VictorJuiz/thesis huggingface dataset:
Computing stationary distributions : perron vectors, random walks, and ride-sharing competition

Stationary distributions appear in a wide variety of problems in areas like computer science, mathematics, statistics, and economics. The knowledge of stationary distribution has a crucial impact on whether we are able to solve such problems, or how efficiently we can solve them. In this thesis, I present three of my projects which have a common theme of dealing with stationary distributions. In the first work, called Perron-Frobenius theory in nearly linear time, we give a nearly linear time algorithm for computing stationary distribution of matrices characterized by the Perron-Frobenius theorem. Through our algorithm, we non-trivially extend the class of matrices known to be solvable in nearly linear time by graph Laplacian solvers. In the second work, called high precision small space estimation of random walk probabilities, we try to make a step toward derandomization of the complexity class RL or randomized log space, which is a long-standing open problem in complexity theory. In this context, the knowledge of stationary distribution for directed graphs seems to be a barrier in achieving such a result. While we are not able to resolve L vs. RL problem, we give a small space deterministic algorithm to estimate random walk probabilities to high precision in undirected graphs, as well as directed Eulerian graphs. In the last work, with the rise of ride-sharing platforms, we study a set of important questions naturally arise in this context. Although we use a different set of technical tools compared to the previous two works, we still deal with characterizing equilibria in stationary systems. One of the main questions we answer is whether the competition between two platforms can lead to market failure by pushing the drivers out of the market

Keywords: Management Science and Engineering.
Advisor: Saberi Amin 
Sidford Aaron 
Charikar Moses
Ugander Johan
Conditional independence testing for variable selection and causal inference

Conditional independence testing is a central statistical topic, and here we report on recent advances leveraging such tests for variable selection and causal inference. First, we consider the generation of model-X knockoffs, developing an efficient sampler for arbitrary graphical models as well as proving a lower bound on the computational complexity of knockoff sampling. Our new knockoff sampler enables the deployment of the principled model-X knockoff framework for variable selection for a wider range of problems. Second, we turn to variable selection with compositional data, developing a penalized fitting procedure and a conditional inference procedure to asses goodness-of-fit. We also briefly discuss the connections between model-X knockoff testing and conditional inference. Lastly, we consider the selection of causal variables in genetics. Using data from parent-offspring trios, we formulate inheritance as a high-dimensional randomized experiment, explain how this corrects for confounders in genome-wide association studies, and develop a set of conditional independence tests compatible with multiple testing procedures to check for causal variants in multiple regions of the genome

Keywords: Statistics.
Advisor: Candès Emmanuel J. (Emmanuel Jean)
Tibshirani Robert
Wager Stefan
Confronting Settler Colonial Histories: Education, Race and Politics in the Hawaiian Kingdom

What was the role of Hawaiian aliʻi in establishing educational institutions and encouraging literacy prior to the overthrow of the Hawaiian Kingdom in 1893? Existing literature on the history of education in Hawaii portrays a linear narrative of foreign domination in which missionaries arrived in Hawaii and imposed western modes of learning and governance on Native Hawaiians. More recently, Hawaiian scholars have countered these dominant narratives by documenting the Hawaiian monarchy’s agency in actively adapting western political strategies, in part to protect their sovereignty from foreign imperialism. This thesis builds upon this recent Hawaiian scholarship and shows how Hawaiian leaders supported early missionaries as teachers of literacy and Christianity as part of an ongoing project of cultural and political adaptation. Using the framework of settler colonialism, I address how existing literature ignores Hawaiian agency and explicitly supports the American project of occupation. I then challenge this dominant narrative, relying on primary materials that show the major role of Hawaiian ali'i and teachers in the adoption and spread of literacy in Hawaii. I argue that the aliʻi supported Western education in the Hawaiian Kingdom as part of a foreign policy strategy to resist Western imperialism. An analysis of archival, primary source material indicates that the aliʻi supported palapala as a political tool, resulting in Western education as a crucial component of leadership and government positions.

