VictorJuiz/thesis huggingface dataset:
Unsupervised Text Generation and its Application to News Interfaces

Recent progress in automated text generation relies predominantly on the use of large datasets, sometimes requiring millions of examples for each application setting. In the first part of this thesis, we advance the field by developing novel text generation methods that balance the goals of fluency, consistency, and relevancy without requiring any training data. We achieve this objective on tasks such as text summarization and simplification by directly defining a multi-component reward, and training text generators to optimize this objective. The novel approaches that we introduce perform better than all existing unsupervised approaches and in many cases outperform those that rely on large datasets./nThe second part of the thesis incorporates text generation into interfaces to help news readers navigate complex, unfolding news topics. We build a novel representation of news stories at scale and integrate new summarization, question generation and question answering modules into a chatbot and an automated interactive podcast. Human evaluations confirm that even though imperfect systems introduce friction for the user, they can serve as powerful tools to stimulate reader curiosity and help readers dive deeper into unfolding topics.

Advisor: Hearst, Marti A
Canny, John F
Molecular Insight into Nonlinear Transport Behaviors

Nonlinear response occurs naturally when a strong perturbation takes a system far from equilibrium. Despite of its omnipresence in nanoscale systems, it is difficult to predict in a general and efficient way. Here we introduce a way to compute arbitrarily high order transport coefficients of stochastic systems, using the framework of large deviation theory. Leveraging time reversibility in the microscopic dynamics, we relate nonlinear response to equilibrium multi-time correlation functions among both time reversal symmetric and asymmetric observables, which can be evaluated from derivatives of large deviation functions. This connection establishes a thermodynamic-like relation for nonequilibrium response and provides a practical route to its evaluation, as large deviation functions are amenable to importance sampling. Two important features of this new method are highlighted in this work. Firstly, its efficiency is demonstrated by comparison with direct nonequilibrium simulations, the Green-Kubo method, and brute-force evaluations of the higher order correlation functions. Secondly, its utility in generating molecular insight is showcased in a couple of examples, including the field-dependent conductivities in electrolyte solutions, and thermal rectification in nonlinear lattices./nIn addition to the methodology development, we also explore how molecular insight into nonlinear transport behaviors can provide us with design principles for nanoscale devices. This is done by introducing a thermodynamically consistent, minimal stochastic model for complementary logic gates built with field-effect transistors. We characterize the performance of such gates with tools from information theory and study the interplay between accuracy, speed, and dissipation of computations. This work provides a platform to study design principles for low dissipation computing devices harnessing the theoretical developments in stochastic thermodynamics.

Advisor: Limmer, David T.
An inhibitory brainstem input to dopamine neurons encodes nicotine aversion

Decades of research implicate dopamine neurons as the brain’s center for reward, which drugs of abuse “hijack” to cause addiction. Indeed, nicotine acts on nicotinic acetylcholine receptors on ventral tegmental area dopamine neurons to increase dopamine release and consequently, feelings of reward and pleasure. However, recent research has revealed that a subset of dopamine neurons signal aversion, contrary to the popular belief that dopamine neurons solely mediate reward. At high doses, nicotine is aversive, and understanding how this dose-dependent switch in valence may lead to novel insights for treating nicotine addiction. To dissect the neural circuits that mediate nicotine’s aversive effects, I performed a detailed anatomical, electrophysiological, and behavioral investigation on VTA dopamine neurons, their inputs from the brainstem, and outputs to the nucleus accumbens. With in vivo calcium imaging, I demonstrate that a high dose of nicotine encodes aversion both by suppressing DA release in the canonical reward-signaling lateral mesolimbic pathway and by increasing DA release in the aversion-signaling medial pathway. I introduce an inhibitory input from the brainstem’s laterodorsal tegmentum (LDT) to the VTA that drives aversive behaviors when stimulated and is activated by an aversive dose of nicotine./nImportantly, when this LDT GABA population is ablated, I observed blunted DA release patterns in the nucleus accumbens in response to aversive nicotine compared to animals with an intact LDT. Together, this work provides novel insights into the circuit mechanisms of how a high dose of nicotine may induce aversion by both increasing aversion signaling and reducing reward signaling, and that an inhibitory input from the brainstem may be an important modulator of the mesolimbic pathway in the context of nicotine response.

