VictorJuiz/thesis huggingface dataset:
Four approaches to combining data [electronic resource]

This thesis is an amalgamation of four projects that study how data from different sources can be meaningfully combound. Exactly what it means to combine data will vary from chapter to chapter. All of the work had biological data as a motivating factor and most of the projects directly address high dimensional datasets.

Keywords: Statistics.
Advisor: Tibshirani Robert primary advisor. Thesis advisor
Hastie Trevor advisor. Thesis advisor
Holmes Susan
From execution traces to specialized inference [electronic resource]

We often envision a future where computers answer our questions. This is inference: coming to conclusions about the world based on a limited amount of information. One formulates a hypothetical world (model), then simulates and analyzes its behavior with respect to evidence. Probabilistic programming languages are a recent approach where we can express any hypothetical world as a program with random choice primitives. However, this descriptive power often sacrifices performance of inference. In my work, I explore execution traces as a solution that enables high performance while preserving descriptive power. This leads to three subsequent developments. The first is Shred, a tracing compiler that generates efficient Metropolis-Hastings MCMC code from probabilistic programs. Performance was seen to be competitive with hand-coded MCMC in some cases. Like the tracing just-in-time (JIT) compilers that served as the inspiration, there is a sacrifice of efficiency in representing multiple control flow paths. Unlike with traditional JIT compilers, the execution target of probabilistic programming language traces is not limited to straightforward execution on a low-level language, but also includes state-of-the-art inference engines. I developed Solitaire, a language for procedural content generation with constraints, combining trace graph compilation with SMT solving and probabilistic languages. Finally, rather than being limited to an intermediate representation, execution traces can also be treated as abstract objects of inference. The third development is model accretion, a stochastic search-based MAP inference algorithm that improves performance of procedural content generation by re-using previous executions.

Advisor: Hanrahan P. M. (Patrick Matthew) primary advisor. Thesis advisor
Aiken Alexander advisor. Thesis advisor
Goodman Noah (Noah D.) advisor. Thesis advisor
From Summer Slide to Summer Glide? Shifts in Low-Income and Minority Students' Attitudes toward Education throughout Participation in a Summer Learning Program

The current achievement gap between low- and higher-income students in the United States reveals disparities between standardized test scores, grades, graduation rates, college enrollment rates, and entrance into STEM fields (Chen, 2013; Clark, 1986; Kena et al., 2015; Reardon, 2013; Stark & Noel, 2015). According to Cooper et al. (1996), summer learning loss is a major contributor to the achievement gap. Many summer learning programs have arisen to combat summer learning loss in low-income students. This study examines the experiences of low-income and high-achieving middle school students participating in a six-week long summer program. Key findings were that student perceptions on education and STEM were consistently positive, although they strongly preferred learning in the summer environment; students' future plans to take advanced STEM courses or have a career path in STEM fluctuated; and students had mixed views on whether the program had prepared them sufficiently with social and study skills. From this data, recommendations can be made for future summer programming, including maintaining academic rigor with hands-on and discussion-based learning; providing teachers that students can see as near-peer role models; and addressing students' anxieties and concerns about their academic careers.

Keywords: honors thesis
low-income students
qualitative study
summer learning
summer learning loss
summer learning programs
Stanford University Graduate School of Education
Thesis
Advisor: Langer-Osuna Jennifer M.
Willinsky John
O'Keeffe Jamie
From superteacher to 'bad teacher' [electronic resource] : goals 2000, comic book films, and changing depictions of educators in the movies

Since 1939, 46 eddies, or fictional movies about primary or secondary schooling that foreground a teacher, have been released in the United States. From the 1950s through the 1990s, eddies often featured two interconnected and dominant tropes: the separation of home and school, and a "superteacher, " or a dedicated educator who uses unconventional teaching methods. However, many of the eddies made after 2000 blur or wholly erase the boundary between home and school, and nearly half of the 15 eddies made after 2000 feature unsavory or morally ambiguous teacher protagonists. This dissertation explores the contexts surrounding the genre's shift in tropes, and asserts that changes in eddies coincide with broader changes within the film industry, as well as with changes in educational policy and rhetoric. Specifically, generic changes in eddies coincide with the rise of the comic book film in the early 2000s, and President Bill Clinton's 1994 Goals 2000: Educate America Act, through which the Clinton administration framed education reform as a systemic problem requiring federal interventions and gained the public's support for federally led reforms. By the early 2000s, caped crusaders had begun proving lucrative at the box office, and the federal government had gained unprecedented traction in schools. Concurrently, the cinematic teacher--with no mask, no cape, and no federal authority—was increasingly depicted as a drug addict, a coward, or a cheater who brought the dysfunction of her home life into the classroom.

