VictorJuiz/thesis huggingface dataset:
Choreographic legacies [electronic resource] : (dis)embodied assemblages of queer and colonial histories

As many of the pioneers of American modern dance have passed away in recent years, the dance field has become intensely preoccupied with the issues surrounding the role of choreography in artistic afterlives. While contemporary concern with Legacy plans points to the desire to curate the history of the choreographer through the afterlife of the choreography, popular attention to the marginalization of women and people of color from artistic institutions also points to a contemporary effect of historical assertions of control over dancing bodies. This project focuses on the lowercase legacies; the legacies that have persisted invisibly, subtly shaping the landscape of possibility within performance. Shifting the popular orientation of our contemporary preoccupation with Legacy to include the assemblage of racist, sexist, and homophobic legacies that have contoured the Western canon, I focus on the violent imperial legacies that have become choreographically embedded within dance history. By the very nature of their embeddedness, these legacies circulate prolifically throughout dance history, across the genres of ballet and modern dance, to impact dance production across the globe. My focus on the transmission of these embedded legacies over more than a century of dance history and across three continents also attends to the persistent issue of dance's temporality. The debate surrounding dance's ontological relationship with ephemerality compels a necessary characterization dance not as a performance of disappearance, but of endurance. The shift from Legacies with a capital "L" to the embedded legacies on which this dissertation focuses invites a new consideration of legacy that is dependent on the medium of performance itself. These legacies prove dance's temporal endurance and influence within sociopolitical constructs that uphold the power of the dominant. This analysis of the temporalities of dance performance and afterlife points towards new considerations of dance's transmission and durability.

Keywords: Theater and Performance Studies.
Advisor: Ross Janice primary advisor. Thesis advisor
Menon Jisha
Phelan Peggy advisor. Thesis advisor
Chromatin accessibility dynamics during C. elegans development reveal regulatory complexity and identify novel enhancers [electronic resource]

Chromatin accessibility, a crucial component of genome regulation, has primarily been studied in homogenous and simple systems, such as isolated cell populations or early development models. Whether chromatin accessibility can be assessed in complex, dynamic systems in vivo with high sensitivity remains largely unexplored. In this study, I use ATAC-seq to identify chromatin accessibility changes in a whole animal, the model organism C. elegans, from embryogenesis to adulthood. Chromatin accessibility changes between developmental stages are highly reproducible, recapitulate histone modification changes, and reveal key regulatory aspects of the epigenomic landscape throughout organismal development. Further, chromatin accessibility measurements near transcription start sites are predictive of steady-state gene expression, and ATAC-seq dynamics are correlated with gene expression changes. Importantly, my analysis of dynamic changes in chromatin accessibility within whole organisms sensitively identified novel cell-type- and temporal-specific enhancers, which I functionally validate in vivo. Furthermore, by integrating transcription factor binding motifs into a machine learning framework, I identify EOR-1 as a potential early regulator of chromatin accessibility changes. My study provides a unique resource for C. elegans, a system in which the prevalence and importance of enhancers remains poorly characterized, and demonstrates the power of using whole organism chromatin accessibility to identify novel regulatory regions in complex systems.

Keywords: Genetics.
Advisor: Brunet Anne
Fire Andrew Zachary advisor. Thesis advisor
Kundaje Anshul
Wysocka Joanna
Circle Tracking Game: Testing Coordination

In an effort to study perspective taking in VR (VRPT) as part of the Virtual Human Interaction Lab, a post treatment questionnaire was conducted which examined Selfishness, Distrust and Coordination in negotiation in the from of games. In the scope of this, we created the Circle Tracking Game, a new game designed to test coordination.

Keywords:  Department of Communication
Coordination Game
Circle Tracking Game
VRPT
VHIL
Stanford
Communication
Media Studies
Thesis
Advisor: Bailenson Jeremy
Citizenship Contestation and Reprisal Violence in sub-Saharan Africa

Why do governments choose to challenge the citizenship of ethnic minority groups? Why do some of these cases result in violence, but not others? My research shows that governments choose to challenge the citizenship when the exclusion of the group benefits the government's political project regardless of a democratic transition, and that affected groups will react with violence when there is an intersection of a political opening and a lack of credible exit options. I examined multiple case studies of ethnic minority groups bisected by international borders in sub-Saharan Africa: the Banyarwanda in Congo/Zaire, the Banyarwanda in Uganda, the Dioula in Côte d’Ivoire, the Bamileke in Cameroon, and black Africans in Mauritania. I analyzed key historical points of citizenship contestation and extension to understand the variation of event outcomes within these countries.

