estimating the basis coefficients in a linear basis expansion via least squares. Nevertheless, selecting appropriate basis functions is usually challenging. In contrast, we develop a fully nonparametric method to estimate the value function by incorporating "soft information" into the estimation algorithm, such as knowledge of convexity, monotonicity, or Lipchitz constants. In the presence of such information, a nonparametric estimator for the value function can be computed that is provably consistent as the simulated time horizon tends to infinity. As an application, we implement our method on pricing tolling contracts in energy markets.

Keywords: Management Science and Engineering.
Advisor: Glynn Peter W. primary advisor. Thesis advisor
Giesecke Kay advisor. Thesis advisor
Ye Yinyu advisor. Thesis advisor
Singular hyperbolic structures on pseudo-Anosov mapping tori [electronic resource]

We study three-manifolds that are constructed as mapping tori of surfaces with pseudo-Anosov monodromy. We use Danciger's half-pipe geometry to regenerate hyperbolic structures when the monodromy has orientable foliations and its induced action on cohomology does not have 1 as an eigenvalue. We also include some discussion on Agol's veering triangulation construction.

Keywords: Mathematics.
Advisor: Kerckhoff Steve primary advisor. Thesis advisor
Church Thomas (Thomas Franklin) advisor. Thesis advisor
Mukamel Ronen E. advisor. Thesis advisor
Smuggling, state-building, and political economy in coastal China, 1927-1949 [electronic resource]

This study looks at Nationalist China's war on smuggling from 1927 to 1949 to explore the transformation of state authority and the larger socioeconomic impact of state-building. The recovery of tariff autonomy in the late 1920s empowered the Nationalist government to raise duties on foreign goods for the first time in nine decades. Higher tariffs and stricter controls on trade provided the new state critical revenues to meet an array of urgent domestic needs and foreign threats, but they also created a full-blown smuggling epidemic by making smuggling a very profitable enterprise. To meet this challenge to its authority, the state fought back with an extensive campaign to stamp out smuggling, created new definitions of legal trade, and asserted its prerogative to police borders. This study argues that the suppression of smuggling was more than a law enforcement issue: it was integral to broader state efforts to extract fiscal resources, broadcast central authority, and delineate new boundaries of legality. Merchants and other smugglers, meanwhile, did not passively accept growing state strictures but adopted a range of responses, from compliance to evasion, that helped shape the contours of an emerging legal regime. How the state asserted its prerogative to tax, regulate, and police trade--and how mercantile circles responded to this expansion of state power--are questions at the core this study. Using diverse sources such as customs records, legal cases, government correspondences, and popular press reports from ports along coastal China, this study chronicles both the campaign to fight smuggling from the top, as well as the range of reactions to official efforts from the bottom. In addition to issues in Chinese studies, I also engage with wider research in legal and economic history in examining the creation and enforcement of new legal categories as well as strategies merchants employed in response to changing business environments.

Keywords: History.
Advisor: Sommer Matthew Harvey
Yeh Wen-Hsin advisor. Thesis advisor
Wigen Kären
Some results on K-theory, topological Hochschild homology, and parameterized spectra [electronic resource]

This thesis comprises three separate papers. The first proves a duality result relating the topological Hochschild homology of a ring spectrum to the Spanier-Whitehead dual of the topological Hochschild homology of the Koszul dual ring spectrum. The second, proves an additivity result for the transfer A-theory of infinity topoi, as introduced by Barwick. The third presents partial results of joint work with John Lind. In the full joint paper we create a machine which has as input 2-Vector bundles and as output parameterized ku-modules.

Keywords: Mathematics.
Advisor: Blumberg Andrew J. primary advisor. Thesis advisor
Cohen Ralph L.
Carlsson Gunnar
Galatius Søren
Sovereign and forgotten bodies [electronic resource] : performing French and trans-atlantic baroques, 1581-1653

"Sovereign and Forgotten Bodies: Performing French and Trans-Atlantic Baroques, 1581-1700" is a study of mimesis in embodied practices, images and world-making. It takes up records of late sixteenth and seventeenth-century French performances, usually titled ballets, that pre-date modern concepts of media specificity. I study texts, prints and drawings from 1581-1653 that expose silences, idealizations, and processes of invisibility in the medium's historiography, addressing figures and performances that defy contemporary conceptions of ballet. These "counterfeit, " "disorderly, " and "topsy turvy" roles have been relegated to the margins of dance and theater history. Through close readings of landmark works in the early baroque ballet corpus, I argue that the perception and unruly character of the moving body were subjects of repeated seventeenth century attempts to order and harmonize dance and spectacularity, marshaling performance towards consolidating power and authority. In this context, the notion of the orderly constitutes an ideological and political metaphor of empire and absolutism. It emphasizes coordinations of movements as political organizations of state and media, as well as modes of knowing, within theatrical dance.