Keywords: settler colonialism
education
Hawaii
Hawaiian Kingdom
Thesis
Advisor: Biestman Karen
Connecting America: An Analysis of the FCC's Connect America Fund Phase II Auction

The FCC’s Connect America Fund (CAF) Phase II auction is the largest broadband expansion program to date, awarding $1.5 billion in subsidies over the next 10 years. The FCC set two policy objectives for this program: (1) achieve universal internet service access; and (2) maximize the value Americans receive, balanced with cost efficiencies. This thesis analyzes the extent to which the CAF auction achieved the FCC’s second policy objective by estimating the effects of reserve price per household on predicting which census block groups received bids in the CAF auction. Internet service providers placed more bids in areas with a higher reserve price per household, not in areas with higher expected demand. While cost efficient, this bidding behavior does not maximize the total value Americans will receive from the auction. To better align future internet expansion programs’ results with the FCC policy objectives, I make the following recommendations: (1) encourage more satellite-based providers to participate in future auctions; (2) re-evaluate reserve prices to align providers’ and the FCC’s estimates of costs; and (3) limit the total amount of support a provider may bid for in the auction.

Keywords: Broadband Expansion
Connect America Fund
Universal Coverage
Maximizing Benefits
Cost Efficiency
Thesis
The constraints of progress : college feminization and the value of the college degree

This dissertation investigates how the status and value of the college degree as a credential are constructed and evaluated in response to the changing social demographic compositions of colleges and universities. A large body of scholarship shows that occupations with a higher proportion of women have lower average rewards for both women and men—a finding many gender scholars argue is the result of the devaluation of work associated with women. In this dissertation, I ask whether a similar process occurs when women earn a higher proportion of college degrees. One notable implication of women's rising educational attainment is that many colleges and universities, like occupations, are increasingly understood in public and academic discourse to be undergoing a feminization of their own. How does the feminization of colleges and universities shape perceptions of college graduates from institutions where women earn most degrees? Is the value assigned to their credentials lower than that assigned to credentials from non-feminized institutions? I draw on original survey-experimental data collected from a representative sample of U.S. adults to test how the gender composition of men's and women's degree-granting institutions affects their chances of being selected for a job interview. This research offers evidence that the feminization of colleges and universities has very different labor market consequences for male and female graduates. I find that college feminization shapes perceptions of college value in the labor market in two distinct, but interrelated, ways. Unlike occupational feminization, college feminization does not lead to an across-the-board devaluation of the college credential. Rather, devaluation unfolds as a gendered process. Although college feminization has little impact on whether women are recommended for an interview, men who have attended feminized colleges are penalized in interview recommendations. Next, I show that college feminization and applicant gender shape the ways in which college and non-college-educated participants construct merit when evaluating job criteria as important factors in the screening process. This work suggests that the specific job criteria that are tied to employment outcomes for applicants is highly dependent both on the college status of evaluators and the context in which their characteristics as applicants are evaluated. Together, this work highlights the emerging role of feminization in the higher education landscape and suggests several paths forward for scholarship on feminization and its role in exacerbating existing inequalities among college graduates

Keywords: Sociology.
Advisor: Correll Shelley Joyce
Jackson Michelle R. (Michelle Renee)
Pedulla David S.
Contact, conflict, and social cohesion

Can intergroup contact build social cohesion? A rich literature demonstrates that intergroup contact typically reduces prejudice, but we have little evidence on whether contact can change behaviors in real-world settings. This is particularly true when ethnicity is highly salient. This dissertation provides causal evidence on these questions by leveraging studies of Iraqis displaced by ISIS, American schoolchildren, and British soccer fans. I find that diverse forms of contact — from face-to-face contact to virtual exposure — generally improve intergroup relations, even after ethnic violence. I also find, however, meaningful variation in the extent to which these effects extend to social contexts outside of the intervention. I propose that the salience of intergroup conflict moderates the returns to contact. The positive impacts of contact may struggle to change intergroup relations where such change is most needed, but can nonetheless build the micro-foundations of social cohesion in important ways. In shedding light on how contact operates, this dissertation enriches our ability to generate expectations about the effectiveness of prejudice reduction interventions, and ultimately brings us closer to understanding the policy tools available to reap the rewards of intergroup cooperation

Keywords: Political Science.
Advisor: Blaydes Lisa
Weinstein Jeremy M.
Hainmueller Jens
Laitin David D.
Continuous Improvement in Practice: Findings from Schools and Districts in California

Prepared for Policy Analysis for California Education (PACE), this research brief reports effective strategies that enable continuous improvement capacities at the school and district levels. Through comprehensive analysis of case studies and interviews with school leaders, this brief highlights salient practices that are visible within four lenses of continuous improvement. The findings of this report can be shared with instructional leaders who are hoping to utilize improvement science within their organizations and can be replicated or adjusted given different school or district contexts.

