VictorJuiz/thesis huggingface dataset:
Digital filters with quantized coefficients [electronic resource] : optimization and overflow analysis using extreme value theory

Parks-McClellan filter designs optimally minimize the maximum magnitude ripple in specific frequency bands for a given filter order. There are simple tools available for estimating the minimum order of a Parks-McClellan filter to meet a specific ripple requirement. However, many real-world filter implementations must first quantize filter coefficients, which can drastically reduce the performance of a Parks-McClellan design by increasing the maximum ripple. By making changes in the filter design specification within a very small range, a very large number of filter realizations with quantized coefficients can be generated. The problem is to choose the best design in the spirit of the original specification. For a Parks-McClellan specification, the best choice minimizes the peak of the ripple. Finding the best design out of perhaps millions of possibilities can be aided by making use of a statistical theory of extreme values. Extreme Value Theory is the study of the statistics of the maximum value or extreme outliers in a random process. We apply the theorems of Extreme Value Theory to the magnitude response of quantized filter designs with the goal of modeling the PDF of the maximum ripple in a particular frequency band. We find that the Generalized Extreme Value distribution, a fundamental distribution of Extreme Value Theory, well models the maximum ripple in quantized filters. This model can be used to estimate the filter order required to achieve a specific performance level for quantized Parks-McClellan designs. In addition, we present algorithms for generating fixed-point Parks-McClellan filters with improved performance, and compare the new algorithm to existing MATLAB tools. Secondly, we introduce a model for the distribution of extreme outliers at an arbitrary point within a digital system. Accurate estimates can be made of the probability that the signal is above a specific threshold, without knowledge of the exact PDF of the signal at that point. This model is useful for overflow analysis, as it can estimate the rate that a fixed-point signal will exceed its maximum representable value. Algorithms are presented and compared that can efficiently use this model on large datasets for automated overflow analysis.

Keywords: Electrical Engineering
Advisor: Gill John T.
Widrow Bernard
Schafer Ronald W.
Directed learning [electronic resource]

In machine learning, it is common to treat estimation of model parameters separately from subsequent use of the model to guide decisions. In particular, the learning process typically aims to maximize ``goodness of fit'' without consideration of decision objectives. In this dissertation, we propose a new approach -- directed learning -- which factors decision objectives into the model fitting procedure in order to improve decision quality. We develop and analyze directed learning algorithms for three classes of problems. In the first case, we consider a problem where linear regression analysis is used to guide decision making. We propose directed regression, an efficient algorithm that takes into account the decision objective when computing regression coefficients. We demonstrate through a computational study that directed regression can generate significant performance gains, and establish a theoretical result that motivates it. This setting is then extended to a multi-stage decision problem as our second case, and we show that a variation of directed regression, directed time-series regression, improves performance in this context as well. Lastly, we consider a problem that involves estimating a covariance matrix and making a decision based on that estimate. Such problems arise in portfolio management among other areas, and a common approach is to employ principal component analysis (PCA) to estimate a parsimonious factor model. We propose directed PCA, an efficient algorithm that accounts for the decision objective in the selection of components, and demonstrate through experiments that it leads to significant improvement. We also establish through a theoretical result that the possible degree of improvement can be unbounded.

Keywords: Electrical Engineering
Advisor: Boyd Stephen P. primary advisor. Thesis advisor
Van Roy Benjamin primary advisor. Thesis advisor
Hastie Trevor advisor. Thesis advisor
Discovering novel roles for the RNA binding protein Whi3 during stress [electronic resource]