Keywords: Theater and Performance Studies.
Advisor: Apostolidès Jean-Marie primary advisor. Thesis advisor
Orgel Stephen primary advisor. Thesis advisor
Ross Janice primary advisor. Thesis advisor
Franko Mark advisor. Thesis advisor
Sparse and low-rank structures in robust principal component analysis, compressed sensing with corruptions, and phase retrieval [electronic resource]

In this dissertation, we discuss three related problems: robust principal component analysis, compressed sensing with corruptions, and signal recovery from quadratic measurements. Robust principal component analysis (RPCA) is a computational framework that aims to decompose a matrix as the sum of a low-rank component and a sparse component. We prove that under mild technical assumptions, a tractable convex optimization works for an exact decomposition. In the case in which there are missing entries, we propose another convex optimization and show that a low-rank matrix can be exactly recovered from a small portion of entries with a constant proportion of corruptions. Further, this dissertation improves some existing results in compressed sensing with grossly corrupted measurements in the literature. For both the Gaussian and non-Gaussian sensing matrices, we derive theorems showing that by weighted L1 minimization, a sparse signal can be recovered from a few linear observations with constant proportion of corruptions. Finally, we discuss the problem of signal recovery from intensity measurements. For general signal recovery, we improve existing results in the literature, showing that the signal can be recovered exactly up to a global phase factor provided the number of measurements is in the order of the dimension of the signal. For sparse signal recovery, we derive both necessary and sufficient conditions for the number of Gaussian measurements, such that a natural convex relaxation works for the recovery of the signal.

Keywords: Mathematics.
Advisor: Candès Emmanuel J. (Emmanuel Jean) primary advisor. Thesis advisor
Papanicolaou George advisor. Thesis advisor
Ye Yinyu advisor. Thesis advisor
Sparsity and shrinkage in predictive density estimation [electronic resource]

We develop new perspectives on the roles of sparsity and shrinkage in predictive density estimation under Kullback-Leibler loss. Our results explain and extend some recently observed information theoretic connections between predictive density estimation and the well-studied normal mean estimation problem. We find new phenomena in sparse minimax prediction which contrast with point estimation theory results and are explained by the new notion of risk diversification. We generalize these new uncertainty sharing ideas to address the nature of optimal shrinkage over unconstrained parameter spaces. Our density estimates can be used to construct competitively optimal probability forecasts and our results give some theoretical support to log-optimality based forecasting techniques used in the fields of weather forecasting, financial investments and sports betting. Motivational stories and examples from the world of sports, stock markets and wind speed profiles are used to suggest the scope of the theory developed in this thesis.

Keywords: Statistics.
Advisor: Johnstone Iain primary advisor. Thesis advisor
Diaconis Persi advisor. Thesis advisor
Donoho David Leigh advisor. Thesis advisor
Spatial phenomena in xenopus cell-free extracts [electronic resource]

Not only do biological systems consist of an extraordinarily complex cast of molecules, these molecules are well-organized in space: first into compartments, which form cells, which act in concert as tissues, which finally make up organisms. This thesis focuses on specific examples of how complicated biological systems create and maintain their intricate spatial organization. The tools of mathematical modeling have greatly assisted scientists' understanding of spatial patterning. In particular, models can help to distill a complicated phenomenon into its core logic. Chapter 1 is an overview of two types of spatial phenomena, Turing patterns and trigger waves, in which a relatively simple mathematical model is able to capture the most salient characteristics of the spatial pattern. Chapter 2 details how trigger waves of mitotic activity help to spatially coordinate the events of mitosis across the relatively large Xenopus laevis egg. We present a simple mathematical model that shows the plausibility of such waves, as well as a detailed experimental study on the existence and dynamics of such waves in Xenopus eggs and extracts. In Chapter 3, I discuss methods that greatly enhance the ability to visualize Xenopus extract using fluorescence microscopy. Traditional methods are only able to visualize a fixed cell cycle state or a single transition from one state to another. The method presented takes advantage of the fact that Xenopus extracts execute many more cell cycles on Teflon versus other materials such as glass and polydimethylsiloxane (PDMS). Using a Teflon-coated glass coverslip, we were able to achieve high-resolution imaging using spinning disk confocal microscopy on extracts that can execute multiple (about six at a minimum) cell cycles.

