VictorJuiz/thesis huggingface dataset:
Causal Distillation for Language Models
Keywords: Natural language processing (Computer science)
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Thesis

Distillation efforts have led to language models that are more compact and efficient without serious drops in performance. The standard approach to distillation trains a student model against two objectives: a task-specific objective (e.g., language modeling) and an imitation objective that encourages the hidden states of the student model to be similar to those of the larger teacher model. In this paper, we show that it is beneficial to augment distillation with a third objective that encourages the student to imitate the causal computation process of the teacher through interchange intervention training(IIT). IIT pushes the student model to become a causal abstraction of the teacher model - a simpler model with the same causal structure. IIT is fully differentiable, easily implemented, and combines flexibly with other objectives. Compared with standard distillation of BERT, distillation via IIT results in lower perplexity on Wikipedia (masked language modeling) and marked improvements on the GLUE benchmark (natural language understanding), SQuAD (question answering), and CoNLL-2003 (named entity recognition).
Causal Structure and Horizon Stability of Black Holes in Curved Spacetimes
Keywords: Physics
de Sitter
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Thesis

The causal structure of spacetime encodes basic information about how different events influence each other, allowing us to better understand our universe. In this thesis, we study the causal structure of Schwarzschild and Reissner–Nordström (RN) black holes in de Sitter (dS) and Anti-de Sitter (AdS) spacetimes. We find that the inner horizon of RN black holes is highly unstable and analyze how its conformal diagram evolves from the Schwarzschild conformal diagram. We illustrate the Penrose diagrams for uncharged and charged black holes within the constant curvature spacetimes and analyze their properties. We examine the smallest black holes in dS, finding their probability of nucleation, as well as the largest dS black holes, which lead to the Nariai solution. We demonstrate two methods for finding the Nariai geometry of RNdS, with the caveat that the inner horizon remains highly unstable. Finally, we find a parallel between gravitational and matrix methods, confirming that the underlying holographic description of dS relies on matrix quantum mechanics.
Causes and consequences of damaging mutation accumulation in cancer
Keywords: Biology.

Cancer develops from an accumulation of somatic mutations over time. While a small subset of these mutations contribute directly to tumor progression, the vast majority of the remaining mutations that accrue in cancer - which can often reach up to thousands and even tens of thousands - are thought to have little functional relevance to tumor growth. However, a growing body of literature also supports that many of these mutations could instead be damaging to cancers - potentially through gene loss of function, immune surveillance, or induction of protein misfolding stress. This dissertation explores the causes and consequences of damaging mutation accumulation in cancer in two parts. First, I use a combination of evolutionary simulations from population genetics modeling and analysis of empirical cancer sequencing data to demonstrate that Hill-Robertson interference causes negative selection to become rapidly inefficient in most cancers. I find that low mutational burden tumors, which experience weak linkage effects, demonstrate strong patterns of positive and negative selection, while high mutational burden tumors, which endure strong linkage effects between mutations, exhibit patterns of neutral tumor evolution. Collectively, these results suggest that the vast majority of tumors (> 95%) are accumulating damaging mutations which are not being removed. Second, I explore how tumors can successfully survive the deleterious consequences of this damaging mutation accumulation. I use functional genomics and statistical analysis to examine how tumors phenotypically respond to damaging mutation accumulation by examining changes in gene expression. I combine this analysis with loss-of-function experiments in cancer cell lines to demonstrate that high mutational burden cancer cell lines maintain their viability by utilizing mechanisms that largely mitigate and prevent protein misfolding stress. Ultimately, these results elucidate potential mechanisms and physiological consequences of inefficient negative selection in somatic evolution, and add to potential therapeutics that can be applied to target high mutational load tumors
Cell Surface Sialylation Modulates Neuronal Excitability and Network Integration
Keywords:  Department of Biology
Biology
glycocalyx
sialic acid
electrophysiology
microglia
neuroinflammation
voltage imaging
Stanford ChEM-H
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Thesis

