VictorJuiz/thesis huggingface dataset:
Towards neural graph databases

Graph databases are the primary workhorse for storing and organizing structured information over real-world entities. The core task on graph databases is query answering. The objective is to execute a given query of interest and retrieve answers to the query from the underlying graph. However, a major challenge is that data in graph databases are often massive, noisy, and incomplete. Relationships between entities keep changing, which is extremely hard to keep track of. Execution of a query over noisy and missing data leads to answers of poor quality. This significantly limits the application of graph databases in many scenarios. Neural graph query answering algorithms aim to address the challenge via embeddings and representation learning. The idea is to map complex queries and graph data to a latent space. This field has witnessed substantial growth, with extensive research focusing on both theoretical and practical dimensions, addressing various queries and graph types with efficient systems. In this thesis, we introduce the concept of Neural Graph Databases (NGDBs) where neural graph query answering is at its core. NGDB consists of a Neural Graph Storage and a Neural Graph Engine, extending the idea of graph databases. Under NGDB, we provide a collection of neural graph query answering methods, datasets, systems, metrics, and broad applications. In Chapter 2, we start with the definitions of different types of graphs, graph queries, fuzzy logic, and graph representation learning. This serves as the foundation and background of the thesis. In Part I, we discuss two works on query embeddings, Query2box and BetaE. Query2box introduces the first neural graph query answering algorithm that models existential quantification, disjunction, and conjunction operations. BetaE further extends its capabilities to include the negation operation. In Part II, we design the first and most scalable system, SMORE, which allows for the training of neural graph query answering algorithms on extremely large graphs. In Part III, we introduce the overall framework and components of NGDB. We further provide a unified taxonomy of existing neural graph query answering algorithms from the perspectives of graphs, modeling, queries, and datasets. Together the thesis introduces the task of neural graph query answering and the framework of NGDB, presents two novel algorithms, and points out promising directions, unsolved problems, and applications of NGDB.

Keywords: Engineering.
Advisor: Leskovec Jurij
Liang Percy
Ma Tengyu
Towards perceptually realistic gaze-contingent virtual and augmented reality displays

Virtual and augmented reality (VR/AR) display systems strive to generate perceptually realistic user experiences, that is, the ability to render digital objects that a human observer cannot distinguish from a real object. Current-generation systems have made significant progress towards this goal, however still struggle to match the spatio-temporal and depth sensing capabilities of human vision, constrained by the limited compute budgets, hardware, and transmission bandwidths of wearable computing systems. Gaze-contingent rendering and display paradigms have emerged as a promising solution. Enabled by recent developments in wearable eye tracking systems, this suite of techniques utilizes real-time eye movement sensing to adjust content to reduce bandwidth requirements or improve visual experience. In this dissertation, we introduce and evaluate several approaches that aim to create more perceptually realistic VR and AR experiences using gaze-contingent display techniques. We model both the spatio-temporal sensitivity of the human visual system and how perception is affected by the distribution of visual attention. In both cases we demonstrate that exploiting these effects could significantly improve potential bandwidth savings of existing approaches. Next, we demonstrate how these bandwidth savings are directly dependent on the latency of the gaze-contingent display system, showing that reducing the latency of current generation systems could enable up to double the bandwidth savings. Finally, we describe how gaze-contingent stereoscopic rendering can improve the accuracy of disparity and depth rendering, including improving shape distortion in VR and alignment of physical and digitally rendering objects in AR

Keywords: Engineering.
Electrical Engineering.
Advisor: Wetzstein Gordon
Horowitz Mark (Mark Alan)
Kellnhofer Petr
Towards quieter supersonic flight : a computational aeroacoustic study of high-speed jets