Whi3 is an RNA binding protein that regulates cell cycle entry by binding to mRNA of the G1 cyclin CLN3 and to the cyclin-dependent kinase Cdc28. Cln3 binds to Cdc28 to promote passage through Start. whi3[delta] cells have a small size phenotype, and Whi3 may regulate cell size by sequestering CLN3 mRNA and Cdc28 protein in the cytoplasm to delay G1 entry (Wang et al., 2004). We observe that Whi3 reversibly localizes from the cytosol to cytoplasmic puncta in response to glucose deprivation and heat shock. This phenotype is shared by components of stress granules (SGs), which are large RNP complexes that form in yeast in response to various stress conditions; SGs sort and process mRNAs during the stress response (Buchan et al., 2008). Because Whi3 shares several characteristics with known SG components, including an RNA binding domain and stress-dependent relocalization, we hypothesize that Whi3 is a novel component of SGs. We show that Whi3 colocalizes with SG markers in response to glucose deprivation and heat shock. Preventing SG formation inhibits Whi3 foci formation. Like SG components, Whi3 is enriched in insoluble cell fractions during stress. Whi3 is not required for SG formation, but may be targeted to SGs to carry out a previously unknown function. We conclude that Whi3 is a novel component of yeast stress granules. This observation suggests an alternative model for Whi3 function: that Whi3 might regulate mRNA translation during stress by transporting mRNA to stress granules. We demonstrate that Whi3 regulates many of its interacting RNAs, and that this regulation may promote stress-dependent survival.

Keywords: Biology.
Advisor: Cyert Martha S.
Sarnow P. (Peter) advisor. Thesis advisor
Simon Michael (Biology professor) advisor. Thesis advisor
Skotheim Jan
Discovery and analysis of long noncoding RNAs in the DNA damage response [electronic resource]

Recent advances in transcriptome analysis have revealed a large number of non-protein coding transcripts that have previously been uncharacterized. A subset of these molecules, termed long noncoding RNAs (lncRNAs), has been implicated in the regulation of chromatin states. Here, we detail a journey of lncRNA discovery and analysis, beginning from the de novo discovery of lncRNAs within the promoters of cell cycle genes, followed by the functional characterization of select candidates. We characterize two examples that regulate the p53-mediated DNA damage response. LncRNA PANDA blocks the apoptosis pathway by inhibiting the transcription factor NF-YA, and lncRNA DINO regulates the p53 transcriptional response by regulating SET7-mediated post-translational modification. Altogether, these studies support a model whereby pervasive lncRNA transcripts, previously discarded as transcriptional byproducts, function through diverse mechanisms as critical regulators of biological pathways.

Advisor: Chang Howard
Fire Andrew Zachary advisor. Thesis advisor
Khavari Paul A. advisor. Thesis advisor
Wysocka Joanna
Discrete sampling in continuous time, band-limited signals [electronic resource]

During more than 60 years, the paradigm implied by the celebrated Shannon sampling theorem has been the basis of most ADC and DAC architectures, with the exception of the so called oversampling converters. The improvements in semiconductor technology allowed for little change in these design architectures while faster, lower power converters and new generations of manufacturing processes were developed. Over the last 5 to 10 years, the point of diminishing returns with respect to scaling seems to have been reached. As a result, there is a renewed interest in researching alternative sampling paradigms to Shannon's. Discrete Sampling is one of the numerous sampling alternatives proposed recently. In this research we show how Discrete Sampling can be extended to work with the class of continuous time band-limited signals. In addition to several mathematical results on the matter, the actual implementation of the paradigm is also considered. It will be shown that the proposed scheme results in a particular type of Hybrid Filter Bank. Several examples of such banks are presented together with their performance when sampling and reconstructing real life audio signals.

Keywords: Electrical Engineering
Advisor: Osgood Brad primary advisor. Thesis advisor
Pauly John (John M.) primary advisor. Thesis advisor
Smith Julius O. (Julius Orion) advisor. Thesis advisor
Dissecting mechanisms of bacterial pathogenesis using chemical probes [electronic resource]