Keywords: International Relations Program
Banyarwanda
citizenship
Zaire
Uganda
Dioula
Côte d'Ivoire
Bamileke
Cameroon
Mauritania
Thesis
Advisor: WEINSTEIN JEREMY
City of Facebook: How East Palo Alto community leaders struck unprecedented $20 million deal with Facebook

In December 2016, Facebook announced an unprecedented agreement to commit $20 million toward affordable housing in the Bay Area. The work by the community coalition, Envision Transform Build EPA, and Facebook’s decision to bargain with a motley group of activists, reflects a new dynamic among residents, city councils, and Facebook – one in which community members are increasingly demanding services from local companies that city governments fail to provide. Members of ETB say the agreement, the single largest contribution that Facebook has made directly towards housing, marks a shift in how the company regards its role in the Bay Area’s affordability crisis. It also highlights the impressive capacity of this grassroots movement to strike a deal with one of Silicon Valley’s most powerful companies.

Keywords:  Department of Communication
Stanford University
Journalism
Communication
Thesis
Advisor: Zacharia Janine
Civic Education and Political Empowerment Among South Korean Youth

South Korea’s democratic consolidation over the past half-century has been accompanied by the proliferation of information related to democratic practices and democracy itself. Scholars of democracy agree that a robust democracy requires well-informed and active citizen participation, and young South Koreans between the ages of 18 and 29 have access to historically unprecedented amounts of information about politics. Yet recent survey has revealed that youth reporting feeling that politics and governance are difficult to understand. Given the sprawling extent of South Korea’s democratic development, why do feelings of being able to understand politics among the nation’s youth remain so low? This investigation turns to civic education in South Korea to answer this question—to understand not only whether students are learning about democracy, but also how democracy is taught in schools. This investigation proceeds in five parts: An introduction to the research question, a discussion of methods employed, a brief history of democratic education on the peninsula, close readings of history and society textbooks at the secondary school level and a discussion of the results emerged from close reading and their implications for the future of South Korean democracy.

Keywords: democracy
South Korea
youth
political empowerment
political efficacy
civic education
secondary school
textbooks
close reading
Thesis
Advisor: Moon Yumie
Cohesive sediment flocculation in a partially-stratified estuary [electronic resource]

This research is focused on understanding cohesive sediment dynamics and transport in the San Francisco Bay-Delta (SFBD) estuary, which is a partially-stratified estuary. Cohesive sediments play an essential role in coastal systems because they act as carriers for contaminant transport, affect aquatic organisms through turbidity, and cause build-up in navigation channels. One of the fundamental challenges in the study of this multi-faceted chemical, biological, and physical problem is the dynamic process of cohesive sediment flocculation. We studied cohesive sediment flocculation using high-resolution transect and stationary measurements of stratified turbulence and floc properties collected between 2008 and 2015. We make the following main observations. First, we show that the expected floc fall velocity is O(0.01-1) mm/s, which is at least two orders of magnitude higher than the expected fall velocity of its disaggregated constituents. Second, we show that the floc size is not significantly affected by changes in salinity, sediment concentration, or biological activity. Moreover, a comparison between the freshwater and saltwater flocculation dynamics shows that the traditional notion of enhanced floc aggregation at the onset of salinity is not appropriate in this estuary. Third, and most importantly, we conclude that the physical processes are the most dominant control on floc size, rather than the biological or chemical factors. Using the turbulent shear rate (G), we show that the floc size scaled inversely with the strength of G. Over tidal timescales, the smallest floc sizes are typically observed during slack water, and the largest floc sizes are typically observed at peak current velocities. However, while G is the primary control on floc size changes in time, we found that other physical processes, such as differential settling, cannot be ignored. These secondary effects are most evident during the tidal transitions, coinciding with when stratification is at its strongest and the largest top-bottom difference in floc sizes is observed. In previous laboratory and field studies, this interplay between turbulence, stratification, and differential settling on flocculation has often been ignored either by design or was not accounted for.

Advisor: Monismith Stephen Gene primary advisor. Thesis advisor
Fringer Oliver B. (Oliver Bartlett) advisor. Thesis advisor
Manning Andrew J. advisor. Thesis advisor
Ouellette Nicholas (Nicholas Testroet)
Collaborative learning at scale [electronic resource]

We introduce an online learning platform that scales collaborative learning. We study the impact of team formation and the team formation process in massive open online classes. We observe that learners prefers team members with similar location, age range and education level. We also observe that team members in more successful teams have diverse skill sets. We model the team formation process as a cooperative game and prove the existence of stable team allocations. We propose a polynomial-time algorithm that finds a stable team allocation for a certain class of utility functions. We use this algorithm to recommend teams to learners. We show that team recommendations increase the percentage of learners who finish the class.

Keywords: Management Science and Engineering.
Advisor: Saberi Amin primary advisor. Thesis advisor
Goel Ashish advisor. Thesis advisor
Johari Ramesh
Colorful: A Modern Day Epistolary

This creative thesis though the Stanford FGSS department is my way of presenting my findings on trauma in the psyche of black-gay males in contemporary America. The novel is a dark-comedy that follows the life of a black-gay teenager during his senior year of high school. The companion essay shows how I imbued my research into the novel.

