VictorJuiz/thesis huggingface dataset:
Tiny Homes and Big Money: Options for the City of Oakland, California to Support the Construction of Additional Accessory Dwelling Units

This paper explores options for the City of Oakland, California to help its residents finance the construction of Accessory Dwelling Units (ADUs) as a means to boost the supply of affordable housing. This paper finds that private finance options are limited for homeowners with limited incomes and home equity. The Department of Housing and Urban Development’s Section 108 loan program, combined with local funding sources, are the most readily accessible options for Oakland to support ADU construction. More innovative options, such as real estate crowdfunding and ADUs-as-a-service, may one day provide viable alternatives for Oakland to encourage ADU construction.

Keywords:  Public Policy Program
Stanford University
Humanities and Sciences
Public Policy Program
Accessory Dwelling Unit
In-law unit
ADU
laneway house
granny flat
ADU finance
municipal finance
affordable housing finance
Oakland
Bay Area housing crisis
Section 108 loan
real estate crowdfunding
ADUs-as-a-service
real estate innovation
revolving fund
secondary unit.
Thesis
Advisor: Cain Bruce
Tit for Tat: The Influence of Resource Dependence on China's Foreign Relations

Existing literature argues that China cultivates relations with resource-rich nations in order to access and procure energy exports. However, this neomercantilist hypothesis inaccurately defines China’s relations as a limited quid pro quo exchange. This thesis expands upon neomercantilist arguments by examining the extent to which energy needs influences China’s foreign relations with resource exporters. Energy relations are examined through quantitative and qualitative methods. A regression analysis is performed to test the strength of China’s oil and gas as an explanatory variable of indicators of political cooperation. Additionally, this thesis examines the evolution of China’s relations with three resource-rich countries of varying oil export levels: Angola, Republic of Congo, and Gabon.
This study finds that neomercantilism is a necessary but insufficient framework for understanding the role of China’s energy dependence. In the regression analysis, energy dependence is a statistically significant predictor of how frequently China aligns with another country in UN voting but not of other indicators of political cooperation, suggesting that resource relations are linked with a limited form of political cooperation. In the case studies, while energy interests may have catalyzed China’s further engagement with resource rich nations, relations quickly evolved beyond resource interests as both African nations and China sought to redefine developmental assistance under the framework of South-South cooperation. Overall, these results suggest the necessity of understanding China’s energy security within the context of its efforts to increase its soft power with resource-rich nations.

Keywords:  Center for International Security and Cooperation
Center for International Security and Cooperation
energy geopolitics
Thesis
Advisor: Blacker Coit D.
Toll road financial performance in the face of revenue risk - a comparative analysis of two cases

Many Public-Private Partnership (P3) project have succeeded in bringing private capital to expedite US infrastructure development, but some of them have faced financial distress and have ultimately filed for Bankruptcy. This thesis describes exploratory research to uncover possible reasons behind struggling toll road P3 projects and their impact on taxpayers by looking into two projects that went through bankruptcy: Southern Connector, and the State Route 125. This thesis develops case studies for each project from sources including court documents, news articles and past studies. By comparing and contrasting the two cases, several conclusions are drawn. First, that P3s can be a tool to shield taxpayers from demand risk if appropriately structured; second, efficient transfer of risk is critical to project's success, especially in aligning incentives to ensure that traffic demand forecasts for toll roads are unbiased; lastly, the 63-20 model is less feasible for P3 projects with high risk profile such as toll roads. While the model transfers demand risk to the concessionaire through the use of project finance, it is less effective in aligning incentives to remove bias in traffic forecasts.

Advisor: Levitt Raymond E.
Topics in high-dimensional statistical learning

Our research explores three topics in high-dimensional statistical learning. First, we consider a regression scenario where it is natural to impose an order constraint on the coefficients. We propose an order-constrained version of l1 -regularized regression for this problem, and show how to solve it efficiently using the well-known Pool Adjacent Violators Algorithm as its proximal operator. We illustrate this idea on real and simulated data. We then consider regression scenarios where it is natural to allow coefficients to vary as smooth functions of other variables. We propose two constrained versions for this problem and show how to solve them efficiently. Last, we study canonical correlation analysis (CCA) in high-dimensional settings and propose a sparse CCA framework, and provide two efficient algorithms. We discuss links between CCA and linear discriminant analysis (LDA). We demonstrate its use on real and simulated data.

