VictorJuiz/thesis huggingface dataset:
Application optimized computing [electronic resource]

All computing systems are power limited, whether it is the 1W limit of a cell phone, or the 100W limit of a server. Triggered by the end of voltage scaling, the restricted power budgets are the result of energy per transistor switch scaling slower than the number of transistors on the chip. Since technology scaling no longer provides the energy savings it once did, to scale performance (operations/sec), we must improve the energy per operation by reducing the number of transistors involved in each operation. This fundamental change is forcing the design community to find new approaches to energy efficient computing. Most designs use pre-designed processor based solutions because of their flexibility and availability. However, they are usually not the most energy efficient solutions. To better understand the potential of producing general-purpose chips with better efficiency, this thesis tries to analyze in detail the types of inefficiencies that exist in general-purpose systems - designs that can be outclassed by up to 3 orders of magnitude in both performance and energy-efficiency by ASIC designs. To collect this data, we classify applications using the dominant sources of energy: compute, control and memory. For compute and control bound applications we gather this data by first identifying the types and magnitudes of energy overheads that exist in a general-purpose Tensilica based extensible RISC chip multiprocessor (CMP) system and then by exploring the architectural support and customizations needed to transform a general-purpose system to have the same energy efficiency as an ASIC. Because the fundamental operations in compute bound applications are generally very low-power, amortization of overheads introduced by programmability requires execution of hundreds of these operations in one cycle. Interestingly, a high percentage of compute bound applications share common data-flow characteristics, which we exploit to create a flexible yet efficient domain specific processor, called the Convolution Engine. Although, control bound applications also operate on low-power control flow operations, sequential dependencies restrict the number of control flow operations fuseable into one instruction to between ten and fifteen. This restriction also defines the extent of achievable efficiency for control bound applications. Unlike the low-power operations abundant in compute and control bound applications, the fundamental cost of a memory fetch is considerable. Improving the system efficiency of memory bound applications not only requires improving the efficiency of the processing elements, but also requires substantially increasing reuse in data fetches.

Keywords: Electrical Engineering.
Advisor: Horowitz Mark (Mark Alan) primary advisor. Thesis advisor
Kozyrakis Christoforos
Richardson Stephen A.
Approaches for local false discovery rates [electronic resource]

Modern hypothesis testing problems involve a large collection of hypotheses H_1, ..., H_N. The Bayesian local false discovery rate is the posterior probability that a hypothesis is null. The local false discovery rate paradigm is therefore an intuitive and attractive approach for deciding which hypotheses to declare as non-null. Accurate local false discovery rate estimation relies on positing an appropriate null distribution, which should be empirically estimated. It is often reasonable to estimate the null distribution from data that is truncated over a region which can safely deemed to be null. This truncation approach is appealing since it enriches the class of models that can be used as candidate null distributions. We propose the use of a log-concave null distribution as a non-parametric extension of earlier local false discovery rate work. Moreover, the truncation approach has a missing data interpretation. For exponential families, a general but simple EM algorithm can be constructed to obtain the maximum likelihood estimates without having to solve the corresponding score equations, which may be awkward in the case of truncation. We verify the correctness of the algorithm by applying Louis' formula (1982).

Keywords: Statistics.
Advisor: Holmes Susan
Efron Bradley advisor. Thesis advisor
Walther Guenther advisor. Thesis advisor
Approximation guarantees for game-theoretic equilibria [electronic resource]

