VictorJuiz/thesis huggingface dataset:
Evaluation of forecasts with applications to meteorology [electronic resource]

Forecast verification is an important topic in meteorology and the methods developed have been applied to evaluating forecasts in other fields, e.g., evaluation of risk assessments in epidemiology and of risk models in banking. Instead of using scoring rules as in the traditional approach, we propose a new approach that uses a more intrinsic loss function. This new approach enables one to construct confidence intervals and tackle other problems of statistical inference, which can not be done in the scoring rule approach without overly restrictive assumptions. We apply the methodology to evaluate weather forecasts. Martingale theory provides an important tool in handling the temporal aspects of the forecasts, while the spatial aspects are handled by clustering into risk buckets.

Keywords: Statistics
Advisor: Lai T. L. primary advisor. Thesis advisor
Shih Mei-Chiung advisor. Thesis advisor
Walther Guenther advisor. Thesis advisor
Evolutionary constraint facilitates interpretation of genetic variation from resequenced human genomes [electronic resource]

I demonstrate how comparative sequence analysis facilitates genome-wide base-pair level interpretation of individual genetic variation, and address three questions of importance for human personal genomics: First, whether an individual's functional variation comes mostly from noncoding or coding polymorphisms; second, whether population-specific or globally present polymorphisms contribute more to functional variation in any given individual; third what is the functional impact of short insertions and deletions in an individual genome. These questions have not been definitively answered by analyses of existing variation data because of a focus on coding polymorphisms, ascertainment biases in favor of common variation, and a lack of base-pair level resolution for identifying functional variants. The data set used in this study consisted of 575 amplicons resequenced in 432 individuals at genomic sites enriched for evolutionary constraint, and variation from 5 published human genomes. Single-site measures of evolutionary constraint derived from mammalian multiple sequence alignments are strongly predictive of reductions in modern-day genetic diversity across a range of annotation categories and across the allele frequency spectrum. I show that putatively functional variation in an individual genome is dominated by polymorphisms that do not change protein sequence, and which originate from our shared ancestral population and commonly segregate in human populations. Furthermore, I demonstrate that selection against short human indels has been shaped by patterns of evolutionary constraint, belying their potential functional importance. These observations show that common, noncoding alleles contribute substantially to human phenotypes and that constraint-based analyses will be of tremendous value to identify phenotypically-relevant variants in individual genomes.

Keywords: Genetics
Advisor: Sidow Arend primary advisor. Thesis advisor
Bustamante Carlos (Carlos D.) advisor. Thesis advisor
Petrov Dmitri Alex
Tang Hua (Geneticist) advisor. Thesis advisor
Evolving the real-time graphics pipeline for micropolygon rendering [electronic resource]

The modern real-time graphics pipeline is a versatile parallel architecture that accommodates a wide range of rendering techniques. The architecture is implemented by heavily optimized graphics processors (GPUs) that employ a mixture of application-programmable and fixed-function processing resources, yet its design lends itself to a simple programming model easily understood by non-expert programmers. A major goal of future graphics systems is rendering geometrically complex, film-quality scenes in real time. Unfortunately, current GPU implementations not only require additional compute capability to handle high-resolution surfaces represented by subpixel-area micropolygons, the fundamental graphics pipeline operations of surface tessellation, rasterization, and shading execute inefficiently under this advanced workload. This dissertation evolves the graphics pipeline architecture and its associated rendering algorithms to increase system efficiency when processing micropolygons. The proposed redesign extends the pipeline with a new parallel algorithm for high-quality, adaptive surface tessellation, making it possible to generate crack-free meshes that represent surfaces accurately, but without excessive numbers of micropolygons. It increases rasterization throughput using micropolygon-parallel processing and analyzes the cost of rasterizer support for motion blur and camera defocus. It also adds pipeline logic to detect and avoid redundant shading computations, reducing shading costs more than eight times. The resulting real-time micropolygon rendering pipeline architecture increases rendering efficiency and, due to its evolutionary nature, maintains the graphics pipeline's simple programming model and the throughput-optimized design of a GPU's programmable processing cores.