Keywords: Education.
Advisor: Labaree David F.
McDermott Ray (Raymond Patrick)
Willinsky John
From thermal to stimulated emission of light [electronic resource]

This dissertation deals with two disparate regimes of light: Thermal emission of light from nanostructured and microstructured surfaces, and light emission and scattering from isolated quantum multi-level systems such as atoms or quantum dots. We show that wavelength-scale structuring of materials can lead to strong modification of light absorption and emission properties, and that such properties can lead to improvements in the efficiency of solar energy conversion and can enable passive cooling via emission of radiation even during the daytime hours. We also study the fully quantum-mechanical interaction of few-photon states with isolated quantum multi-level systems (emitters), whose physical manifestation can take the form of atoms, superconducting qubits, and quantum dots. Through this study we obtain analytical solutions to the propagation of photons through these important system. Specifically, we gain new insight into atom inversion, fluorescence quenching, two-photon state engineering, dissipation, and provide the first fully quantum mechanical description of stimulated emission in the most fundamental case of a single-photon, interacting with a single excited atom.

Keywords: Applied Physics.
Advisor: Fan Shanhui
Harris J. S. (James Stewart)
Mabuchi Hideo advisor. Thesis advisor
From tiger moms to effective teamwork [electronic resource] : how interdependent motivation can power action

In three separate but interrelated sets of studies of this dissertation research, I examine interdependent motivation—or action toward a goal that derives from the input of others. One factor that can facilitate interdependent motivation is an interdependent mindset, or understanding that others are part of the self. Part 1 examines how Asian American compared to European American high school students experience interdependent motivation from the input of close others, namely their mothers, and how interdependence can explain this motivation for Asian Americans. Part 2 examines how the construction of situations of parental influence in the U.S. and India can explain differences in interdependent motivation, and how people's interpretation of these situations reflect their interdependent and independent mindsets. Part 3 compares how Asian American and European American pairs of university students work together on a collaborative task of creative problem solving. It also examines whether manipulating mindsets can facilitate interdependent motivation. We show that people who are likely to have habitual interdependent mindsets—East Asian Americans, South Asians, and South Asian Americans—benefit from the input of others who they feel are a part of themselves and perform relatively well. In contrast, people who are likely to have habitual independent mindsets—European Americans—are more likely to experience others, even close others, as separate from themselves and have more difficulty the input of others to facilitate their performance. Together the three sets of studies have implications for why Tiger Mothers can motivate Asians but not European Americans, and why European Americans often struggle when tasks require collaboration.

Keywords: Psychology.
Advisor: Markus Hazel Rose primary advisor. Thesis advisor
Tsai Jeanne Ling primary advisor. Thesis advisor
Walton Gregory M. (Gregory Mariotti) primary advisor. Thesis advisor
Functional and structural diversity within the human dopamine system [electronic resource]

The mesencephalic dopamine system is essential for a number of basic neural processes, including reward learning, working memory, and motor control. Maladaptive dopamine functioning has been implicated in a number of psychiatric disorders ranging from addiction to impulse disorders and schizophrenia. Understanding the normal function of the dopamine system and its involvement in cognition and behavior is therefore critical for future advances in promoting mental health. Despite the diversity of functions it subserves, a predominant view has been that dopamine neurons are functionally homogeneous and uniformly broadcast reward-related signals as a population to target structures throughout the brain. The work presented here challenges this view by characterizing functional and structural heterogeneity within the dopamine system in humans. In particular, I show that the substantia nigra (SN) and ventral tegmental area (VTA) are activated by aversive events, which is explicitly at odds with the prevailing idea that dopamine neurons homogeneously encode reward prediction error. These regions exhibit differential patterns of functional connectivity during aversive processing, which suggests that they are components of distinct functional networks. I also identify structural diversity between the SN/VTA and striatum with diffusion-weighted imaging (DWI) and tractography methods. I show that diffusivity in the mesolimbic pathway, but not other nigrostrial pathways, is related to trait impulsiveness, which suggests that these pathways subserve distinct functionality. Collectively, this work suggests that there is functional heterogeneity within the dopamine system, and these functional differences are correlated with anatomically distinct white matter pathways.

Keywords: Psychology.
Advisor: McClure Samuel M. primary advisor. Thesis advisor
Dougherty Bob advisor. Thesis advisor
Wagner Anthony David advisor. Thesis advisor
Wandell Brian A. advisor. Thesis advisor
Functional consequences of cohesin complex mutations on normal and malignant hematopoiesis [electronic resource]

Recent studies have identified recurrent mutations in all components of the cohesin complex in acute myeloid leukemia and other myeloid malignancies, and, importantly, have shown these mutations to occur early in disease pathogenesis and in pre-leukemic hematopoietic stem cells. Here, we investigate the impact of these mutations on hematopoiesis and demonstrate that introduction of cohesin mutants into normal human hematopoietic stem and progenitor cells (HSPC) results in blocked differentiation and enforcement of stem cell programs both in vitro and in vivo. These effects were cell context dependent, restricted to immature HSPC populations. Cohesin mutants selectively increased chromatin accessibility and likelihood of occupancy at binding sites for transcription factors known to regulate HSPC including ERG, GATA2, and RUNX1 as measured by ATAC-Seq and ChIP-Seq. Furthermore, epistasis experiments showed that silencing of these transcription factors 2in which mutant cohesin impairs hematopoietic differentiation and aberrantly enforces stem cell programs through the modulation of HSPC chromatin accessibility and transcription factor activity.