Game-theoretic equilibria model natural outcomes of selfish behavior. The concept of the "Price of Anarchy (POA)" captures how well game-theoretic equilibria approximate the socially optimal outcome. In this dissertation, we consider the POA in three different models, as a function of different design parameters and equilibrium concepts. We first consider weighted congestion games where players compete to share resources. The cost of a resource depends on the total weight of the players using that resource and players are allowed to use only certain subsets of the resources. Routing games are a canonical example of such games. We provide a precise characterization of the POA as a function of the resource cost functions. We also explore how the POA is affected by the structure of the permitted strategies for the players. Our bounds apply to pure Nash, mixed Nash, correlated, and coarse-correlated equilibria. We next consider opinion formation games, where players in a social network choose opinions to express to minimize the cost of disagreement with their neighbors' opinions and their own intrinsic beliefs. We obtain bounds on the POA with respect to the pure Nash, mixed Nash, and correlated equilibria. We show that the POA is always at most 2 when the cost functions are convex. We provide a more detailed characterization of the the Price of Anarchy as a function of the costs of disagreement. Finally, we consider combinatorial auctions with item bidding. In this model, several goods are sold simultaneously in independent auctions to buyers who have different values for different bundles of goods. We bound the pure Nash and the Bayes-Nash POA when the individual single-item auctions are second price auctions and buyers' valuations over the bundles are subadditive. We provide the first explicit gap between the worst case pure Nash and Bayes-Nash POA. We also consider how the pure Nash POA varies as a function of the payment rule in the underlying single-item auction.

Advisor: Roughgarden Tim primary advisor. Thesis advisor
Goel Ashish advisor. Thesis advisor
Shoham Yoav advisor. Thesis advisor
The archaeology of reform at a German prisoner of war camp in a Canadian national park during the Second World War (1943-1945) [electronic resource]

During the height of the Second World War pressure from Great Britain resulted in the transfer of thousands of German prisoners of war (PoWs) from British to Canadian control. To house them, Canada built a system of PoW camps, including Riding Mountain Camp in southwestern Manitoba. The PoWs sent there soon realized their good fortune: they lived in warm barracks, ate abundant food, and were able to purchase goods from a mail order catalog. But while the PoWs were well treated, they were at the same time subjected to a concerted reeducation campaign organized by the Allies. This reveals that these Canadian camps were not merely warehouses for the PoWs, but in fact, classic reforming institutions. Initially subjected to ideological training under Nazism, the PoWs were next subjected to another kind of education under the Canadians. Evidence collected from oral history interviewing, archival research, and three seasons of field archaeology combine to reveal that material culture was a key nexus in this competition for the minds of the PoWs. In addition to providing books and teaching courses on history and political science, the Canadians introduced the PoWs to a democratic, capitalistic way of life by familiarizing them with North American consumer goods and by allowing them to fraternize with Canadian civilians. The Nazi bureaucracy, in turn, used material things to try to keep the PoWs from turning to the other side. For example, by sending them crisp new Wehrmacht uniforms from Germany, heartening Christmas cards, and packages filled with German goods adorned with Nazi symbolism.

Keywords: Anthropology.
Advisor: Voss Barbara L.
Hodder Ian advisor. Thesis advisor
Jamieson Ross W. (Ross William)
Asymptotic behavior of eigenvalues and eigenvectors of a random matrix [electronic resource]

This thesis can be mainly divided into two parts. In the first part, we consider an N-by-p data matrix X_N where all the rows are i.i.d. p-dimensional samples of mean zero and covariance matrix Sigma. Here the population matrix Sigma is of finite rank perturbation of the identity matrix. This is the ``spiked population model'' first proposed by Johnstone. As N, p both go to infinity but N/p tends to a fixed ratio, for the sample covariance matrix, we establish the joint distribution of the largest and the smallest few packs of eigenvalues. Inside each pack, they will behave the same as the eigenvalues drawn from a Gaussian matrix of the corresponding size. Among different packs, we also calculate the covariance between the Gaussian matrices entries. As a corollary, if all the rows of the data matrix are Gaussian, then these packs will be asymptotically independent. Also, the asymptotic behavior of sample eigenvectors are obtained. Their local fluctuation is also Gaussian with covariance explicitly calculated. As the second part of the thesis, we study the limiting distribution of the k smallest gaps between eigenvalues of three kinds of random matrices -- the Ginibre ensemble, the Wishart ensemble and the universal unitary ensemble. All of them follow a Poissonian ansatz. More precisely, for the Ginibre ensemble we have a global result in which the k-th smallest gap has typical length n^{-3/4} with density x^{4k-1}e^{-x^4} after normalization. For the Wishart and the universal unitary ensemble, it has typical length n^{-4/3} and has density x^{3k-1}e^{-x^3} after normalization.