Host-pathogen interactions are highly regulated at the post-translational level, making small molecules useful tools for dissecting many aspects of these events. This dissertation describes the development and application of chemical probes to examine aspects of bacterial infection on either side of the host-pathogen interface. We rationally designed a set of inhibitors and activity-based probes to study the substrate recognition and activation mechanisms of the internal cysteine protease domain (CPD) of Clostridium difficile's large gluocosylating toxin TcdB; a major virulence factor of this important nosocomial pathogen. Subsequent work with these tools has helped elucidate the biochemical details of CPD allosteric activation within a eukaryotic environment, and has provided evidence that TcdB contributes to hypervirulence in some C. difficile strains. We also developed an optimized activity-based probe for studying inflammasome-mediated caspase-1 activation, which is a fundamental part of the host's response to intracellular bacterial pathogens. We used this tool to discover that when cells are unable to activate caspase-1 upon intracellular bacterial infection, they instead undergo apoptosis. This work provides insight into a potential intracellular arms race between the host and pathogens capable of suppressing caspase-1 activation, and also highlights the balance that exists between pro- and non-inflammatory cellular responses. Together, these studies show there is much to be gained from adding chemical probes to the repertoire of tools used to study mechanisms of bacterial pathogenesis.

Keywords: Chemical and Systems Biology.
Advisor: Bogyo Matthew
Chen James
Mochly-Rosen Daria advisor. Thesis advisor
Monack Denise M. advisor. Thesis advisor
Dissecting multiple origins of heterogeneity in RNA folding [electronic resource]

Structured RNAs are central to many biological processes. For structured RNAs to carry out their function, they must fold into a correct structure and often undergo conformational changes while carrying out their function. When RNA folding, conformational change and function have been studied at the single molecule level, it has been commonly observed that individual molecules can have distinct properties that persist over long timescales. However, the origins of this molecular heterogeneity were unknown. The research presented in this dissertation uncover that heterogeneity in RNA folding can arise from multiple sources. This understanding helped elucidate features of RNA folding landscapes that were not previously appreciated. Furthermore, it demonstrated that understanding the origins of heterogeneity for a particular RNA is key to developing models that accurately describe the overall folding.

Keywords: Chemical Engineering
Advisor: Herschlag Daniel primary advisor. Thesis advisor
Khosla Chaitan
Spakowitz Andrew James advisor. Thesis advisor
Dissecting the holy body [electronic resource] : between medicine and religion in early modern Europe

This dissertation explains how the body provided proof of holiness in early modern Catholicism. Tradition had long asserted that the bodies of especially saintly or sinful individuals should reveal signs of their elect status. In the early modern period, Church officials sought to make such vague ideas exact: they required medical proof of bodily holiness. This requirement arose out of developments in both medicine and Catholicism. After the Reformation, many Christians doubted how or even if they should venerate the saints. In response, the Catholic Church centralized and formalized canonization procedures. As part of this reform, canonization officials began to require that medical practitioners examine the cadavers of holy individuals. Medical and anatomical knowledge had progressed during this period to the point where dissection was thought to yield unique information about the lifestyle and habits of the deceased. This information could also include signs of a person's spiritual state. The body, interpreted through expert eyes, could now reveal a person's true nature. Together, medical practitioners and canon lawyers in the city of Rome created standards through which to interpret bodily signs of holiness. The methods of proof employed in these examinations presaged many techniques of knowledge production that would become a part of experimental practice in the early modern world. This dissertation therefore demonstrates that instead of being opposed, science and religion worked together to define the boundaries of the natural in human bodies.

Keywords: History.
Advisor: Findlen Paula primary advisor. Thesis advisor
Buc Philippe
Riskin Jessica advisor. Thesis advisor
Stokes Laura
Dissecting the neural mechanisms of cerebellum-dependent learning [electronic resource] : enhanced plasticity and instructive signals