Keywords: Cancer Biology.
Advisor: Majeti Ravindra
Chang Howard
Mitchell Beverly Eileen
Winslow Monte advisor. Thesis advisor
Functional genomics across scale [electronic resource] : from cell free nucleic acids to single chromosomes and single cell genomics

Incorporation of sequencing techniques into molecular biology studies has led to the scaling up of experimental approaches and the generation of "-omics" data types. These studies are driving the discovery of novel diagnostics and biomarkers that has the potential to deliver both preventive and therapeutic value. In this thesis, we explore the impact that the scale of starting material, spanning from nucleic acids in plasma to chromosomes and genome of single cells, has on functional genomics. We will also address the multidisciplinary approaches that integrate microfluidics, bioinformatics, and statistical models that are required to assess effectively the data generated from these ranges of starting material. The thesis will begin with a transcriptome-wide characterization of circulating cell free RNA in plasma. The presence of circulating nucleic acids from fetal sources being detectable in the plasma of pregnant woman has the obvious benefit of being a non-invasive diagnostic tool for fetal health. We used the high-throughput methods of microarrays and next-generation sequencing to characterize the global landscape of circulating RNA in cohorts of human subjects. Using bioinformatics approaches to focus on genes whose expression is highly specific to certain tissues, we were able to infer the relative contributions of these tissues towards circulating RNA and monitor changes in tissue development and health. The second part of the thesis will address the analytical framework of using sequenced reads from single chromosomes isolated using microfluidics to scaffold genomes during de novo assembly. Genomes assembled de novo from short reads are typically highly fragmented and lack chromosome scale contiguity. Here, we used microfluidics techniques to trap single chromosomes for sequencing, and used the sequenced reads from these chromosome preparations as a source of long range information in grouping scaffolds together as chromosomes. The concluding part of the thesis will be on the application of single cell genomics to dissect tumor heterogeneity. Substantial genomic heterogeneity occurs within a given tumor, and to fully understand that diversity requires the ability to perform genomics at single cell resolution. We performed targeted sequencing of a panel of single nucleotide variants (SNVs) and deletions in acute lymphoblastic leukemia (ALL) patients. By accurately segregating groups of co-occurring mutations into distinct clonal populations, we inferred the clonal architecture in these patients.

Keywords: Bioengineering.
Advisor: Quake Stephen Ronald primary advisor. Thesis advisor
Altman Russ advisor. Thesis advisor
Bejerano Gill
Covert Markus advisor. Thesis advisor
Functional map networks for the joint analysis of image and shape collections [electronic resource]

In many machine learning and computer vision problems, data are often easy and cheap to acquire but very expensive to label. For example, it is effortless to collect a large amount of images of the same object using image search engines, but annotating them about where the objects are costs much more work of a skilled human agent. If we can build relationships between data, abundant information can be transported from labeled ones to unlabeled ones. In our work, we use a novel representation of the relationships between images or shapes, called functional maps. Unlike point-based maps, functional maps build correspondences between functions over images or shapes based on their local properties. We also propose a functional map network to jointly analyze collections of images or shapes. Each image/shape is a node in the network and each edge connecting two images/shapes is associated with the map between them. Finally, we proposed three applications of the map network. First, given a collection of images sharing one similar object, segmentations are transferred among the images via functional maps, and the segmentation for the common object emerges if the map network is cycle-consistent. Second, we extend the functional map networks to handle multi-class joint image segmentation, which is more challenging and requires partial similarity constraint because each common object may only appear in a subset of images. Third, we build a functional map network among 3D shapes for joint shape segmentation. Maps between shapes are regularized and improved by partial cycle-consistency and the shared structure across the collection is discovered, corresponding to the meaningful shape parts. For all applications, experimental results on various benchmark data sets are provided to demonstrate the effectiveness of the proposed approaches.