Neurons are coated in a thick layer of glycoproteins and glycolipids called the glycocalyx. The neuronal glycocalyx is highly sialylated, and depletion of these surface sialosides is associated with neuroinflammatory disorders through an uncharacterized mechanism. The basic role of the glycocalyx in affecting electrical activity in neurons also remains unknown despite studies demonstrating that global desialylation leads to a reduction in action potential firing rate. This is due in part to the dual technical challenge of manipulating glycans in a subpopulation-specific manner and measuring the internal electrophysiology of several neurons simultaneously. To meet these challenges, this work aims to develop a voltage imaging platform to investigate how network activity in mouse neuron cultures change in response to linkage-specific sialoside removal. We also characterize a pathway by which activated microglia, the resident phagocytes of the brain, alter the functional connectivity of nearby neuronal networks via secretion of extracellular vesicle-bound Neuraminidase 3 (Neu3). Altogether, these results reveal that distinct subpopulations of sialosides play critical roles in network activity and uncover a new molecular mechanism by which microglia may influence neuronal electrophysiology. These discoveries present Neu3 as a potential therapeutic target for neuroinflammatory conditions and demonstrate the importance of glycosylation in neuronal communication.
Centering the Voices of First-Generation Immigrant Youth: Multilingual NLP Methods in the Translanguaging Context
Keywords: Computer Science
Translanguaging (Linguistics)
Education
Natural language processing (Computer science)
Multilingualism
Multilingualism in children
Transcription
Interviewing
Spanish language
Native language and education
Children of immigrants > Attitudes
Children of immigrants > Education (Elementary)
Zapotec language > Study and teaching (Elementary) > Spanish speakers
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Thesis

Translanguaging, or the act of using multiple languages within a speech utterance (e.g., sentence and/or word), is a global phenomenon for multilingual communities. In the context of the United States, translanguaging is a frequent occurrence among Latin American immigrant communities. While there are several large multilingual models such as XLM-RoBERTa and multilingual BERT, these models have been trained on and evaluated with parallel monolingual data. Upholding parallel monolingualism as the standard definition of multilingualism erases the language practices of many communities of color, including Latin American immigrants in the United States. The consequences are even worse for racialized children in the schooling system who may be labeled as English Language Learners (ELL) for the very notion that their fluency in multiple languages must be separate and apart. This ELL label has immediate consequences regarding future classes they have access to, as well as their own sentiment around and through their language practices. Moreover, there is currently no labeled NLP dataset that includes translanguaging between Spanish and English for the task of sentiment analysis. In collaboration with the Stanford Graduate School of Education, this research aims to center the voices of first-generation Indigenous Latin American immigrant students in NLP research through the task of sentiment analysis. Specifically, this thesis constructs the Interview Transcripts Dataset, an innovate trilingual dataset composed of transcribed interview data that contain instances of translanguaging, as well as a framework for developing these datasets. The findings of this project provide a promising starting point, and emphasize the need to leverage current pre-trained models on similar domains as well as develop a more robust large-scale dataset that centers translanguaging. Ultimately, translanguaging remains an open problem in NLP research tasks.
Challenging the State: Western European Regionalism in the Era of Financial Crisis
Keywords: Law
Regionalism
Nationalism
Global Financial Crisis (2008-2009)
Economic Voting
Electoral Manifestos
Western Europe
Spain
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Thesis

The Global Financial Crisis and its aftershocks have substantially altered the Western European political landscape. But while the literature has extensively focused on the impacts of the economic hardship on traditional party competition, it has often failed to consider the center-periphery dimension. This thesis addresses both the demand for and supply of regionalist ideologies during the crisis. Using an original dataset containing 8 countries, 35 regions, and 128 regionalist parties, it finds that voters did not increase their support for regionalist parties during the crisis and may have even turned their backs on these political actors. In addition, I consider the reactions of regionalist parties in three Spanish autonomous communities, Catalonia, the Basque Country, and Galicia, to the crisis. I find evidence of regionalist mobilization on the issue and even some indications of radicalization of regionalist demands. Taken together, these findings raise interesting implications for the impacts of the financial crisis and the interaction between economic indicators, party competition, and voting patterns.
Chance Me!: Competition Culture in Online College Admission Forums
Keywords: Universities and colleges > Admission
Education, Higher
Electronic discussion groups
Reddit
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Thesis

It is no secret that the attainment of a college degree is one of the single most impactful choices in one’s life that has the ability to positively impact lifetime financial and social status. As the technological landscape of the workforce continues to develop exponentially and the demand for qualified employees who can meet and adapt to modern challenges—i.e. college graduates—increases, students are responding to this pressure, enrolling in record numbers year after year. While access to entry into and information about these institutions has been historically stratified by class, race, gender, and other identities, the proliferation of the participatory internet has given rise to a host of readily accessible resources and tools for all students. Discussions about college pursuit have historically been internal amongst schools, education professionals, and families; however, online admissions communities serve as sites where all members of the college application process co-engage with one another, shedding light on their interpretation of the qualities that warrant admission into institutions of higher education. While literature exists about the influences and motivations that allow students of all backgrounds to pursue college, this thesis, through the textual analysis of content submitted to popular college admissions online forums, aims to explicate the nature of admissions discussions in novel spaces online, against the backdrop of an intensely competitive culture. Despite their neutral and beneficial flagging, I find that messages within these platforms can contribute to and reinforce legacies of stratification and exclusion in education. Forum users and moderators can be more active in critically engaging with the messages circulated in these spaces and the systems they serve to benefit.
Changing the meaning of motherhood : gender, family, and politics in Côte d'Ivoire, 1893-1983
Keywords: History.