Advisor: Hanrahan P. M. (Patrick Matthew) primary advisor. Thesis advisor
Akeley Kurt
Dally William
Exalted bodies, Charles Ellis Johnson and the practice of Mormon photography [electronic resource]

On September 24, 1890, the then president, prophet, seer, and revelator of the Mormon Church, Wilford Woodruff, made an announcement. "I have arived [sic], " he declared, "at a point in the History of my life as the President of the Church of Jesus Christ of Latter Day Saints whare [sic] I am under the necessity of acting for the Temporal salvation of the Church." Finally succumbing to almost four decades of the larger nation's anti-polygamy assault, Woodruff sought to save his religion by relinquishing plural marriage. In so doing, however, he profoundly altered the very nature of Mormonism itself. Because in renouncing the practice of polygamy, the LDS church did not simply disavow an unorthodox family structure. To the contrary, it abandoned perhaps the central doctrine of its founding theology -- a theology rooted in an intoxicating vision of the male body and that body's sexualized capacity to do nothing less than make heaven on earth. This dissertation examines both this vision and its loss through the work of the little-known Mormon artist Charles Ellis Johnson (1857-1926). Church photographer, Holy Land traveler, and, perhaps surprisingly, erotic stereographer, Johnson made pictures that both restage Mormonism's original, polygamous dreams and reveal the extent to which the country shattered these dreams when they broke the LDS to monogamy. More than this, Johnson's images simultaneously disclose how the nation's brutal anti-polygamy war rooted itself in not simply terror and revulsion but also a delicious myth of the manly Saint. Focusing on Johnson's Holy Land work and his erotic stereographs, I examine the way in which Mormon polygamy spoke to such collective fantasies of manhood, power, and, ultimately, the creative impulse itself; I examine, in other words, the way in which plural marriage never existed as an isolated religious event but rather belonged to an historical, cultural, and social vista that encompassed phenomena as diverse as minstrelsy, the New Woman, dude ranches, and even Emerson.

Keywords: Art and Art History
Advisor: Wolf Bryan Jay primary advisor. Thesis advisor
Corn Wanda M. advisor. Thesis advisor
Gough Maria advisor. Thesis advisor
Ma Jean
Example-centric programming [electronic resource] : integrating web search into the development process

The Web is fundamentally changing programming. The increased prevalence of online source code--shared in code repositories, documentation, blogs and forums--enables programmers to build applications opportunistically by iteratively searching for, modifying, and combining examples. These Web resources are a ubiquitous and essential part of programming: in one of our studies, programmers spent 19% of their time consuming relevant online information. But our development tools haven't yet embraced these changes. How do we leverage the latent opportunity of Web-based example code in the next generation of programming tools? This dissertation explores the roles that online resources play in creating software, making contributions in three areas. First, it presents a taxonomy of programmer Web usage. Programmers turn to the Web with a variety of goals: they learn new skills, transfer knowledge to new domains, and delegate their memory to the Web. Using our taxonomy, we suggest opportunities for tool support of programmer Web usage. Second, this thesis contributes interaction techniques for lowering the cost of locating relevant example code on the Web. We created Blueprint, a task-specific search engine that embeds Web search inside the development environment. A laboratory study and large-scale deployment of Blueprint found that it enables participants to write significantly better code and find example code significantly faster than with a standard Web browser and search engine, and may cause a fundamental shift in how and when programmers search the Web. Finally, this thesis contributes interaction techniques for helping programmers understand examples. Efficient understanding and effective adaptation of examples hinges on the programmer's ability to quickly identify a small number of relevant lines interleaved among a larger body of boilerplate code. By augmenting the code authoring experience with execution visualization and linking of related lines, programmers can understand examples significantly faster.

Advisor: Klemmer Scott primary advisor. Thesis advisor
Dontcheva Mira
Ousterhout John K. advisor. Thesis advisor
Winograd Terry advisor. Thesis advisor
Excellence for all [electronic resource] : American school reform, 1983-2008

Excellence For All: American Education Reform, 1983-2008 examines the history of school reform in the United States over the past quarter-century. Specifically, the work examines an approach to educational change best characterized by the phrase "excellence for all"—an equity-focused policy phenomenon uniquely situated for the policymaking context of the late twentieth and early twenty-first centuries. The idea of promoting excellence for all students united a broad enough coalition to pursue a truly national reform effort and captured the imaginations of leaders in state and local government, at philanthropic foundations, in colleges and universities, and in school districts across the country. Led by a corps of self-styled educational entrepreneurs aggressively pursuing reforms that they could take "to scale, " the movement sought to remake the American high school piece by piece. The dissertation examines this reform movement through the nation's three largest districts—New York, Chicago, and Los Angeles—and through three particular change efforts: a physical plant reform (the small schools movement), a personnel reform (Teach For America), and a curricular reform (the Advanced Placement Program). The work aims to establish the ways in which this most recent era of school reform represented a departure from previous reform eras, strives to explain the movement's broad appeal, and ultimately, aims to understand its shortcomings by exploring the assumptions underlying the excellence for all approach and the tradeoffs required by it.