Advisor: Saunders Michael A. 
Tibshirani Robert 
Taylor Jonathan E.
Topics in statistical learning with a focus on large-scale data

The widespread of modern information technologies to all spheres of society leads to a dramatic increase of data flow, including the formation of "big data" phenomenon. Big data are data on a massive scale in terms of volume, intensity, and complexity that exceed the ability of traditional statistical methods and standard tools. When the size of the data becomes extremely large, it may be too long to run the computing task, and even infeasible to store all of the data on a single computer. Therefore, it is necessary to turn to distributed architectures and scalable statistical methods. Big data vary in shape and call for different approaches. One type of big data is the tall data, i.e., a very large number of samples but not too many features. Chapter 1 describes a general communication-efficient algorithm for distributed statistical learning on this type of big data. Our algorithm distributes the samples uniformly to multiple machines, and uses a common reference data to improve the performance of local estimates. Our algorithm enables potentially much faster analysis, at a small cost to statistical performance. Another type of big data is the wide data, i.e., too many features but a limited number of samples. It is also called high-dimensional data, to which many classical statistical methods are not applicable. Chapter 2 discusses a method of dimensionality reduction for high-dimensional classification. Our method partitions features into independent communities and splits the original classification problem into separate iv smaller ones. It enables parallel computing and produces more interpretable results. For unsupervised learning methods like principle component analysis and clustering, the key challenges are choosing the optimal tuning parameter and evaluating method performance. Chapter 3 proposes a general cross-validation approach for unsupervised learning methods. This approach randomly partitions the data matrix into K unstructured folds. For each fold, it fits a matrix completion algorithm to the rest K − 1 folds and evaluates the prediction on the hold-out fold. Our approach provides a unified framework for parameter tuning in unsupervised learning, and shows strong performance in practice.

Keywords: Statistics.
Advisor: Hastie Trevor 
Efron Bradley 
Taylor Jonathan E.
Topology optimization of thermo-elastically damped MEMS resonators

Micro-electromechanical systems (MEMS) resonators are becoming evermore ubiquitous. The main loss mechanism in these devices is thermo-elastic dissipation (TED). In this thesis a finite element model is developed to simulate TED behavior and a topology optimization scheme is established to modify the internal structure of the resonator in an effort to reduce damping. Each element of the resonant structure is a variable of density between 0 (void) and 1 (solid). The gradients of these variables are calculated and are used to solve a strictly convex subset of the problem using the method of moving asymptotes. The element densities of the model are updated iteratively until an optimal topology is formed. The algorithm proves to be effective at mitigating the effects of TED. Optimal devices have an improvement in quality factor of nearly 10x. Devices are fabricated in single crystal silicon and tested using a lock-in amplifier. The constituent loss modes are able to be quantified experimentally and there is good agreement between modeled and tested devices. This topology optimization algorithm and other tools can be used to improve all types of MEMS resonators.

Keywords: Mechanical Engineering.
Advisor: Kenny Thomas William 
Lew Adrian 
Tang Sindy (Sindy K.Y.)
Touching heroes [electronic resource] : the homeric construction of intimacy

This dissertation examines the poetics of intimacy in the Iliad and the Odyssey and demonstrates that they employ an observable system when constructing close contact. It does so by first defining 'intimacy' as those moments of extreme physical and emotional closeness between characters, which it situates in archaic Greek epic. It then breaks down these encounters into their three essential elements: stance, physical connection, and verbal intercourse. Together, they make an interaction 'intimate.' Each of these elements is treated in its own chapter, which allows my dissertation to examine all the phrases and formulas that constitute them, as well as their various shades of meaning and thematic implications. Characters do not just stand near one another and touch each other with gesture and speech, they use a variety of stances and actions that, in turn, produce a myriad of effects and associations. They also make themselves vulnerable. My dissertation establishes the fullness of Homer's intimate poetics and, in doing so, brings to light the ambiguity of intimacy inherent to this system. Whether on the battlefield or at home, the poet's description of interaction links care and violence in surprising and disturbing ways.

Keywords: Classics.
Advisor: Martin Richard P. primary advisor. Thesis advisor
Peponi Anastasia-Erasmia advisor. Thesis advisor
Rehm Rush advisor. Thesis advisor
Toward the generation of pure forebrain glutamatergic and spinal cholinergic neurons