Keywords: Continuous Improvement
Improvement Science
School leadership
District leadership
CORE districts
PACE
Stanford Graduate School of Education
Policy Organization and Leadership Studies
Thesis
Advisor: Myung Jeannie
Matheny Kaylee
Control and tomography of phonons in cavity optomechanical nanostructures

Phonons are the quanta of mechanical motion. One possible toolbox for manipulating phonons is provided by the field of cavity-optomechanics, in which light and motion interact via radiation pressure. Of particular importance to applications are cavity-optomechanical nanostructures, whose properties are entirely engineered and which can be integrated on the surface of a chip. In such platforms, new possibilities for the control of phonons emerge. Two key questions arise in these systems where phonons carry information: How can we control the propagation of phonons, and how can we use light to prepare and verify quantum states of mechanical systems? In this thesis, I present three main results using cavity optomechanical nanostructures. First, I will show that phonons confined to a resonator can be made to deterministically couple to an external channel. We propose, and demonstrate via cryogenic measurements, that a particularly simple symmetry-breaking perturbation in nanopatterned silicon allows for the efficient transduction of localized phonons into de-localized phonons. Second, we design and experimentally demonstrate a single-mode phononic wire. Our design incorporates a patterned silicon film with a complete two-dimensional acoustic bandgap. We show through optical measurements that only a single propagating mode is supported for GHz frequency phonons within the bandgap. Low-loss propagation over millimeter length scales is observed. In addition, methods to generate optically induced non-linearities for phonons are discussed. Finally, I describe recent results from our experiment combining photon counting and continuous measurement of mechanical position to perform quantum state tomography. By heralding our measurement on the detection of a single inelastically scattered photon, a single phonon is added to a nanomechanical oscillator. Despite the large thermal occupancy of the oscillator at room temperature, the addition, or subtraction, of a single phonon produces a distinctly non-Gaussian state of motion. The results open up new possibilities for preparing and verifying macroscopic quantum mechanical states using light

Keywords: Applied Physics.
Advisor: Safavi-Naeini Amir H. 
Kenny Thomas William 
Vuckovic Jelena
Controlling color and photoisomerization pathways in photoactive proteins : the role of the protein environment

Proteins are a remarkable class of macromolecules. With a limited number of building blocks, amino acids, they adopt an incredible diversity of three dimensional structures, each with unique functions that are essential to virtually all cellular processes. In many cases, specific small molecules (i.e., ligands, cofactors, substrates, solvent) bound within the three dimensional protein structure are required to help perform that protein's function. The environment created by the protein around the small molecule imparts unique functionality not attainable for the free small molecule alone. For example, fluorescent proteins contain a covalently attached small molecule chromophore that absorbs and emits photons at particular wavelengths. When free in solution, the chromophore is essentially nonfluorescent, but within the protein environment, the chromophore's photon emission efficiency dramatically improves. It is easy to recognize and demonstrate the exquisite control that a protein has over the reactivity of its bound ligands, cofactors, and substrates. However, we do not understand how the protein environment controls function, specifically what factors at the molecular level are important in creating this immense functional diversity. In some cases, crystal structures provide obvious atomic interactions that prove to be essential, such as a particular hydrogen bond or electrostatic attraction. Yet, designing proteins with desired functions is still quite difficult, if not unattainable in many cases, even with current state-of-the-art computational and experimental methods. In my work as a graduate student, I focused on identifying the underlying factors that link a protein's function to its structure and on how to manipulate those factors in a rational way to efficiently achieve a desired function. Using green fluorescent protein (GFP) and its many relatives and derivatives, I have applied various biophysical, spectroscopic, structural, and protein engineering techniques to address this issue, with projects that focus on gaining mechanistic insights into relevant light-induced processes, creating quantitative and predictive models to relate structure and energetics to protein function, and using this deeper understanding to engineer new and improved photoactive protein variants. Together, these projects tell a cohesive story about the functional role of the protein environment on bound molecules and my efforts to elucidate design principles for the engineering of new and improved proteins

Keywords: Chemistry.
Advisor: Boxer Steven G. (Steven George)
Cui Bianxiao
Khosla Chaitan
Convergence concepts : he political construction of stability, legitimacy, and authority