Advisor: Lammel, Stephan
Stone soup: digesting the epigenome through the window of chromatin accessibility

In this thesis, we leverage epigenetic datasets that provide a limited view of the epigenome to understand changes in transcriptional activity across a diverse set of cellular contexts. It is often the case that we would like to learn about an epigenome that is partially characterized by different types of experiments. In our case, the epigenome is often partially characterized using assays that measure chromatin accessibility. In the European fable of Stone Soup, a hungry traveler convinces a village to give them ingredients to make soup; however, all the traveler has available to them are stones. Thus, the stones provide a basis for the soup, as it brings in other crucial ingredients to design a hearty meal. In this thesis, we leverage chromatin accessibility as our stone: the primary ingredient that we leverage to gather a more complete view of the epigenome./nIn the first part of this work, we explore methods designed to increase our understanding of the epigenome, primarily through the identification of genomic locations that are crucial to regulatory activity, including binding sites of transcription factors and modification of histone tails. In particular, we introduce two methods designed to predict such epigenetic events. While the first of these methods is designed to predict epigenetic events from DNA sequence alone, the second method improves upon existing methodology to predict epigenetic events in novel cellular contexts using chromatin accessibility as the primary indicator of context specificity./nIn the second part of this work, we leverage chromatin accessibility, as well as additional transcriptomic epigenetic information, to characterize changes between cellular contexts for various applications. In the first application, we leverage chromatin accessibility and transcriptomics to understand how CD8(+) T cells change after reprogramming cells to a pluripotent state, and how maintenance of the T cell phenotype can ultimately effect outcomes for cancer immunotherapy. Finally, we explore the role of the transcription factor, MORC3, in modulation of the accessible genome in the innate immune system. Together, these applications demonstrate how chromatin accessibility can be leveraged to characterize changes in regulatory activity and gain a more complete understanding of the epigenome.

Advisor: Yosef, Nir
Joseph, Anthony D
Observation and measurement of photon-induced WW production in pp collisions at sqrt(s) = 13 TeV using the ATLAS detector

While CERN's Large Hadron Collider (LHC) is primarily a high-energy proton or heavy ion collider, it can also be used as a high-energy photon collider. This is possible because the highly boosted electromagnetic fields surrounding the circulating ions behaves like a flux of photons. A search for the process $\gamma\gamma\rightarrow W^{+}W^{-}$ was conducted in the 139 fb$^{-1}$ of proton-proton collision data collected in LHC Run 2 between 2015 and 2018. Events were tagged using the $e^{\pm}\nu\mu^{\mp}\nu$ decay channel of the $W^{+}W^{-}$ system, where the event was determined to be photon-induced due to a lack of charged hadronic activity near the leptons. The process was observed with a significance of 8.4$\sigma$, with a measured fiducial cross section of $3.13 \pm 0.31~(\mathrm{stat.}) \pm 0.28~(\mathrm{syst.})~\mathrm{fb}$. This fiducial cross-section agrees with Standard Model expectations. A strategy to improve the \yyWW~measurement with the use of a novel low-\pt~tracking algorithm in ATLAS is also presented. The use of low-\pt~tracks improves the rejection of QCD-induced backgrounds to \yyWW, leading to an expected increase in statistical significance of 3--4$\sigma$.