Keywords: Education.
Advisor: Labaree David F.
Cuban Larry advisor. Thesis advisor
Wineburg Samuel S. advisor. Thesis advisor
Exchange Rates and the Current Account Balance: A Case Study of the Yen

Whenever there exists persistent current account imbalances between countries, the surplus country is often accused of undervaluing its exchange rate to give its exports an unfair advantage, and is thus pressured into letting its exchange rate appreciate. A forensic exploration of the embittered trade history between the United States and Japan is undertaken to refute these claims. This paper seeks to demonstrate that such an accusation is faulty. Firstly, such an accusation does not specify by which measure an exchange rate is undervalued. Secondly, even if an exchange rate is undervalued by a specified measure, it does not follow automatically that an undervalued exchange rate is a deliberate mercantilist policy that gives exports an unfair advantage. Thirdly, even if the exchange rate were allowed to appreciate, there is no evidence to suggest that the current account balance would be restored; a corollary to this is that any restoration of competitive balance need not be accompanied by a change in the exchange rates. Finally, the constant bashing of the surplus country introduces volatility into the system and leads could lead a ‘one-way bet’ on the exchange rate that makes it harder, rather easier, to achieve current account balance. In light of this, the United States should have worked together with Japan in the 1980s and 1990s to stabilize the yen-dollar exchange rate.

Keywords:  Department of Economics
Stanford Department of Economics
current account
trade
United States
Japan
exchange rate valuation
Thesis
Advisor: McKinnon Ronald
Exotic particles in topological insulators [electronic resource]

Recently a new class of quantum state of matter, the time-reversal invariant topological insulators, have been theoretically proposed and experimentally discovered. These topological quantum states of matter are insulating in the bulk, but have gapless edge or surface states protected by the time-reversal symmetry. In particular, topological insulators in three dimensions are characterized by topological field theory which gives rise to the topological magnetoelectric effect, and is analogous to that describing the electromagnetism of the hypothetical particle called axion. In this thesis we will show that in these topologically nontrivial insulators, magnetic monopoles and axions, which are originally postulated in elementary particle physics, may emerge. Firstly we will show that when time-reversal symmetry is broken on the surface of a topological insulator, an electric charge near the surface will induce an image magnetic monopole. The composite particle consisting of an electron and its image monopole forms a dyon and obeys fractional statistics. Secondly, when there is an antiferromagnetic order in the bulk of a topological insulator, the magnetic fluctuations couple to the electromagnetic fields exactly like axions. The physical effect of the dynamical axion and its detection will also be discussed. Then finally we propose transition metal oxide of corundum structure as a candidate for topological magnetic insulators which can give rise to the dynamical axion.

Keywords: Physics
Advisor: Zhang Shoucheng primary advisor. Thesis advisor
Fisher Ian R. (Ian Randal) advisor. Thesis advisor
Kivelson Steven advisor. Thesis advisor
Experimental studies of high-Tc cuprate superconductors with density wave correlations [electronic resource]

High-Tc cuprate superconductors remain the source of central intellectual challenges for condensed matter physicists two decades after their discovery. Accumulating evidence suggests possible ubiquity of coexisting superconducting and density wave correlations in the ground state of these materials. As both correlations in their spatiotemporally incoherent forms can in principle produce a pseudogap in the excitation spectrum, the nature of the pseudogap widely seen in cuprates above Tc comes to forefront of debate. I have been trying to address the relationship triangle between the pseudogap, superconductivity and density waves, by mainly using angle-resolved photoemission spectroscopy (ARPES) to study the momentum spaces of single-layer La-based (La214) and Bi-based (Bi2201) cuprates. In this thesis, I first talk about our ARPES-neutron scattering joint effort (in collaboration with Tohoku University) in the stripe-ordered state of La214. We found around the 1/8 doping level a dual nature of the pseudogap (in LBCO) and a dual nature of the spin stripe ordering ground state. The latter will be discussed in the context of a doping-dependent crossover between localized- and itinerant-spin ground-state physics, as demonstrated for the first time in a condensed matter system (1% Fe-doped LSCO). I then focus on our ARPES findings in both the pseudogap and superconducting states of nearly optimally-doped Pb-Bi2201 obtained over unprecedented momentum, energy and temperature ranges. They suggest that the pseudogap is a broken-symmetry state that is density-wave like and distinct from homogeneous superconductivity; it explicitly coexists with coherent superconductivity below Tc, causing a striking, momentum-dependent distortion of the high-Tc ground state. I also include in the appendix our recent observation of symmetry-distinct states (likely derived from the Cu dz orbital) in proximity to the Zhang-Rice singlet that has so far been generally taken as the only relevant electronic building block for cuprates. This finding might profoundly transform our upper-level understanding of high-Tc superconductivity as discussed above. This thesis ends with a chapter which describes my experimental philosophy, speculations and outlook for the near future of this field.