The focus of this thesis is to understand the contribution of multiple learning mechanisms to cerebellum-dependent motor learning. The studies that contribute to this thesis examine the role multiple learning mechanisms in the context of signaling in the intact circuit of awake-behaving animals. By using a well-parameterized learning paradigm, it is possible to distinguish and separate the contribution of specific learning mechanisms to different aspects of learning. This thesis demonstrates the sufficiency to two learning mechanisms long hypothesized to be important for cerebellum-dependent learning: 1) LTD at the parallel fiber to Purkinje cell synapse in the cortex (Marr 1969; Albus 1971; Ito 1972); and 2) the output of Purkinje cell simple spike activity (Miles & Lisberger 1981). Furthermore, the findings highlight the importance of understanding how learning mechanisms operate in vivo and interact with the on-going activity as well as previous activity in the circuit to determine different learning outcomes. The idea that the properties of a learning mechanism do not operate in isolation to produce learning but must be considered in the context of the intact and functional circuit is a common lesson that could apply to and should be tested in other learning systems of the brain.

Advisor: Raymond Jennifer L. primary advisor. Thesis advisor
Madison Daniel V.
Moore Tirin
Shatz Carla J. advisor. Thesis advisor
Distribution problems in number theory [electronic resource]

Four separate problems are considered. The first chapter concerns the average equidistribution of Heegner points attached to elements of fixed order in the class group of imaginary quadratic fields. Some discussion of the Cohen-Lenstra heuristics is also included. Chapter 2 treats the distribution of the logarithm of two families of L-functions at the central point. The most easily stated consequence is that the central values of L-functions attached to modular forms of large weight converge to 0 in distribution as the weight tends to infinity. Chapter 3 concerns omega results for large sums of Dirichlet characters. The length N of the sum is treated as a parameter that is allowed to vary with the modulus q of the characters. For N small compared to q the large values exhibited are related to the distribution of smooth numbers, while for larger N the results are analogous to omega bounds known for the corresponding L-functions. The final chapter gives a mixing time analysis for the random k-cycle walk on the symmetric group. The main new analytic ingredient is an asymptotic formula for many character ratios evaluated at a k-cycle.

Keywords: Mathematics
Advisor: Soundararajan Kannan
Diaconis Persi advisor. Thesis advisor
Venkatesh Akshay
Does Carbon Pricing Improve Clean Tech Profitability? A Comparative Analysis of the United States and Australia

The literature on optimal climate change abatement policy stresses that a price on carbon dioxide emissions could play a crucial role in driving clean energy technology innovation. The premise underlying this theory is that forcing emissions-intensive energy production to internalize the externality will increase the profitability of clean energy production, thereby enhancing the incentive to innovate. This paper tests that assumption by using event study methodology to evaluate whether political events indicating the prospect of a price on carbon in Australia and the United States increased the share prices of clean energy firms in the two countries. I find that in Australia, investors responded to expectations of a carbon tax by bidding up the valuation of Australian clean energy firms substantially. I identify a similar response in the United States, but these effects are smaller in magnitude and not as statistically robust. I offer two possible explanations for the asymmetry of these results: differing political institutions between the two countries that make policy promises more credible in Australia than in the U.S. and variations in the proposed policies that could have caused investors to project that the Australian carbon tax would be a more effective driver of clean energy than the U.S. cap-and-trade system.

Keywords:  Department of Economics
carbon tax
cap-and-trade
clean energy
event study
Australia
United States
Stanford Department of Economics
Thesis
Advisor: Wolak Frank
Does making a test high stakes for students artificially inflate acheivement gap by race & gender? Evidence from the California High School Exit Exam [electronic resource]