Current practices for disease modeling or drug screening for neurodegenerative genetic diseases rely on human immortalized cell lines or animal models that do not accurately represent the progression of the disease or capture the effects drugs will have in clinical trials. Human neurons induced from stem cells have been shown to accurately capture the effects the drugs will have on the diseases neurons and can serve as a reliable model for the progression of these (Jiménez-Moreno et al., 2017; Jungverdorben et al., 2017). However, current methods for obtaining human neurons for drug testing and disease modeling involve converting readily available cell types such as fibroblasts and blood cells into induced pluripotent stem cells and subsequently differentiating into neurons. These methods often involve multiple lengthy and complicated combinations of morphogens or growth factors and produce neurons at a very low efficiency. Our lab previously reported a facile and rapid method to produce induced neuronal (iN) cells by overexpressing a proneural transcription factor, NGN2, in human embryonic stem cells and induced pluripotent stem cells (Zhang et al., 2013).To determine the neuronal subtypes at a single cell level, we first performed single cells RNA-sequencing (scRNA-seq) for human embryonic stem cells, day 4 and day 28 iN cells. Two transcription factors (ISL1 and PHOX2B) were found to be upregulated in a subpopulation of iN cells which are positive for cholinergic markers such as SLC18A3 and SLC5A7. Immunofluorescence staining of ISL1 and PHOX2B confirmed the scRNA-seq results. We further confirmed overexpression of ISL1 and/or PHOX2B in Ngn2 derived iN cells is sufficient to upregulate in cholinergic genes. The cholinergic fate was partially removed by forcing the induced neurons into a frontal brain neuronal fate that showed an increase in glutamatergic markers. Through this research we have shown that ISL1 and PHOX2B are important regulators of cholinergic cell fate and can be overexpressed or removed to give the desired neuronal cell fate.

Keywords:  Department of Biology
Neurodegenerative
induced neuronal cell
pluripotent
cholinergic
glutamatergic
neuron
Thesis
Advisor: Wernig Marius
Jones Patricia
Towards a deeper understanding of molecular mechanics

The advent of atomistic molecular dynamics simulations held the promise of a complete understanding of biomolecular dynamics. However, this goal has remained elusive, as increased computational power has brought with it larger systems to simulate and an overwhelming number of observables to analyze. In this work, I describe how recent advancements in Markov state modeling have helped overcome this dimensionality problem and enabled the characterization of complex phenomena, such as the folding-upon-binding processes of intrinsically disordered peptides. But is it possible to produce even more insightful models? To this end, I present a method that exploits Markov state models to infer statistically causal drivers of protein dynamics. Finally, I discuss a neural network alternative to Markov models, which yields physically interpretable insights and has the potential to replace expensive atomistic simulations.

Advisor: Pande Vijay 
Das Rhiju
Markland Thomas E.
Towards a holistic language for engineering synthetic morphogenesis [electronic resource]

Biological patterns form in a distributed manner through self-assembly and have the capacity to self-heal. The ability to engineer synthetic morphogenesis will advance our way of patterning. Here, I develop a language to facilitate the engineering of synthetic morphogenesis. This language is motivated by an exercise to design and grow a yinyang-like pattern from a single \textit{Escherichia coli} cell. The language consists of the abstraction and implementation of functions for engineering the curvature, texture, and reliability of cell lineage borders. These border functions are realized holistically, as an emergent consequence of cell physical properties such as growth rate and cell shape, as opposed to an explicit genetic system. I used the border functions to design and grow two-dimensional phases of the moon, pacmans with different size mouths, and a yinyang-like pattern. The holistic language facilitates the engineering of more complex synthetic morphogenesis than previously achieved and serves as a foundation for expanding our ability to engineer synthetic patterns.

Keywords: Bioengineering.
Advisor: Endy Andrew D. primary advisor. Thesis advisor
Frank C. W. advisor. Thesis advisor
Huang Kerwyn Casey
Riedel-Kruse Hans
Towards a Mexican Indigenous Party? A Study of Ethnic Party Formation and Indigenous Mobilization in 20th Century Mexico

In absolute numbers, Mexico is the country in the Western Hemisphere with the largest number of Indigenous peoples. Depending on the definition used, between ten and slightly more than twenty percent of Mexico, a nation of nearly 120 million, is Indigenous. At the same time, Mexico’s Indigenous population has historically been among the most marginalized of the country’s citizens. More than seventy percent live in poverty while also facing persistent discrimination in a nation that has historically lionized its Indigenous roots while neglecting the needs of its contemporary Indigenous population. Despite these factors, Indigenous movements and organizations in Mexico have never coalesced to form a cohesive, viable, national-level Indigenous movement, nor an ethnic political party organized around Indigenous identity and issues. This paper will explore the question of why this has been the case. This paper assesses the question through a comparative approach that considers the theory of ethnic party formation and the factors that allowed such parties to form in other Latin American countries. It then explores the nature of the relationship between Indigenous groups and the federal government in Mexico, how that relationship evolved over the last century, and how institutional and organizational factors affected the relationship and the organization of Indigenous groups themselves. It also discusses whether, given that Mexico’s Indigenous population has not thus far organized into an ethnic political party, whether this is something that should happen.