Keywords: Feminist Gender and Sexuality Studies
Stanford
Black
Gay
Trauma
Queer
Narrative
Thesis
Advisor: Cerankowski Karli
Combinatorial methods in Markov chain mixing [electronic resource]

This thesis is concerned with various aspects of Markov chain mixing. The general problem is to examine the number of steps of a Markov chain required for the chain to be close to its stationary distribution. Chapter 2 discusses the problem of shuffling a large deck of cards, describing how to implement riffle shuffles using only operations which affect fewer cards at a time. It also gives upper bounds on the mixing times of several related shuffling schemes. Riffle shuffles are usually modelled by the GSR shuffle. Chapter 3 presents the results of several hundred physical riffle shuffles, and compares this data to the predictions of the GSR model. Similar analysis is done for mash shuffles. Chapter 4 describes how the convergence of a Markov chain may be affected by interweaving other operations. It gives examples where these modifications can drastically slow down or speed up convergence, and a conjecture regarding the efficient generation of random partitions. The random transposition walk on the symmetric group is well-understood. Chapter 5 extends the known strong stationary time results regarding this walk to a more general walk where at each step, a larger number of cards are chosen at random and shuffled amongst themselves. Chapter 6 introduces mutation times, a new combinatorial technique similar to the method of strong stationary times. Mutation times can give upper bounds on the mixing times of some Markov chains where strong stationary times may be difficult to construct. This chapter uses mutation times to analyse several models of wash shuffles, as well as some classical random walks on the symmetric group. Chapters 7 and 8 examine the convergence of statistics on Markov chains, rather than the convergence of the chains themselves. Chapter 7 describes how coupling may be used to obtain results about the convergence of statistics, and Chapter 8 uses strong stationary times. Both chapters contain a large number of examples. Finally, Chapter 9 presents a likelihood order for simple random walks on Coxeter groups, showing that the weak Bruhat order describes which elements are more or less likely than others after any number of steps.

Keywords: Mathematics.
Advisor: Diaconis Persi primary advisor. Thesis advisor
Fox Jacob
Soundararajan Kannan
Combinatorial signal processing [electronic resource]

We study the problem of interpolating all values of a discrete signal f of length N when d< N values are known, especially in the case when the Fourier transform of the signal is zero outside some prescribed index set J; these comprise the (generalized) bandlimited spaces B^J. The sampling pattern for f is specified by an index set I, and is said to be a universal sampling set if samples in the locations I can be used to interpolate signals from B^J for any J. When N is a prime power we give several characterizations of universal sampling sets, some structure theorems for such sets, an algorithm for their construction, and a formula that counts them. There are also natural applications to additive uncertainty principles. Universal sets are related to the invertible, but possibly poorly conditioned submatrices of a discrete Fourier transform matrix. At the other extreme, we study the problem of finding unitary submatrices of the discrete Fourier transform matrix. This problem is related to a diverse set of questions on idempotents on Z_N, tiling Z_N, difference graphs and maximal cliques. Each of these is related to the problem of interpolating a discrete bandlimited signal using an orthogonal basis.

Keywords: Electrical Engineering.
Advisor: Osgood Brad primary advisor. Thesis advisor
Gill John T.
Montanari Andrea advisor. Thesis advisor
Communication and computation [electronic resource] : new questions about compositionality

The topic of this dissertation is the famous principle of compositionality, stating that the meanings of complex expressions are determined by the meanings of their parts and how the parts are put together. The title belies its intent: rather than advanc- ing a central thesis, it instead asks and provides answers to new questions about compositionality. In particular, these questions arise by shifting from viewing com- positionality as a property of symbolic systems -- where what I call 'status questions' are naturally discussed -- to viewing it from a procedural perspective, as operative in processes of production and interpretation. The questions the dissertation asks arise at successively narrower levels of scale. At the level of our species, I ask: why are natural languages compositional in the first place? At the level of small conversations: what role does compositionality play in the broader theory of communication? And at the level of an individual language speaker: what is the algorithmic interpretation of compositionality and what demands on complexity does it impose? In the pursuit of answers to these questions, a wide variety of methods are employed, from simulations of signaling games, to logic and formal semantics, to theoretical computer science, as appropriately called for.