This dissertation defines a broad class of normative political concept - the 'convergence concept' - named to highlight the distinctive mode by which these concepts are evaluated: the evaluation of convergence concepts at the collective scale of the polity derives from the consolidation and convergence of individual citizens' normative judgements. Thus, convergence concepts reflect citizens' own conceptual definitions and assessments, as well as the processes of both private and discursive reasoning which guide these judgements. These concepts are of central concern in the study of political coordination and cooperation (as well as crisis and conflict), since citizens' judgements and behaviors can either establish and reinforce, or undermine and erode, shared structures of governance and coercive political authority. This project investigates three such concepts: stability, legitimacy, and authority. It offers a normative framework for conceptualizing these concepts, and presents an empirical approach by which to investigate political processes of discursive conceptual reasoning

Keywords: Political Science.
Advisor: McQueen Alison (Alison E. J.) 
Ober Josiah
Chapman Emilee
Conversion and braiding rules of band-structure nodes

Topological semimetals are characterized by topologically protected band-structure nodes. One prominent example is the Weyl semimetal, characterized by Weyl points carrying topological Chern numbers. In this dissertation, we explore the topology of band-structure nodes with three ingredients: crystal symmetry, non-Hermiticity and periodic driving. First, we show that point group symmetry facilitates a new type of topological invariant from relative homotopy theory, which determines the rules for converting generic band nodes to nodes at high-symmetry momenta (and vice versa) as we tune the lattice Hamiltonian. Secondly, we show that exceptional lines in non-Hermitian bands act as Alice strings. This is manifested by the reversal of the topological charge of a node, if it is braided around an exceptional line. Finally, we discuss the Nielsen-Ninomiya no-go theorem in Floquet bands and the possibility of simulating chiral Weyl particles in the adiabatic limit

Keywords: Physics.
Advisor: Qi Xiaoliang 
Fan Shanhui
Kivelson Steven
Convex projective geometrically finite structures

In this thesis, we explore two phenomena involving geometrically finite hyperbolic manifolds, and extend them to convex projective geometry. The first phenomenon involves the limit set of a Zariski dense geometrically finite structure. Greenberg studied limit sets of geometrically finite hyperbolic manifolds in order to understand their commensurators, and Mj extended his result to symmetric spaces. We extend this line of results to convex projective geometry, where our motivation is to understand when two geometrically finite structures define similar limit sets. We show that, when the limit of a Zariski dense geometrically finite structure is not the entire boundary at infinity, it determines the structure up to a finite index. The second phenomenon involves the characterization of geometrically finite structures. We introduce the notion of generalized geometrically finite structures, following the works of Danciger-Guéritaud-Kassel on convex cocompactness and Ballas-Cooper-Leitner on generalized cusps. We show an equivalence between a geometric and a dynamical description of such structures, similar to Bowditch's work on geometrically finite hyperbolic manifolds

Keywords: Mathematics.
Advisor: Danciger Jeffrey 
Trettel Steve J.
Cortical Development in a Human 3D Cellular Model of 22q11.2 Deletion Syndrome

22q11.2 deletion syndrome (22q11DS) is a multi–system disorder characterized most frequently by a 3 Mb hemizygous deletion on chromosome 22. This disorder is the most common chromosomal microdeletion in humans and leads to significantly increased rates of neuropsychiatric disorders. Defects in corticogenesis are hypothesized to play a role in pathogenesis and have been investigated through MRI studies, postmortem studies, and mouse models, but have not been studied in human cells. Here, we investigated corticogenesis in 22q11DS using human cortical spheroids (hCS) differentiated from human induced pluripotent stems cells derived from 22q11DS and control subjects. We found that hCS differentiation showed no major differences in morphology and size between 22q11DS and control subjects. Transcriptional profiling of hCS using single–cell RNA–sequencing revealed similar cell composition and highly correlated gene expression. We found that genes within the 22q11.2 deletion exhibited, on average, a 50% reduction in 22q11DS patient derived hCS, including DGCR8, a miRNA processor. Differentially expressed genes, including 9 from the 22q11.2 locus, were enriched for transcriptional regulation, specifically of mRNA and RNA metabolic and catabolic pathways in gene ontology analysis. These findings indicate that early cortical differentiation may not be a significant contributor to developmental defects in 22q11DS, which makes hCS a reliable cellular model to study this disorder. Furthermore, we show that gene expression within the 22q11.2 locus, including DGCR8, is significantly downregulated and may play a role in dysregulating transcription in 22q11DS patient derived hCS.

Keywords:  Department of Psychiatry and Behavioral Sciences
22q11.2 Deletion Syndrome
human cortical spheroids
single-cell RNA-sequencing
Thesis
Advisor: Pasca Sergiu