Using large-eddy simulations (LES) and the Ffowcs Williams-Hawkings (FW-H) method, this thesis studies aeroacoustic phenomena in high-speed jet flows from supersonic aircraft engines. The work is divided to two parts. The first part focuses on jet screech in an underexpanded rectangular jet plume—a challenging aeroacoustic resonance emitting disruptive tonal noise. A detailed numerical study identifies optimal mesh designs and FW-H sampling, yielding accurate screech results with moderate computational and storage costs. This investigation reveals that screech involves energy transfer between the upstream-traveling guided jet mode and the downstream-traveling Kelvin-Helmholtz wave. Distinct regions in the spatially developing jet can be identified based on the wave energy of oppositely-moving waves. The near-nozzle region is found to be related to the receptivity of the initial shear layers, followed by a region further downstream where the wave energies reach maximal values. The SPOD modes can be used to reconstruct the amplitude and directivity of the fundamental screech tone with Lighthill's acoustic analogy. The second part of the thesis centers on dual-stream coaxial nozzles with internal mixing geometries for noise reduction in supersonic business aircraft. Analysis of nearfield flow turbulence highlights internal shear layers and wakes introduced by the mixing geometry, impacting the near-nozzle external jet flow even in absence of the temperature and velocity differences between the two streams. Two coaxial nozzles with an internal center plug and a mixing duct are studied: one with a 16-lobe mixer and one without. A comparison of the coaxial jet with its fully mixed equivalent single jet condition shows that the coaxial jet is louder in the downstream direction. The equivalent single jet emits acoustic tones in the upstream direction, likely due to the excitation of instability waves in the shear layers. Overall, this study improves the understanding of screech generation and coaxial jet aeroacoustics, offering insights for quieter supersonic aircraft design in the future.

Keywords: Engineering.
Aeronautics and Astronautics.
Advisor: Lele Sanjiva K. (Sanjiva Keshava)
Alonso Juan José
Bres Guillaume
Moin Parviz
Toxic positivity : integrating folk music and digital instrument design

This dissertation focuses on the interactive dynamics between electronic and acoustic instruments fused with the rich and diverse folkloric sounds of Turkey. The performance practices of folk instruments are incorporated into Western symphonic instruments and their capabilities are extended through technological means. Unpredictable pairings of acoustic and electronic instruments are explored to create unconventional timbres as well as subvert traditional instrumental roles. Multiple contrasts merge: Digital vs. Acoustic and Western vs. Folk

Keywords: Humanities and Sciences.
Music.
Advisor: Berger Jonathan
Alessandrini Patricia
Ulman Erik
Tracing T cell clonal responses to chronic antigen stimulation using single-cell T cell receptor sequencing approaches

T cells play a central role in the immune response, protecting the host against immune challenges while maintaining self-tolerance. During acute infection, naïve T cells are activated in response to antigen and differentiate into memory precursors and effector T cells. Upon antigen clearance, effector T cells undergo apoptosis while memory cells survive and persist as long-lived memory T cells that are ready in case of subsequent infection. In settings where antigen stimulation persists, as in chronic infections and cancer, T cell development is modulated, such as through the development of exhausted T cell states characterized by limited effector function and high sustained expression of inhibitory receptors. How T cell responses to chronic antigen stimulation develop and are maintained are not well understood, especially at the level of individual T cell clones. Recently, the development of single-cell genomics technologies has enabled high-resolution profiling of the T cell compartment at the clonal and phenotypic levels. In particular, the ability to sequence the T cell receptor (TCR) of individual cells in parallel with gene expression allows for the dissection of the TCR repertoire in the context of cell states and finer interrogation of T cell clonal dynamics. Here, we dissect various aspects of the T cell response to chronic antigen stimulation by tracing clones using TCR sequencing methods. First, we demonstrate that CD4 T cell responses are maintained during chronic viral infection by a memory-like progenitor population. Then, we profile the T cell response to immune checkpoint blockade and characterize the regional distribution and cell states of T cell clones within the tumor, lymph nodes, and peripheral circulation of patients with lung cancer. Altogether, this work demonstrates how clonal tracing through single-cell TCR sequencing technologies and computational approaches can be leveraged to uncover features of T cell responses to chronic infection and cancer, and how this approach can be extended to other settings of immune challenge.