In a prior study of high school exit exams, my co-authors and I found that socio-economically disadvantaged students -- female, low income, English Language Learners (ELLs) and students of color -- are less likely to pass a high school exit exam than their more socio-economically advantaged peers, even when controlling for prior and concurrent achievement on a similar exam with no individual stakes for students (Reardon, Atteberry, & Arshan, 2011). These findings raise significant concerns about the accuracy of standardized test scores and the role they may play in reproducing societal and educational inequality. In this dissertation I use the same data to more thoroughly explore the achievement gaps on the high stakes California High School Exit Exam (CAHSEE) and low stakes California Standards Test (CST). I posit that the reasons we may observe a CAHSEE/ CST gap fall into three broad categories. The first category consists of statistical artifacts resulting from measurement error and violations of statistical assumptions. The second category of explanations consists of unintended consequences to policy decisions. These decisions may exacerbate achievement differences between groups but do not stem from performance differences between different groups introduced along with the high stakes of the test. If there is no evidence that the CAHSEE/ CST gaps are driven by true differences in ability -- either due to differences in student knowledge (including test prep) or differences in rigor of content or preparation—then these gaps are most likely the direct result of the "high stakes" nature of the exam. I use student level administrative data from three large California districts to examine these possibilities. I demonstrate that these measures are not driven by school segregation or measurement error using school fixed effects, multiple measures of ability, test scores shrunken to the group mean and instrumental variables. I find that women overperform on the English Language Arts (ELA) exam and underperform on the mathematics exam. Other groups underperform on both exams. Breaking down the exams by the content substrands, I find that the writing sample, which is included in the high stakes CAHSEE, but not the low stakes CST, drives the female overperformance on the ELA section. I conclude that the patterns of these gaps, including dramatic differences by school attended, are consistent with a stereotype threat explanation. In an era of increasing accountability for students, these performance differences on meaningful tests need to be considered both by policymakers as a possible negative unintended consequence to student level accountability and by educators as an impediment to the current of future success of their students.

Keywords: Education.
Advisor: Reardon Sean F. primary advisor. Thesis advisor
Cohen Geoffrey L. (Geoffrey Lawrence) advisor. Thesis advisor
Loeb Susanna advisor. Thesis advisor
Domesticating Prince Shōtoku [electronic resource] : Tokugawa sacred geography and the construction of a national landscape

The cult of Prince Shōtoku in the ancient and medieval periods was developed through the geographical logic of a satellite (Japan) struggling to break free from a superpower (China). Over time, the prince's images accreted numerous sacred and powerful layers as a national symbol in response to the political, religious, and cultural opportunities of each new age. After the encounter with Europe and the shift in the socio-political structure of the country, the burden of Shōtoku's image as a national symbol also changed accordingly. Shitennōji Temple in Osaka, as a hub of the Shōtoku cult, had always been at the middle of the cult's transformations. After surviving tough times including the turbulence of the Oda-Toyotomi decades in the late sixteenth century, Shitennōji was integrated directly into the new Tokugawa regime by Tenkai, a Tendai monk and the key architect of Ieyasu's new religious policy. Tenkai's vision was more than a mere revival of Shitennōji's physical plant or a stabilization of its role as a center of the Shōtoku cult. Rather, Shitennōji was designated as one of the most politically important temples to ensure success in institutionalizing Buddhism under the Tokugawa regime. To further that project, Tenkai appropriated Shōtoku narratives in order to construct a new national ideology for deifying Ieyasu by combining Buddhism and Shintō. Tenkai's thoroughly designed scheme caused an unintentional discourse-battle between Tenkai and Hayashi Razan. As a representative Tokugawa scholar, Razan attempted to reorganize Japan's national landscape based on Neo-Confucianism and Shintō, and he severely attacked Buddhism, criticizing Shōtoku narratives. The legacies of this battle for the next generations included new functions for Shōtoku narratives. One was as agencies to support Shintō Japan--rather than Buddhist or Confucian Japan. Another was as gazetteers, or travel guidebooks. Under the Tokugawa publishing boom, Shōtoku-related gazetteers contributed to the popularity not only of Shōtoku-related sites but also of other pilgrimages all over Japan. Thus, the broader public could start recognizing concrete geographies of Japan, while at the same time imagining Japan as a unified sacred field. Meanwhile, Tokugawa intellectuals began to struggle with conceptualizing sacred Japan in the world. Needless to say, Shōtoku narratives also responded to this movement, serving to legitimate Shintō Japan and confirming the construction of a national landscape.

Keywords: History.
Advisor: Wigen Kären
Bielefeldt Carl advisor. Thesis advisor
Uchida Jun advisor. Thesis advisor