Advisor: Garcia-Sciveres, Maurice
Shapiro, Marjorie D
Japan and Germany after 1945: Parties, Politicians and World War Two Legacies

How did the Japanese and German politicians approach their nations’ problematic pasts? Whatroles did the Japan Socialist Party (JSP) and the Social Democratic Party (SDP) of Germany play in the memory and reconciliation politics of their countries? Why did their approaches differ? This dissertation provides answers to these questions. In the first chapter, I investigate how the JSP approached the reparations agreements with Southeast Asia in the 1950s. By studying Diet debates and controversies surrounding the negotiations of these treaties, I show that the Japanese Socialists exhibited much less contrition and understanding of Asian grievances than expected. In the second chapter, by contrast, I demonstrate the critical role of the German SPD in bringing about the Luxembourg Treaty – a reparations agreement between West Germany and Israel – and facilitating reconciliation with the Jewish nation. In the final chapter I analyze how the SPD approached the problem of Nazi criminals in the postwar era. Through the analysis of court trials and parliamentary debates, I show that the SPD pushed consistently for greater acceptance of the nation’s past mistakes and the need for their atonement – including judicial prosecution of the guilty. All chapters of this dissertation demonstrate that the German and Japanese Socialists played an important role in the memory making of their nations. Despite similar ideological outlooks and the positions they occupied in their domestic political systems, however, their approaches to WWII legacies differed. I argue that the reason for this lies in the different carryovers that the leftist movements brought with them from the pre-1945 era. Through the study of biographies of individual politicians, I show that the SPD’s prewar history of resistance, imprisonment, and exile significantly impacted its thinking about memory and reconciliation politics in the postwar period. By the same token, the lack thereof in the Japanese Socialist camp had serious implications for its behavior after the war. Overall, this dissertation illustrates that if we want to understand the behavior of political elites particularly in the field of public memory making, we need to know who these elites were, what they did in their past and what beliefs they held.

Advisor: Vogel, Steven K
Realization of a Fully Integrated Electronic-Photonic Sensor-Receiver Array for Endoscopic Ultrasound

Ultrasound imaging remains an indispensable tool in numerous medical disciplines ranging from oncology to cardiology and from dermatology to ophthalmology. Imagers employing piezoelectric and capacitive micromachined transducers have long been the golden standard when it comes to traditional ultrasonography procedures such as abdominal, pelvic or obstetric scans. However, when used in endoscopic, intravascular, and catheterized applications, traditional receiver implementations have demonstrated serious shortcomings in terms of power dissipation and achieved form factor./nThe focus of this thesis is on the development and realization of an electronic-photonic ultrasound receiver system capable of tackling modern miniaturized endoscopic probe specifications. It begins with an overview of the existing electrical and optical ultrasound imaging technologies, which spotlights the need for an alternative approach to endoscopic ultrasound sensing and proposes a electronic-photonic array system based on micro-ring resonator (MRR) sensors as a promising candidate. Subsequently, the operating principle of MRR ultrasound sensing is presented, accompanied by theoretical analysis and finite element model (FEM) simulations of the transduction mechanisms. The developed theory is backed by proof-of-concept experimental results. The initial analysis is followed by the design and fabrication of a first-of-its-kind ultrasound receiver array on a silicon photonic chip with highly sensitive, micro-scale optical MRR sensors in its core. Such a system can be ultra-low power and size, ensuring safe operation inside the human body without sacrificing key system attributes, such as image resolution and system bandwidth. Configured in 2-D beamforming arrays of thousands of elements, these optical sensors, can perform real-time, 3-D imaging and pave the way towards miniaturized optical ultrasonic reception probes with form factors below 5mm^3, compliant to modern endoscopic probe specifications. After presenting measurement results of this electronic-photonic system-on-chip (EPSoC) prototype, the thesis discusses architectures that will further enhance the overall system sensitivity through the use of coherent detection and higher quality factor MRRs.