Keywords: Medicine.
Microbiology and Immunology.
Advisor: Satpathy Ansuman
Curtis Christina
Davis Mark
Jerby Livnat
Transformations of methane and carbon dioxide to chemical feedstocks, fuels, and materials

Global warming and associated climate change effects are the defining issue of the 21st century and decarbonization of all sectors is imperative to mitigate the worst consequences of climate change. Of particular importance are new, cost-effective, and greenhouse-gas-emissions-free chemical transformation processes to convert CO2 into chemicals, fuels, and materials. This is in contrast to today's processes for producing chemicals, fuels, and materials, as nearly every such process produces direct and/or indirect CO2 emissions. As a result, the paradigm shift that needs to occur is the transition from fossil-based sources for chemicals, fuels, and materials production to the use of CO2 itself to produce these products, as this would allow for negative emissions by sequestering CO2 in solid form. However, due to CO2's negligible value from a thermodynamic standpoint; nearly every CO2 transformation is endothermic, requiring energy. This required energy can take the form of clean, emissions-free electricity obtained from solar and wind, for example, but widespread proliferation of renewable sources of electricity generation has yet to occur and the challenge of grid-scale energy storage has not yet been adequately addressed. A better alternative for this required energy exists in the form of a co-reactant with high enthalpy, such as CH4. CH4 is arguably the most advantageous co-reactant due to its abundance and relatively low cost. Therefore, CH4 and CO2 are expected to be the feedstocks of the future to produce fuels, chemicals, and materials. Three such processes to transform CO2 and CH4 to chemical and fuels are discussed at length in this dissertation: 1) low temperature CO2 utilization via reverse water-gas-shift chemical-looping, 2) CH4 pyrolysis for the production of CO2-free H2 and carbon nanotubes, and 3) photocatalytic direct CH4 to CH3OH

Keywords: Engineering.
Mechanical Engineering.
Advisor: Majumdar Arunava
Chueh William
Zheng Xiaolin
Translation matters : tracing the transmission of medieval texts from manuscripts to MOOCs

This dissertation meets at the convergence of three areas of interest: Old English acts and attitudes of translation, manuscript studies both traditional and through a digital humanist lens, and, finally, the pedagogical opportunities that aim to equip and inspire future generations of learners. Using the Oxford English Dictionary's different meanings of the word "translation," it traces translation through acts of conversion, movement, transfer, and transformation. Part One describes these areas of interest and provides an introductory framework for the project. In the sections of Part Two, I examine translation as conversion. In focusing on translation as conversion, this assessment looks particularly at narratives of conversion and translation as described in Bede's Ecclesiastical History through notable figures such as Augustine of Canterbury, King Oswald of Northumbria, and Cædmon of Whitby. In Part Three, I discuss the notion of translation as movement. This section builds on the robust research of manuscript provenance, but this exploration also envisions how this line of inquiry can be reshaped and enriched in the digital age. It does so by discussing a digital mapping project that visualizes manuscript movement—or, the lives of manuscripts. In the next section, I introduce the role of manuscript digitization and curation, paleography, and online learning, specifically through a series of MOOCs created in a collaboration between Stanford University and Cambridge University called "Digging Deeper." Part Five contains a manuscript description of selected manuscripts of the Old English version of the Gospels, giving special consideration to newly discovered and identified artifacts since the publication of a critical edition of this medieval text. I conclude this study looking backward and forward: backward to the traditional mode of manuscript studies in detailed descriptions of textual artifacts, and forward to future opportunities of collaborative, often digital, work. Understanding the relevance of early translation will help new scholars appreciate translational echoes found in an increasingly accessible and inviting scholarly community. Breaking the glass on hermetically sealed texts and their histories both expands how Old English can be accessed by the masses and how Old English can be carried to new heights by non-traditional scholars, celebrating an elevation through equity.