Advisor: Papanicolaou George primary advisor. Thesis advisor
Dembo Amir advisor. Thesis advisor
Johnstone Iain advisor. Thesis advisor
Asymptotically valid and exact permutation tests [electronic resource]

Given independent samples from P and Q, two-sample permutation tests allow one to construct exact level tests when the null hypothesis is P = Q. On the other hand, when comparing or testing particular parameters [theta] of P and Q, such as their means or quantiles, the classical permutation tests need not be level [alpha], or even approximately level [alpha] in large samples. Under very weak assumptions, this dissertation provides general test procedures whereby the asymptotic validity of the permutation test holds even when the assumption of identical distribution is unknown, while retaining the exact rejection probability [alpha] in finite samples when the underlying distributions are identical. A quite general theory is possible based on a coupling construction, as well as a key contiguity argument for the multinomial and multivariate hypergeometric distributions. The mathematical and statistical foundations for understanding permutation tests are laid out. Based on these technical arguments, the ideas are broadly applicable and generalizations have been made to the k-sample problem of comparing general parameters, the two-sample U-statistics, and d-dimensional multivariate cases and multiple testing. In the U-statistics case, we consider the Wilcoxon statistic or some rank statistics where the parameter of interest is a function of the joint distribution [theta](P, Q) and not just a simple difference [theta](P) - [theta](Q). In multivariate case, we apply the modified Hotelling's T^2-statistic as well as tests based on the maximum of studentized absolute differences. In the latter case, we must employ a bootstrap prepivoting operation, which leads to a bootstrapping after permuting algorithm. Then, we apply these tests as a basis for testing multiple hypotheses simultaneously by invoking the closure method to control the Familywise Error Rate. Monte Carlo simulation studies illustrate how the classical permutation tests and the proposed new permutation tests perform under various scenarios of underlying distributions with small, moderate, and large samples. Lastly, we also present some economic empirical applications where the permutation tests are utilized for testing some parameters of the underlying distributions.

Keywords: Economics.
Advisor: Romano Joseph P.
Hong Han advisor. Thesis advisor
Wolak Frank A. advisor. Thesis advisor
At the center of the periphery [electronic resource] : oil, land, and power in Baku, 1905-1917

At the turn of the twentieth century, the output of the Baku oilfields accounted for half of the world's crude oil. This was not accomplished by government fiat or the workings of a monopoly, but by a large and variegated group of workers and entrepreneurs within well-defined market structures, a development all the more remarkable for its rarity in Russian history. However, the oil industry was already threatened by the seeds of its own success. As oil made the transition from a source of illumination to a source of energy, it became the subject not only of increased demand but of intense political contestation as well. The fate of the oil industry became entangled with the outcome of broader debates within Russian society about the proper role of the government in protecting the public interest and the legitimacy of private property. This dissertation recounts how these struggles played out and demonstrates their impact at the local and translocal levels: productive plots found no lessees, workers went on strike, restive villagers dug their own wells, and increasingly antagonized ethnic groups killed each other in growing numbers. All the while, the oil industry in Baku continued to decline, the first oil industry to do so under the weight of political pressure.