Keywords: Philosophy.
Advisor: Benthem Johan van
Icard Thomas advisor. Thesis advisor
Potts Christopher
Skyrms Brian advisor. Thesis advisor
Competitive intelligence [electronic resource] : drivers and consequences of executives' attention to competitors in enterprise software

In this dissertation, I investigate executives' attention to competitors and the implications for firm innovation. Using a hand-collected dataset on competition, innovation, and executive experience in the full population of public U.S. enterprise infrastructure software firms, I examine attention to competitions in three empirical papers. In the first paper, I show that attending to competitors that activate opportunity-based rather than threat-based views of competition has a positive relationship with product innovation. In the second paper, I show that executives are more attentive to competitors at the periphery of an industry when the experience of the executive team amplifies (i.e. mirrors) the experience of the CEO. In the third paper, I use social network analysis to show that personal similarities between CEOs can influence competition between firms. As a whole, my dissertation suggests that executives can be strategic in how they think about competition, with tangible benefits for firm performance.

Keywords: Management Science and Engineering.
Advisor: Katila Riitta primary advisor. Thesis advisor
Byers Thomas (Thomas H.) advisor. Thesis advisor
Eesley Charles advisor. Thesis advisor
Eisenhardt Kathleen M. advisor. Thesis advisor
Computational investigation of DNA methylation and C2H2 zinc finger transcription factor binding [electronic resource]

DNA binding regulatory proteins known as transcription factors (TFs) and biochemical modifications to DNA such as DNA methylation play a key role in regulating gene activity. In my thesis, I develop computational methods for leveraging novel datasets to gain insight into how these processes affect gene regulation. I first describe a new method for finding genetic differences that are associated with variation of DNA methylation across individuals. I then describe methods for revealing the DNA binding preferences of one of the most ubiquitous but poorly understood class of TFs known as C2H2 zinc finger TFs. I present a case study in which I train and interpret deep convolutional neural networks to reveal how mutations in CTCF, an important C2H2 zinc finger TF, affect its binding preferences.

Advisor: Fraser Hunter B. primary advisor. Thesis advisor
Kundaje Anshul
Bejerano Gill
Snyder Michael
Computational methods using large-scale population whole-genome sequencing data [electronic resource]

Advancements in next-generation low-cost, high-throughput DNA sequencing technologies have made it possible to sequence a large number of human genomes. To date, at least tens of thousands of individuals have been whole genome sequenced. Even more large-scale population sequencing projects are actively underway or will be launched in the foreseeable future. This vast amount of genomic data undoubtedly advances the characterization of human genome variation and supports disease studies across diverse cohorts. However, the challenging problem of how to efficiently and precisely determine individual-level genomic differences from this huge amount of sequencing data exists. This natural first step of leveraging sequencing data for genomic analyses can be computational intensive, while the quality of the restored genomes influences a wide variety of downstream applications, such as association studies, personalized medicine, and population genomics. In this dissertation I present computational methods to approach this fundamental problem in the context of ever-increasing sequencing data volume and demonstrate the effectiveness and efficiency of these methods using real data from latest population sequencing projects. First, I present a new method that maps reads of newly sequenced human genome to a large collection of genomes, aiming to reduce the inherent biases induced by aligning to any single reference genome. Second, I introduce an approach, named Reveel, for single nucleotide variant calling and genotype calling of large cohorts that have been sequenced at a low coverage, that aims for computational efficiency as well as accuracy in capturing linkage disequilibrium patterns present in rare haplotypes. Third, on the basis of the Reveel framework I present a reference-based approach that effectively incorporates genotypes from completed projects to improve the genotyping quality of new datasets while maintaining low computational costs. Finally, I demonstrate an application of genotype information for improving the efficiency of identity-by-descent detection from a large cohort.

Advisor: Batzoglou Serafim primary advisor. Thesis advisor
Kundaje Anshul
Pritchard Jonathan (Jonathan K.) advisor. Thesis advisor
Computational modeling of the brain [electronic resource] : development, health, and disease

The brain is our most complex yet least understood organ, and many questions remain as to its development and the intricate relation between form and function. The characteristic wrinkling of the human brain is the result of both biological and mechanical processes during development, so it is crucial to incorporate soft tissue mechanics in our quest to address relevant developmental and medical questions. A major challenge in modeling the mechanical processes that influence brain development is the significant difference between traditional engineering materials and soft, growing biological tissues. In particular, it is not possible to natively model growth, or the addition of mass, using the traditional finite element method. In response to this challenge, this thesis elaborates on the applicability of computational tools and theoretical frameworks to the modeling of soft, growing materials. Combining the theory of finite growth, continuum mechanics, and finite element analysis allows for the incorporation of biological phenomena in FE simulations; helps distinguish between the behavior of soft, growing materials and their stiffer, non-growing counterparts; and enables the quantification of experimental and clinical data for validation. Beyond continuing work on the physiological and pathological development of the brain, these computational and theoretical advances on the modeling of soft, growing materials lead to many possibilities for future work on other soft tissues.

Keywords: Mechanical Engineering.
Advisor: Kuhl Ellen
Levenston Marc Elliot advisor. Thesis advisor
Pinsky Peter M. (Peter Michael)