Keywords: Humanities and Sciences.
Advisor: Treharne Elaine
Algee-Hewitt Mark
Albritton Benjamin
Translational cardiovascular surgical engineering for enhanced biomechanics and device development

Valvular heart disease is a significant cause of global morbidity and mortality, and most of these diseases are rooted in nuanced biomechanical changes. While surgical intervention has been a mainstay for treatment of many conditions, techniques and devices have been developed primarily based on anatomic principles and guided by appearance and function of the diseased valve, yet new innovations in ex vivo cardiac simulation have enabled the rapid and safe testing of surgical operations and therapies, offering new insights into the nuances of valvular disease and repair. This dissertation contributes to and expands upon the field of study of valvular diseases and surgical treatments and devices as well as modeling modalities and the engineering tools to study these diseases and innovate new solutions for a wide range of diseases including mitral valve prolapse, systolic anterior motion, annular dilation, rheumatic mitral valve, COVID-19, and various aortic pathologies. The following research work has resulted in a significant clinical impact on valvular repair as well as prosthesis and device design, and this work will continue to serve as a foundation for the future expansion of translational cardiovascular surgical engineering, bringing science to art to improve patient care around the world.

Keywords: Engineering.
Mechanical Engineering.
Advisor: Levenston Marc
Woo Joseph
Wu Sean
Translatome analysis reveals microglia and astrocytes to be distinct regulators of inflammation in the hyperacute and acute phases after stroke

Ischemic stroke is a leading cause of death and long-term disability. Neuroin-flammation after stroke can significantly affect stroke outcomes¬--it can clear dead tissue and aid neuroplasticity but also exacerbate cell death. However, the exact astrocytic and microglial signaling pathways initiating neuroinflammation after stroke are unresolved and will be critical for developing immunomodulatory stroke therapies. In Chapter 1, I give background on the progression of stroke, status quo of treatments, and the genetic tools used to profile gene expression changes in microglia and astrocytes. Furthermore, I lay out the key gaps in knowledge and give an overview of how this dissertation fills those gaps. In Chapter 2, to parse the astrocytic and microglial response from that of infil-trating cells in the brain after stroke, we used the RiboTag technique to separately obtain astrocyte and microglia-derived transcriptional responses. By crossing floxed RiboTag mice with Aldh1l1-CreER or Cx3cr1-CreER mice, we tagged astrocytic or microglial ribo-somes, respectively, and then isolated cell-specific mRNA from ribosomes immunopre-cipitated from brain tissue. We performed RNA-sequencing on astrocyte or microglia-specific transcripts obtained from peri-stroke cortex in male and female mice 4 hours and 3 days after distal middle cerebral artery occlusion or sham surgery. Few sex differences were observed. Microglia initiated a rapid response to stroke at 4 hours by adopting a proinflammatory profile associated with the recruitment of immune cells while the astro-cyte profile was dominated by stress response, as well as proinflammatory genes. By 3 days, microglia have dampened their inflammatory response in exchange for a prolifera-tive, phagocytic state. At this timepoint, astrocytes have enhanced their pro-inflammatory response and may be doing this through transcriptional regulation. Taken together this data comprehensively describes the astrocyte and microglia-specific translatome re-sponse in the hyperacute and acute period after stroke and identifies pathways critical for initiating neuroinflammation. Chapter 3 summarizes the findings, provides additional discussion, and comments on future directions to be taken

Keywords: Medicine.
Advisor: Buckwalter Marion
Wyss-Coray Anton
Gentles Andrew J.
Kaltschmidt Julia
TrkA-ing pain : an optobiological approach for probing the NGF/TrkA pathway in relation to pain