Advisor: Stojanović, Vladimir
Interrogating Genetic Networks Using Barcoded Expression Reporters

Systematically profiling the effects of genetic perturbations is a powerful approach that has revealed the molecular basis for a wide range of biological phenomena. The simple, programmable DNA recognition of CRISPR-Cas9 enables genome-wide genetic analysis in human cells and many other systems. Cas9 is guided by a short RNA to a complementary sequence in the genome, where it can introduce mutations or alter gene expression. Pooled libraries of guide RNAs (gRNAs) that individually target each gene in the genome allow us to introduce genetic perturbations systematically into a population of cells. A key challenge is measuring the phenotypic effects caused by individual guides in these pooled libraries and linking these phenotypes back to the associated gRNA, thereby finding the gene that is responsible. Gene expression changes provide a clear and sensitive phenotypic measure for many cellular processes. We sought a general approach to profile how the expression of a particular gene of interest changed when other genes were perturbed. We began with a library of gRNAs, each disrupting one gene, and linked these guides with an expression reporter containing a guide-specific nucleotide barcode. gRNAs that alter reporter expression will change the abundance of the expressed RNA barcode specifically associated with that guide. Deep sequencing of these expressed barcodes quantifies each of these guide-specific reporter expression effects individually within a pooled, complex population. We have implemented this strategy by combining CRISPR interference (CRISPRi) with barcoded expression reporter sequencing (CiBER-seq). CiBER-seq profiling in yeast recapitulated known regulation across a range of promoters. Notably, interrogation of the integrated stress response (ISR) revealed both well-studied and uncharacterized modes of regulation. While uncharged tRNAs activated the ISR, tRNA insufficiency also activated the reporter, independent of the uncharged tRNA sensor. By uncovering alternate triggers for ISR activation, we illustrate how precise, comprehensive CiBER-seq profiling provides a powerful and broadly applicable tool for dissecting genetic networks. We extend the CiBER-seq paradigm to interrogate mammalian systems and to explore new protein-centric biological questions.

Advisor: Ingolia, Nicholas T
She Got Game: A Participatory Action Research Evaluation of Intersectional Surveillance in Collegiate Women's Basketball

This dissertation is a study of agency and liberatory practices for Black women’s basketball players within a holistically surveilled, predominantly White institution (PWI). Central to this study is the exploration of the dynamics surrounding Black labor in sport, particularly how the regulation and confinement of the body, mind, and spirit of Black student athletes allows for their continued exploitation by the institution of sport in U.S. higher education. I use Afrocentric feminist epistemology to design and execute a participatory study that flips the proverbial script on student athlete research: empowering Black student athletes to critically evaluate their own lived experiences while simultaneously exploring ways of disrupting the tools of regulation currently confining their agency and autonomy. In doing so, this dissertation highlights both how the regulation and control of Black female student athletes is inextricably linked to power, race and gender, and identifies where we can collectively build towards increased freedoms./nI built the participatory action research (PAR) methodology utilized in this study upon the conceptual intersections of Black feminisms and surveillance studies. As such, I also leveraged the site of data collection was also leveraged as a space for participants to identify opportunities to secure and exercise agency and bodily autonomy in real time—a process fellow PAR scholars refer to as the design serving as the intervention. I argue that by empowering Black women to authentically tell their own narratives we can disrupt an institution’s ability to uphold exploitative labor and domestication practices. This work serves as a call to action; in identifying opportunities for student athlete agency and bodily autonomy within a surveilled system. This call likewise challenges institutional actors to increase support for current student athletes in their quest to defiantly look back. While this dissertation primarily centers experiences of surveillance at the site of the institution of sport within U.S. higher education, findings also interrogate the holistic regulation and control of the Black woman’s body in society at large. The study includes a focus on timely issues surrounding biometric technologies and their implications on data privacy and consent policy, understanding the role and influence of sports media in confining Black womanhood, tracking the sustained emotional and cultural labor experienced by Black women in predominantly White spaces, and exploring emerging digital media tools that enable Black women to reimagine the possibilities of storytelling and resistance.