Keywords: History.
Advisor: Weiner Amir
Naimark Norman M. advisor. Thesis advisor
Astourian Stephan H. advisor. Thesis advisor
Attentional bias in social phobia [electronic resource]

Social phobia (SP) affects more than 10% of American adults in their lifetime. A negative attentional bias is one of the best studied factors that contributes to the maintenance of SP; many studies have demonstrated that individuals with SP show biases to attend preferentially to social threat. Recently, researchers have begun to demonstrate that manipulating attentional biases can induce anxiety in non-anxious individuals or alleviate anxiety in anxious individuals. Therefore, it is important for both researchers and clinicians to gain a better understanding of the attentional biases that characterize SP. In the current research, participants with SP and healthy control participants with no history of mental illness completed three tasks: a behavioral attentional cueing task that yields separate measures of engagement with and disengagement from social threat; a free-viewing eye-tracking task in which positive, negative, and neutral emotional faces were presented for the participants to view over a 15-second period; and an antisaccade task that tests participants' ability to control the shifting of attention to positive and negative emotional stimuli. The results demonstrate a deficit in attentional control in individuals with SP on exposure to social threat stimuli, followed by avoidance of these stimuli. At long exposure times, attentional deployment seems to be influenced more by elaborative processes than it is by SP.

Keywords: Psychology.
Advisor: Gotlib Ian H. primary advisor. Thesis advisor
Frank Michael C. (Professor of human biology) advisor. Thesis advisor
Gross James
Attitude determination of passively magnetically stabilized nano satellites [electronic resource]

The work in this thesis enables attitude determination to be performed on passively magnetically stabilized nano satellites using only a measurement of the solar vector. Existing state of the art methods can achieve an accuracy of one degree using a full attitude sensor suite. The methods presented in this thesis achieve an accuracy of five degrees at a reduced mass and power cost, opening up new mission opportunities for nano satellites and providing a backup capability for existing designs. Two approaches to attitude determination are presented. Firstly, a batch algorithm is described that simultaneously estimates both satellite attitude and unknown parameters in the satellite's attitude dynamics model. Secondly, an online attitude determination capability is developed by extending the commonly employed multiplicative extended Kalman filter (MEKF) for situations where no gyros are present. Both approaches were applied to actual flight data from NASA's O/OREOS and the University of Michigan's RAX-1 nano satellites and results verified against independent data.

Keywords: Aeronautics and Astronautics.
Advisor: Rock Stephen M. primary advisor. Thesis advisor
Close Sigrid
Enge Per advisor. Thesis advisor
Automated handling of Drosophila for biological investigation [electronic resource]

The fruit fly, Drosophila melanogaster, is a key model species for biological research. Trained humans can manipulate, inspect and dissect individual flies, but these operations are often rate-limiting bottlenecks for screening and experimentation. Here I present a high-speed, economical robot for handling non-anesthetized adult flies. Using machine vision the robot tracks a fly's thorax and gently grabs it ~400 ms after targeting. The robot can then translate and rotate the picked fly, inspect its phenotype, dissect or release it, and thereby rapidly prepare multiple flies sequentially for a wide range of experimental formats. In one illustration, the robot restrained flies and dissected the cuticle to permit two-photon imaging of neural dynamics. In another, the robot sorted flies by sex. The robot's tireless capacity for accurate, repeatable manipulations will enable experiments and biotechnology applications that would otherwise be totally infeasible, especially those requiring high-throughput capture, testing and assessment of individual fly attributes.

Keywords: Electrical Engineering.
Advisor: Schnitzer Mark Jacob
Shenoy Krishna V. (Krishna Vaughn) primary advisor. Thesis advisor
Clandinin Thomas R. (Thomas Robert)
Automatic mesh adaptation using the continuous adjoint approach and the spectral difference method [electronic resource]

In this thesis, mesh adaptation using continuous adjoint is tested on two-dimensional Euler equations. Both the flow solver and the adjoint solver are implemented with the high order spectral difference (SD) method. Both h and p adaptation are studied. The test cases include a half-cylinder in subsonic flow and a NACA 0012 airfoil in subsonic and transonic flows. It is found that h-refinement is more suitable for flow discontinuities while p-refinement offers a better performance in smooth flows. Both adaptation methods lead to a faster functional convergence than uniformly h or p refined meshes. In addition, the adapted meshes show similar patterns as those arrived at using the discrete adjoint method. Comparisons between different adjoint target output functionals are also made.