Chronic pain is a prevalent problem that plagues modern society, and there is a need for better understanding its mechanisms to produce alternative therapeutics for managing pain. Nerve Growth Factor (NGF) and its primary receptor, Tropomyosin Receptor Kinase A (TrkA) are known to be potent mediators of chronic pain, but there is a lack of established methods for precisely perturbing the NGF/TrkA signaling pathway in the study of pain and nociception. Optobiological tools that leverage light-induced protein-protein interactions allow for precise spatial and temporal control. Previously, our lab reported a blue-light activated version of TrkA generated using the improved Light inducible Dimer (iLiD) system, opto-iTrkA, and demonstrated its ability to activate similar downstream survival and differentiation pathways to native NGF/TrkA signaling in a cellular model. This work aims to extend the use of opto-iTrkA as a tool to studying nociceptive pathways \textit{in vitro} and pain \textit{in vivo}. We show that opto-iTrkA activation orthogonal to NGF/TrkA activation is able to sensitize the Transient Receptor Potential Vanilloid 1 (TRPV1) channel in cellular models, cause the transduction of phospho-ERK signals from axonal terminals to the soma in cultured sensory neurons, and also induce mechanical sensitization in mice expressing opto-iTrkA in the peripheral nervous system. We hope that this demonstrates the utility of opto-iTrkA as a tool to expand the toolbox for dissecting nociceptive pathways and pain.

Keywords: Humanities and Sciences.
Chemistry.
Advisor: Cui Bianxiao
Bertozzi Carolyn
Boxer Steven
Trust, Sovereignty, and Social Lives of Displacement in Iraq

How can those who have experienced violence establish a system of order and survival when the state authority fails? This dissertation explores the motivations and moral beliefs of internally displaced Iraqi Arabs who make informal sponsorship agreements with Iraqi Kurds to ensure protection, residency, jobs, and resources for themselves, their families, and acquaintances in the Kurdistan Region of Iraq [KRI]. It challenges the common belief that civil wars lead to the breakdown of neighborliness. Instead, this dissertation demonstrates that these sponsorship agreements enable displaced Iraqi Arabs to maintain a mutual sense of obligation and trust with the Iraqi Kurdish community while remaining separate from an interior domain of Kurdish life. It argues that by redefining colonial and state power, Iraqis who enter into such sponsorship agreements create a less-explored form of sovereignty, in which the founding sovereign act is not the exclusion of bare life, but the conditional integration of the ethnic other into social life. Drawing from two years of ethnographic fieldwork and archival research in the Sulaymaniyah Governorate of the Kurdistan Region and the adjacent disputed territories, the dissertation weaves together stories of overlapping narratives of displacement in peri-urban neighborhoods, narratives of everyday encounters with authorities in checkpoints, theological ruminations of Kurdish tribal leaders around compassion and engaged humanitarianism, the bitter nihilism and disengagement of young Kurdish men, deeply exhausting travails of fugitive displaced Iraqis falsely accused of terrorism, and the remarkable agency exercised by displaced women in keeping their families together, among others. At a monumental time when social hierarchies are deeply in flux, it provides a lively portrait of how the fragmentation of authority is experienced, imagined, and narrated by Iraqis.

Keywords: Humanities and Sciences.
Anthropology.
Advisor: Hansen Thomas Blom
Esmeir Samera
Ferguson James
Tambar Kabir
Truth-vetting & mathematics : sense-making practices in an inequitable world

Increasing students' performance in school-based mathematics is a constant focus that is fueled by differences in students' performance outcomes. Research that examines students' experiences with learning mathematics has shown that students take on different ways of knowing that either align or are at odds with the type of classroom instruction they receive. The research has shown that these preferences tend to fall along gendered lines. This study uses student interview data to argue that knower types (ways of knowing) fall more generally along social identity lines, and that this phenomenon is influenced by the interaction of identity and social construction. The framework and findings of this project also provide a new lens for understanding and interrogating "gaps" in students' math performance and differences in math trajectories.

Keywords: Education.
Advisor: Valdes Guadalupe
Boaler Jo
Langer-Osuna Jennifer