Keywords: Applied Physics
Advisor: Shen Zhi-Xun primary advisor. Thesis advisor
Fisher Ian R. (Ian Randal) advisor. Thesis advisor
Kivelson Steven advisor. Thesis advisor
Explicitly minimizing clinical risk through closed-loop control of blood glucose in patients with type 1 Diabetes Mellitus [electronic resource]

Type 1 Diabetes Mellitus or Juvenile Onset Diabetes is currently a permanent, incurable disease that removes the ability of the patient's body to control blood glucose levels. This loss of automatic control greatly increases the patient's exposure to clinical risks of high and low blood glucose levels. These risks can be mitigated through tight, regulation of blood glucose levels using insulin injections, but only at the price of paying frequent attention to the blood glucose levels and manually providing accurate dosing decisions. This can be very trying for all patients, especially teenagers and children. Recent technological advances enable automatic external regulation of patient's blood glucose levels. Pumps can infuse insulin into the subcutaneous tissue to lower blood glucose levels. Continuous glucose monitors can sense subcutaneous glucose levels, specifically the rises caused by meals and the drops caused by insulin. This has caused a flurry of control and modeling research, in the hopes of mitigating the clinical risk without the price of constant human attention. The most common approach, and the one taken here, is to use model predictive control, where the predictions from a model of glucose dynamics are optimized against a cost function using the future insulin injections. We directly minimize the asymmetric clinical risk instead, and recognize that our control authority (the potential effects of injecting insulin) is largely limited to reducing the blood glucose level. We further consider likely future blood glucose measurements, since we both respond better to positive disturbances than negative ones, and because negative disturbances are more risky. Also, we explicitly estimate the uncertainty of predictions, since glucose dynamics incorporate uncertainty from the complex biology, stochastic patient behaviour, and extrapolation. More uncertainty should mean more cautious insulin injection. Lastly, since meals occur faster than insulin acts and can raise the blood glucose by 2 to 4 times the width of the acceptable range, this work develops a novel Bayesian framework for detecting meals and estimating their effects. This work improves prediction root mean squared error by 20% relative to predictions excluding meals for prediction horizons from 1 to 4 hours and improves robustness to meals. These prediction improvements alone reduce the avoidable clinical risk by 38% relative to predictions excluding meals. When the improvements to the predictions are combined with minimizing clinical risk under uncertainty and measurement anticipation the avoidable clinical risk is reduced by 30% relative to a published MPC controller that has privileged information and tunes independently for each patient.

Keywords: Aeronautics and Astronautics
Advisor: Gerdes J. Christian primary advisor. Thesis advisor
Niemeyer Gunter primary advisor. Thesis advisor
Buckingham Bruce A. advisor. Thesis advisor
Lall Sanjay advisor. Thesis advisor
Exploring Direct Sampling and Iterative Spatial Resampling in History Matching

We explore multiple methods to history match a porosity field by using both production data and a secondary data set. In this paper, seismic impedance is used as secondary data but any data set with identical dimensions as the primary data can be used. The task is formulated as an inverse problem where the production data is estimated through an upscaled ow simulator. Co-located permeability values are obtained though an empirical relationship from the well logs. The secondary seismic data is treated in two ways. Firstly, it is used as conditioning data to further constrain the porosity simulation. This means that the production data is the only data that has an objective/mist function. In the second method, porosity and seismic impedance are simulated simultaneously. This corresponds to an objective function with combined production and seismic data. If the second method is used, a more constrained porosity field is obtained in which channels follow the seismic more closely, whereas when the first method is used the channels are slightly thinner and more spread out. Because increased amount of conditioning data yields a more constrained a posteriori distribution it is likely that the optimization takes requires less steps to reach an optimum compared with the case where both seismic and production data is matched. In addition, frequency information is also incorporated into the objective function. However, because this information seems to conflict with the previous information, the convergence to an optimal point is decreased. This is a problem that could be mitigated with the right choice of the training image is the geospatial simulation.

Keywords:  Department of Energy Resources Engineering
School of Earth Energy &amp; Environmental Sciences
Thesis
Advisor: Mukerji Tapan