Keywords: Chemical and Systems Biology.
Advisor: Ferrell James Ellsworth primary advisor. Thesis advisor
Huang Kerwyn Casey
Meyer Tobias advisor. Thesis advisor
Skotheim Jan
Spatio temporal regulation of cell cycle transcription [electronic resource]

The Start checkpoint regulates cell cycle commitment and associated transcription in the budding yeast, Saccharomyces cerevisiae. It was previously shown that commitment to cell division corresponds to activating the positive feedback loop of G1 cyclins controlled by the transcription factors SBF and MBF. Around this pivotal cell cycle event, over 300 genes (G1/S regulon) are expressed to facilitate the G1/S transition. Despite its importance, little was known about distinct temporal regulation within the G1/S regulon. We found that SBF and MBF target genes have a well-defined distribution of transcriptional activation times. We also showed that activation of G1 cyclins precedes the activation of the bulk of the G1/S regulon, which we named 'feedback-first' regulation. In budding yeast, feedback-first regulation ensures that commitment to cell division occurs before large-scale changes in transcription. Thus, the transition can be viewed as a two-step process whereby the decision to divide precedes synthesis of the cellular machinery required for division. Furthermore, we found that feedback-first regulation is conserved in the related yeast S. bayanus as well as human cells. This finding highlighted the importance of understanding the molecular mechanisms through which co-regulated genes can have distinct activation dynamics. We showed that timing is partially explained by the combinatorial use of SBF and MBF transcription factors, which implement a logical OR function for gene activation. In addition to combinatorial use of transcription factors, we analyzed genome-wide chromosome conformation capture data to examine the potential link between the timing of gene expression and 3-D genome architecture. The early-activated genes of the G1/S regulon are significantly enriched for the number of physical contacts to the rest of the genome. Further analysis revealed two main clusters, whose interactions co-vary and whose activation time distributions are distinct. Taken together, these our work explains a significant amount of timing variation within cell cycle-dependent gene expression. Thus, we concluded that the cell utilizes both genome architecture and the combinatorial use of transcription factors to implement feedback-first regulation ensuring that commitment to cell division precedes genome-wide cell cycle-dependent transcription.

Keywords: Applied Physics.
Advisor: Block Steven
Skotheim Jan
Fisher Daniel S. advisor. Thesis advisor
Spatiotemporal dynamics from interlinked positive-and-negative feedback loops [electronic resource]

Positive and negative feedback loops are two of the most ubiquitous network motifs in biological systems. When a positive feedback loop and a negative feedback loop are coupled together, rich dynamics can emerge. Among these, oscillations in time and space, and pulses of protein activity are some of the commonly observed phenomena in a biological system. In this thesis, we started by computationally study the benefit of a positive feedback in an oscillator, and concluded that oscillators running on interlinked positive-and-negative feedback loops are more robust and tunable in period than the oscillators with only the negative feedback. We then focused on the Xenopus laevis embryonic cell cycle oscillator, a well characterized biochemical oscillator that runs on interlinked positive-and-negative feedback loops. We identified a transition of oscillator topology during Xenopus early development, from the long first cell cycle that depends critically on Wee1/Cdc25 mediated positive feedback, to the short subsequent cell cycles in which the positive feedback is dispensable. Using the human neutrophil-like HL60 cells, we studied the spatiotemporal dynamics of cytoskeleton proteins. We identified a perfect coupling between the protruding front and the retracting rear of a migrating HL60 cells. Myosin exhibits dynamic flashes at the rear of the cell, and the time scale of the flashes depends on local positive and negative feedback loops. When the duration of the myosin flashes is perturbed, the cell exhibits difficulties in turning and has inefficient chemotaxis. We also performed a statistical study comparing the shape and migration dynamics of HL60 cells, and provided evidence of a close correlation between the two phenotypes. Our results showed that the spatiotemporal protein dynamics allowed by proper regulation of interlinked positive-and-negative feedback loops is important in many examples in biology.

Keywords: Chemical and Systems Biology.
Advisor: Ferrell James Ellsworth primary advisor. Thesis advisor
Theriot Julie primary advisor. Thesis advisor
Meyer Tobias advisor. Thesis advisor
Skotheim Jan
Spudich James A.