Keywords: Electrical Engineering.
Advisor: Guibas Leonidas J. primary advisor. Thesis advisor
Girod Bernd advisor. Thesis advisor
Leskovec Jurij advisor. Thesis advisor
Functional Properties of the Hippocampus in Siberian Hamsters: Illuminating the Relationship between Circadian Rhythms and Learning

Circadian rhythms comprise a recurring pattern of behavioral and biological processes organized by a central pacemaker, the suprachiasmatic nucleus (SCN). Abnormal activity of this brain structure is associated with impaired hippocampal-dependent memory in both humans and animal models, but the process by which this occurs is unknown. Therefore, we used extracellular field potential recording techniques to assess the functional properties of the isolated hippocampus in circadian entrained and arrhythmic Siberian hamsters. This study finds evidence for plastic change in the hippocampus as a result of chronic non-circadian SCN activity. Input/output curves, paired-pulse tests, and induction of long-term potentiation were used to determine that intrinsic hippocampal circuitry and capacity for plasticity are conserved. Further examination in the presence of carbachol establishes that arrhythmia induces a change in cholinergic modulation of dentate gyrus function. For granule cells activated by perforant path stimulation, carbachol effected less depression of the population spike, and less paired-pulse facilitation, in arrhythmic animals compared to controls. Our findings are consistent with the hypothesis that a non-circadian firing pattern of SCN neurons could over-inhibit the medial septum, with learning deficits arising from attenuated septohippocampal signaling. Mitigating the cognitive detriment associated with circadian disruption is enormously relevant to shift workers, transmeridian flight crews, dementia patients, and the aging. Our model has high translational value and the present findings point to areas for pharmacological intervention as a therapeutic strategy. The relationships established here bring us closer to resolving learning deficits associated with circadian decline, and to understanding memory processes more broadly.

Keywords:  Department of Biology
Biology
Circadian rhythm
Dentate gyrus
Electrophysiology
Hippocampus
Memory
Plasticity
Siberian hamster
Stanford University
Thesis
Advisor: Madison Daniel
Fernald Russell
Functionary [electronic resource] : learning to communicate mathematically in online environments

This study posed and studied a solution to a prevailing tension in online education: the online medium is fundamentally connective and yet students often report feelings of social isolation. The study compared two online interventions -- both into a student's fluency in the language of functions and graphs, a major focus of a student's transition from arithmetic to algebra. The "traditional" intervention had students perform auto-graded recall-based work common to current online education platforms, and experience didactic instruction. The "Functionary" intervention, meanwhile, had students perform communicative work, taking turns drawing and describing a graph with an online partner, and experience instruction in response to their need. These interventions were studied using a pretest-posttest 3 x 2 factorial design with three levels of the between-subject condition variable ("traditional, " "Functionary, " and "null") and two levels of the within-subject time variable ("pre" and "post"). Students were counterbalanced between conditions according to their pretest scores, which assessed their proficiency in various elements of precision in describing and drawing graphs. An analysis of variance determined that students perceived the Functionary intervention to be significantly more social than the traditional intervention. In the aggregate, both the traditional and Functionary interventions learned significant amounts, with neither learning significantly more than the other. An analysis of student descriptions of a graph revealed that the Functionary condition saw a significant increase over time in the number of students who used a correct coordinate. The other conditions didn't see the same gains. Aspects of Functionary's design may therefore be useful to instructors and instructional designers in both online and face-to-face classrooms. This study also revealed the challenges students faced taking up conventional mathematical notation, adding to our pedagogical content knowledge of the language of functions and graphs. Implications for instructional designers, math teachers, and math education researchers are discussed.

Keywords: Education.
Advisor: Boaler Jo
Grossman Pamela L. (Pamela Lynn)
Schwartz Dan
Wineburg Samuel S. advisor. Thesis advisor
Gender segregation in the workforce and the role of worker preferences [electronic resource]

We use matched employer-employee data from Census's Longitudinal Employer-Household Dynamics (LEHD) database to uncover substantial shifts in the distribution of gender shares across firms in the U.S. between 1992 and 2010. This is despite our finding that indices of gender segregation declined only slightly over this period. Systematic segregation (segregation above what would be expected from random allocations of workers to firms) is shown to exist. Most, but not all, of this is found to be attributable to sorting across industries. Estimates of systematic segregation are shown to be sensitive to the choice of reference group used to normalize segregation measures, demonstrating that the extent of systematic segregation may have been overestimated in previous studies. We also provide a model in which profit maximizing firms have an incentive to hire workforces with a gender balance that is desirable to future employees whom they would like to hire. An analysis of hiring and separations patterns suggests that firms hire and workers separate in such a way that a steady state share of workers is maintained, but that these steady states differ by firm. An examination of the probability with which individual workers separate uncovers the counter-intuitive finding that the greater the share of one's own gender within the firm, the more likely men and women are to separate. Alternative theories to explain this finding are discussed.

Keywords: Business.
Advisor: Lazear Edward P. primary advisor. Thesis advisor
Benkard C. Lanier advisor. Thesis advisor
Oyer Paul E. (Paul Edward)