Queen mothers and women warriors figure prominently in African tradition. In modern African political systems, however, women's influence often appears marginal. This dissertation examines this apparent gulf between "tradition" and "modernity" by tracing the history of changing meanings of motherhood in Côte d'Ivoire in the twentieth century. Motherhood has long been the source of moral and political authority for women in African societies. Beyond connotations of reproduction and caregiving, African motherhood is a social institution that encapsulates women's political, economic, and ritual responsibilities in their communities. In excavating the relationship between motherhood and politics, this study demonstrates how maternal authority emerged as both a site of female power and a locus of political contestation in Côte d'Ivoire. Over the course of the twentieth century, motherhood empowered women to make potent political claims, most notably in resistance to colonial rule. But as colonial officials, missionaries, and Ivoirian leaders vied for power against a backdrop of turbulent political change, meanings of motherhood began to shift. From public mothers, to domestic housewives, to citizen-mothers, the ideal Ivoirienne took on new forms as women and men debated whether to harness or suppress women's authority. As women sought recourse in public motherhood, those opposed to or threatened by their action leveraged changing meanings of motherhood in order to coopt their militancy. Through careful readings of colonial archives, interviews, and news media, this dissertation follows women as they negotiated and resisted these conflicting imperatives
Characterizing the greenhouse gas impacts of natural gas resources : a life-cycle assessment and evaluation of new aerial technologies
Keywords: Energy Resources Engineering.

Greenhouse gas emissions from oil and natural gas production will need to be reduced as society transitions to a renewable energy economy and production declines. However, the energy system has significant inertia: even in a world meeting 1.5 ºC of warming targets, natural gas consumption is estimated to be 50% of 2020 levels in 2050. Previous research has shown that significant differences can exist in production emissions between different fossil fuel resources, and thus it is critical to develop metrics to minimize emissions during the energy transition. Based on an updated synthesis of measurements from component-level field studies, in Chapter 2 we develop a new inventory-based model for CH4 emissions, for the production-segment only, that agrees within error with recent syntheses of site-level field studies and allows for isolation of equipment-level contributions. We find that unintentional emissions from liquid storage tanks and other equipment leaks are the largest contributors to divergence with the US EPA Greenhouse Gas Inventory. If our proposed method were adopted in the United States and other jurisdictions, inventory estimates could better guide CH4 mitigation policy priorities. In Chapter 3, we calculate life-cycle emissions for natural gas production in the United States at the producing-county level. Results are aggregated and reported by basin. The bottom-up model from Chapter 2 is combined with an open-source life-cycle emissions calculator. We find that in both gas and oil rich basins, carbon intensity of the produced gas is dominated by methane emissions in all cases except when there is exceptionally high flaring. For dry gas fields (such as the Appalachian basin), carbon intensity is dominated by equipment leaks and pneumatic device venting. For mixed and oil dominant fields (such as the Williston basin), carbon intensity of the produced gas is dominated by tank emissions and flaring. We demonstrate that allocation choices (i.e., whether particular emission sources are assigned to oil and/or gas) have a large impact on the resulting carbon intensity. In Chapter 4, we perform a single-blind evaluation of the quantification capabilities of three aerial, airplane-based technologies (Bridger's Gas Mapping LiDAR, Carbon Mapper's Global Airborne Observatory, and GHGSat-AV) in blinded, controlled release trials with a focus on large emitters (10-2,000+ kg hr-1 CH4). In two 2021 campaigns, metered natural gas was released concurrently with overpasses by the tested technologies. Results were submitted by operators in a three-stage unblinding process. Detection rates of non-zero releases were 100%, 85%, and 86% for Bridger, Carbon Mapper, and GHGSat, respectively. The teams report parity slopes of 0.35 to 1.06, with R2 values of 0.35-0.78. We discuss implications for measurement methods and practical emissions reductions
Characterizing the mechanism of sensorial perception of biomechanical changes in human skin
Keywords: Mechanical Engineering.