Advisor: Scott, Janelle
Van Rheenen, Derek
Quantifying the Impact of Environmental Stimuli on the Structural Dynamics of Cesium Lead Iodide Perovskite

Metal halide perovskite is a new generation of semiconducting materials that providing promise for the development of efficient optoelectronic devices such as solar cells, light-emitting diodes (LEDs), and lasers due to its outstanding optical and electronic properties. In particular, all-inorganic cesium lead iodide (CsPbI3) presents great promise for photovoltaic applications due to its suitable bandgap for single and multi-junction solar cells, and its enhanced thermal stability compared to organic-based metal halide perovskite. However, exposure to environmental stimuli such as ambient moisture tends to structurally transform CsPbI3 perovskite (high-T) into a nonperovskite (low-T) phase that has a larger bandgap. Thorough understanding of the influence of the environmental stimuli is key in predicting solar cell stability and in designing more stable devices. By directly monitoring the high-T to low-T CsPbI3 phase transformation under controlled relative humidity, I am able to quantify the dependence of phase transformation processes on relative humidity, extract the associated nucleation barriers, and uncover the rate-limiting process. Furthermore, I find heating under general solar cell operating temperature to be a potential method of mitigating moisture-induced phase transformation. In addition, I demonstrate that illumination using above band-gap continuous-wave laser transforms high-T phase CsPbI3 to low-T phase in ambient conditions. In the presence of moisture, laser induces structural phase transformation at rates order of magnitude much faster than moisture-induced phase transformation. In the absence of moisture, laser does not trigger phase transformation, but introduces long-lasting defects that lower the photoluminescence emission and accelerate phase transformation upon exposure to moisture. Finally, I demonstrate direct visualization of phase growth in individual single-crystals utilizing a continuous-wave laser via photoluminescence imaging, as well as in situ heating in cathodoluminescence microscopy coupled with scanning electron microscopy. I find that initial growth direction and shape show correlation to the interface migration speed. These studies all contribute to the fundamental understanding of phase transformation energetics of CsPbI3, which can serve as references for device applications of CsPbI3 and for future designs of stable photovoltaics systems.

Advisor: Yang, Peidong
Dynamic Response and Seismic Mitigation of Floor-Anchored Nonstructural Components

Failure of nonstructural components during an earthquake can cause widespread property damage, lead to lengthy downtime of the structure, and pose a life-safety threat to the occupants. Current code provisions aim to minimize the life safety threat by specifying lateral force demands and anchoring requirements. These code requirements are based on a simplified equation that does not fully consider the component attachment’s contribution to its overall dynamic response. Research suggests that the component attachment is an important parameter that determines its dynamic properties. Most analyses of the dynamic response of floor-anchored nonstructural components use an idealized single-degree-of-freedom system with a concentrated mass. Nonlinear behavior is included in the component force-displacement relations while the boundary conditions remain fixed based to the floor. Assuming a nonlinear behavior of the attachment changes the fixed-based boundary conditions and results in uplift at the base of the model. Models that include uplift at the base can be found for analysis of rocking structures and soil-structure interaction, but are rarely applied for analyzing nonstructural components. This dissertation focuses on acceleration-sensitive equipment and examines the attachment design of floor-anchored mechanical and electrical nonstructural components. The dissertation includes three parts. (i) An extensive experimental shaking-table test study of a nonstructural experimental model that is attached via several attachment designs to a concrete slab. The experimental results demonstrate that the selected attachment properties govern the boundary conditions of the nonstructural component and strongly influence its dynamic response. (ii) A mechanics-based numerical modeling approach for floor-anchored nonstructural components attached via steel channel connections. It defines a generalized analytical approach to estimate the force-displacement relations of the attachment and offers a simple approach for the engineer to estimate the contribution of the attachment design to the dynamic amplification of the component. (iii) A numerical study that examines the mechanics-based modeling approach with a wide range of input motions, component parameters, and attachment properties.

Advisor: Moehle, Jack P