Keywords:  Center for Latin American Studies
Stanford Center for Latin American Studies
Latin American Studies
Mexico
Indigenous issues
ethnic parties
Indigenous mobilization
20th Century Mexico
Thesis
Advisor: Frank Zephyr
Towards clinically viable neural prostheses through innovations in neuroscience, decoders, and interfaces

Millions of people in the United States live with paralysis due to spinal cord injury or neurological diseases. The motor impairment limits the patients' independence and in some cases the ability to communicate. Brain-computer interfaces (BCIs) translate signals from the brain into useful control signals, manipulating end-effectors such as computer cursors or robotic arms. BCIs can help restore lost motor capabilities and improve the quality of life for people with paralysis. Intracortical BCIs (iBCIs) have shown promising results in clinical trials, making them the prime candidate as an assistive device for people with severe paralysis, such as tetraplegia. However, for most applications iBCIs need further improvements to be suitable for clinical use. In this dissertation, I aimed to advance the main three components of the iBCI system: the neural interface, the user estimation decoding algorithm, and the user interface. I advanced the three components using multidisciplinary tools from neuroscience, statistics, and engineering. I believe that the studies which comprise this dissertation are a step forward towards the goal of clinical viability of iBCIs.

Keywords: Electrical Engineering.
Advisor: Shenoy Krishna V. (Krishna Vaughn) 
Goldsmith Andrea
Okamura Allison
Towards Fairness in the Wild: Controlling Disparities in Machine Learning Systems with Human Interaction

The problem of fairness in machine learning (ML) systems has become increasingly important as algorithmic decision making is permeating society, from social media applications with billions of users to the criminal justice system. We consider two aspects of fairness in ML systems that have received relatively little attention in the literature. First, many real-world ML systems are “online” and are fed data continuously over time, resulting in an amplification of initial disparities. Second, the particular demographic groups we often seek to be fair across depend on specific case-settings, and are not sufficient in capturing all possible groups that may suffer from an unfair system. We therefore present two new methods of understanding fairness in machine learning systems that interact with humans: 1. We develop a technique based on distributionally robust optimization to control for losses faced by minority groups at each time step of an online ML system, and we demonstrate improvements in minority group satisfaction in a real-world text autocomplete task, and 2. We demonstrate a clustering algorithm that groups data by a model’s expected loss, allowing human users to determine which high-loss groups present fairness concerns for the particular system. Together, these approaches allow us to address fairness in ML systems as not only just a small number of high-stakes fairness cases, but also as an inherently social problem.

Keywords:  Department of Computer Science
artificial intelligence
bias
fairness
machine learning
human interaction
Thesis
Advisor: Liang Percy
Towards industry-ready high-order overset methods on modern hardware

While computational fluid dynamics (CFD) has enabled a significant reduction in wind tunnel testing during the aircraft design process, the methods used in industry have largely stagnated in recent years. Traditional CFD methods are not well suited to vortex-dominated flows or flows where boundary layer transition and separation play a key role. In addition, the nature of modern high-performance computing (HPC) hardware has changed in recent years, requiring a fundamental shift in algorithm development to fully utilize the computing power available on modern clusters. This thesis presents the development of an overset CFD solver to tackle the above problems. First, the artificial boundary (AB) overset approach is presented, including a new interpolation method developed to reduce the error inherent in inter-grid interpolation. Numerical analysis and experiments are presented to show that the AB approach is more accurate and efficient than traditional methods. The second part of this thesis presents a new overset hole-cutting algorithm to reduce the overhead associated with moving overset grids. Based upon a direct cut approach, the algorithm was developed specifically to handle curved grids and to leverage the massive parallelism available on GPUs. The method is shown to be fast and robust enough to be applicable to large-scale problems of industrial interest. Finally, two large-scale, 3D, unsteady, compressible Navier--Stokes simulations are presented on both static and dynamic overset grids: the Taylor--Green vortex breakdown, and the flow around static and spinning golf balls. The Taylor--Green results are shown to agree extremely well with an `exact' solution, even on dynamic overset grids. A review of previous literature on golf ball flow physics is also presented, with the present results shown to agree well with a variety of both experimental and computational studies.

Keywords: Aeronautics and Astronautics.
Advisor: Jameson Antony
Alonso Juan José
Farhat Charbel
Towards Ultracold Strontium Atoms

Ultracold atoms give physicists a system dominated by quantum mechanical effects with considerable experimental control, and as such are used for quantum simulation and precision measurement experiments. In order to get atoms down to ultracold temperatures (nanokelvin), many different techniques and stages are required. In this thesis, we present two different developments towards obtaining ultracold strontium for precision measurement purposes. We frequency lock three lasers used in the laser cooling process to a strontium cell. We explore painted potential evaporative cooling techniques and calculate the micromotion for different modulation frequencies.

Keywords:  Department of Physics
AMO
Physics
Quantum
Ultracold
Strontium
Thesis
Advisor: Hogan Jason
Hollberg Leo