Keywords: Aeronautics and Astronautics.
Advisor: Jameson Antony
MacCormack R. W. (Robert William)
Pinsky Peter M. (Peter Michael)
Axl as a therapeutic target in metastatic ovarian cancer [electronic resource]

ABSTRACT Axl, Sky, and Mer receptor tyrosine kinases (RTKs) are increasingly implicated in a host of cellular responses including cell survival, proliferation, migration, phagocytosis, chemoresistance, and epithelial-mesenchymal transition (EMT). Furthermore, the Gas6/AXL system is implicated in several types of human cancer as well as inflammatory, autoimmune, vascular and kidney diseases. Since the discovery of Gas6/AXL in 1988 in chronic myelogenous leukemia, many more cancers have been found to express AXL. In chapter 1, I will describe my contribution to the field that includes identifying the role of AXL in metastatic ovarian cancer and validating the therapeutic target in ovarian cancer. In the second chapter, I have investigated the role of AXL in chemoresistance in ovarian cancer. Within the past decade, AXL crosstalk has emerged as a dominant pathway for ligand-independent activation. With the recent identification of AXL as an important factor in mediating tyrosine kinase inhibitor resistance, understanding this cross-talk is important. There has been a recent report of c-MET and AXL cross-talk in breast cancer. c-MET has become a potential target for cancer therapy with numerous clinical trials using c-MET inhibitors as monotherapy or in combination with other targeted agents or chemotherapy. I have further explored this cross-talk in ovarian cancer. In my final chapter, I have identified AXL expression in ovarian cancer tumors formed in a conditional genetically modified invasive ovarian cancer mouse model. In the future, AXL therapy should be further investigated in patients with metastatic ovarian cancer.

Advisor: Giaccia Amato J. primary advisor. Thesis advisor
Cochran Jennifer R. advisor. Thesis advisor
Hu Mickey advisor. Thesis advisor
Sweet-Cordero Eric advisor. Thesis advisor
Balancing stem cell self-renewal and differentiation in the skin [electronic resource]

The skin is a classical example of a tissue maintained by stem cells, but the identity of the stem cells that maintain the different epidermal compartments and the signaling mechanisms that control their activity remain unclear. Using lineage tracing and quantitative clonal analyses, we show that the Wnt-target gene Axin2 marks epidermal stem cells that compete neutrally and require Wnt/[beta]-catenin signaling to proliferate. By RNA in situ hybridization, we show that the Axin2-expressing stem cells produce their own self-renewal signals in the form of Wnt proteins. These cells also express secreted Wnt inhibitors, including Dkks, which accumulate at high levels around more differentiated cells. We propose a new model for skin maintenance, in which epidermal stem cells produce short-range Wnt signals to maintain their own identity and function, while simultaneously secreting longer-range inhibitors that suppress Wnt signaling to promote differentiation of the stem cell progeny.

Keywords: Developmental Biology.
Advisor: Nusse Roel
Bejerano Gill
Kingsley David M. (David Mark) advisor. Thesis advisor
Oro Anthony
Bank dominance: Financial sector determinants of sovereign risk premia

This paper investigates the persistence, extent and nature of the correlation between banking and sovereign credit risk in the European financial crisis. I use Credit Default Swap (CDS) premia on sovereigns as a measure of sovereign risk while using a specially constructed CDS Banking Risk Index (BRI) to measure the financial sector risk of each country. This paper finds that there is “bank dominance” in the determination of sovereign risk premia in the European financial crisis even when fiscal variables are included in the estimation. The Banking Risk Index is the primary statistically significant determinant of sovereign risk premia in the crisis period. Moreover, this paper finds that the correlation between banking and sovereign risk increases with an increase in the financial sector risk, measured by the BRI—in times of greater financial sector risk, banking and sovereign risk are jointly evaluated in the market, even more so than usual.

Keywords:  Department of Economics
Stanford Department of Economics
Thesis
Advisor: Duffie Darrell