The mechanism by which humans perceive biomechanical changes in the outer layer of their skin, the stratum corneum (SC), has not been previously described. The SC, consisting of a network of lipids and corneocytes, interacts with the external environment and its mechanical behavior is sensitive to these interactions. Solar damage, low relative humidity, and damaging topical treatments cause water loss and shrinkage of the SC. Volume changes in the SC result in the development of tensile stresses in the SC, which are perceived as skin tightness. This dissertation first elucidates the mechanism by which SC stresses are transduced by cutaneous mechanoreceptors and their corresponding neurons by demonstrating computationally how stresses in the SC cause the propagation of strains to underlying skin where cutaneous mechanoreceptors reside. A relationship between strain and firing rate of slowly adapting type I (SAI) neurons is used to predict neural activity from computed strains in various skin morphologies. The effects of SC stresses induced by cleansers and moisturizers, which are quantified experimentally, are simulated to predict neural activity specific to each cleanser and moisturizer. A strong linear trend is observed between predicted SAI activity from each topical treatment and skin tightness perception scores reported in a large clinical survey. Next, this dissertation explores the effect of skin layer mechanical properties, skin layer thicknesses, and skin surface topographies on the magnitudes of computed SAI neuron firing rates. Each of these parameters is found to influence the predicted SAI neuron firing rates. Additionally, parameters affecting sensitivity in SAI neuron firing rates to distinct SC contraction amounts are investigated. The topography of the skin surface was found to be especially influential in these studies of sensitivity. Finally, this dissertation evaluates whether it is expected that an individual would maintain the ability to distinguish the unique effects of cleanser and moisturizer treatments when a full thickness skin tensile strain is combined with the SC contractions induced by the topical treatments. This is studied in three distinct skin regions, and it is concluded that the perceptual acuity would be maintained with a stretching of the skin for skin sections with a topography that is not relatively flat. This additional scenario strengthens the conclusion that individuals are capable of perceiving biomechanical changes in the SC through activation of SAI neurons. Overall, this dissertation details the mechanism by which mechanical changes in the SC are perceived and describes relevant parameters for this perception. This provides novel information for the perception of skin tightness, which is not characterized in detail in literature
Charitable Giving and the Housing Market after Hurricane Sandy in New York City
Keywords: Housing
Climatic changes
Flood damage
Hurricane Sandy (2012)
Elections
Economics
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Thesis

Extreme weather events often have consequences not only economically and financially,
but also in terms of more complex social changes. How people respond to
disasters in their risk-taking, prosociality, and other social behaviors dependent on
group membership is stilla a somewhat open question. This paper explores changes
in charitable giving among New York area neighborhoods with significant exposure
to flood damages from Hurricane Sandy after the storm. While the existence of any
major shift in giving levels is unlikely, there is the possibility of a differential effect
between Republicans and Democrats, with the former increasing contributions while
the latter see no change. Additionally, I provide further evidence to suggest a strong
price discount on single family homes in the Sandy flood zone following the hurricane,
but do not find evidence of changes in rents.
Chiral algebras in physics and mathematics
Keywords: Physics.

Chiral algebras and vertex algebras are ubiquitous structures in physics and mathematics. They form the symmetry algebras of two-dimensional conformal field theories, they describe the universal long-distance physics of statistical systems near second order phase transitions, they arise on the world-sheets of string theories, they encode information about protected sectors in higher-dimensional quantum field theories, and they constitute an important mathematical bridge between various subjects in pure mathematics, like number theory and finite group theory. This thesis collects a few vignettes from my research on chiral algebras: it explores classification, exceptional objects, and some hints from mathematics that there are beautiful new structures waiting to be discovered
Chromatin activity identifies differential gene regulation across human ancestries
Keywords: Biology.

Current evidence suggests that cis-regulatory elements controlling gene expression may be the predominant target of natural selection in humans and other species. Detecting selection acting on these elements is critical to understanding evolution but remains challenging because we do not know which mutations will affect gene regulation. To address this, I co-devised an approach to search for lineage-specific selection on three critical steps in transcriptional regulation: chromatin activity, transcription factor binding, and chromosomal looping. Applying this approach to lymphoblastoid cells from 831 individuals of either European or African descent, I find strong signals of differential chromatin activity linked to gene expression differences between ancestries in numerous contexts, but no evidence of functional differences in chromosomal looping. Moreover, I show that enhancers rather than promoters display the strongest signs of selection associated with sites of differential transcription factor binding. Overall, this work indicates that some cis-regulatory adaptation may be more easily detected at the level of chromatin than DNA sequence. This thesis provides a vast resource of genomic interaction data from diverse human populations and establishes a novel selection test that will benefit future study of regulatory evolution in humans and other species