VictorJuiz/thesis huggingface dataset:
Hardware acceleration For graph neural networks
Keywords: Electrical Engineering.

Traditional deep neural networks (DNNs) rely on regularly structured inputs such as vectors, images, or sequences. This reliance on regularity makes them difficult to use in domains where data is naturally irregular, such as connections on social media. Graph neural networks (GNNs) extend DNNs to operate on arbitrarily structured graph-valued data. However, GNNs do not accelerate efficiently on CPUs, GPUs, and DNN accelerators such as a TPU, due to their irregular and input-dependent pattern of computation. As a result, GNNs have much higher inference latency than other types of DNNs in practice. This limits their use to applications where inference can be precomputed off-line. This dissertation presents hardware and software techniques to reduce the inference latency of GNNs. To this end, we make the following three contributions. First, we introduce a decomposition of GNN inference into a series of three computational phases: aggregate, combine, and update. This decomposition permits a simple representation for a broad class of GNNs we call GReTA. Second, we introduce a GNN accelerator architecture called GRIP. GRIP alleviates the bottlenecks in each phase by using separate memory subsystems specialized for the different access patterns in each phase of inference. Finally, we introduce optimizations to reduce the working memory and bandwidth requirements for GNN inference including caching partitions of feature data, inter-phase pipelining, and merging computation. We also introduce a novel optimization called vertex-tiling that substantially improves latency by increasing the reuse of weight values during inference. Taken together, these techniques significantly reduce the latency of GNN inference over existing state-of-the-art implementations. Evaluated on a broad range of models and datasets, our accelerator reduces latency by 7-70x compared to a CPU and GPU baseline
High precision photoemission study of overdoped Bi2212 superconductors
Keywords: Applied Physics.

High-temperature superconductivity in the cuprates is a complex and enduring problem. The complexity is evidenced by the phase diagram, where superconductivity is intertwined with a plethora of unconventional states in the pseudogap regime. In this thesis, we try to disentangle superconductivity from such states to better understand its nature. Using angle-resolved photoemission spectroscopy, we first study the cuprate phase diagram near the pseudogap critical doping in Bi2Sr2CaCu2O8+δ (Bi2212). With increasing doping, we find a temperature-independent boundary across which the pseudogap ends and quasiparticle-like excitations recover. The result challenges presumptions associating the pseudogap with a quantum critical point and suggests a relatively simple region in the phase diagram where superconductivity emerges from a Fermi-liquid-like normal state. In the second part, we focus on this pseudogap-free region to study the superconducting phase transition. We discover that the transition temperature coincides with the most rapid drop of zero-energy spectral intensity instead of the opening of the superconducting gap. We also observe a strong momentum anisotropy in the spectral signatures associated with the transition. These observations are consistent with the scenario that the superconducting transition in overdoped Bi2212 is driven by phase fluctuations
High-valent copper-dioxygen assemblies : synthesis, characterization, and potential relevance to biological systems
Keywords: Chemistry.

Biological enzymes utilize various copper-based active sites to activate dioxygen creating a variety of copper-dioxygen assemblies. These assemblies carry out highly selective and difficult oxidative transformations vital to biological life. Insight into how Nature has optimized these active sites can be gleaned by studying synthetic structural mimics and has potential to be of great benefit to the industrial design of catalysts. While the resting structures of many of these active sites are known, the nature of the active oxidants are often less well-defined. In this thesis, efforts towards the cryogenic synthesis and spectroscopic characterization of copper(III)-containing oxidants, formed directly via dioxygen activation of biomimetic copper precursors, will be discussed. This work demonstrates both the kinetic and thermodynamic accessibility of the copper(III) oxidation state under biological ligation, which challenges existing assumptions in the literature through the identification of reactive intermediates
Holistic battery management system design for lithium-ion battery systems via physics-based modeling, estimation, and control
Keywords: Energy Resources Engineering.

Lithium-ion battery systems used in electric vehicles and stationary grid storage applications are composed of numerous batteries that are interconnected to create a battery pack that can satisfy the high energy and power requirements of the desired application. However, the current research in the battery modeling and control community has focused mainly on lithium-ion batteries at the single cell-level in an isolated environment where the cell-to-cell interconnections and pack heterogeneities are not accounted for. Merely applying the existing knowledge of a single cell to such a large-scale battery pack assumes "modularity", wherein modularity is defined as the ability to extrapolate the behavior of a battery pack from a single cell. Recent experimental studies presented in the literature show evidence that the assumption of modularity, in terms of electrical, thermal, and aging behavior, does not hold true. The literature further highlights that a pack reaches its end-of-life sooner than a single cell, the thermal and aging gradient behavior of the pack is non-uniform and aggravated in comparison to a single cell, and the performance of a pack is adversely affected due to cell-to-cell heterogeneities induced by manufacturing variances. As a result, the design of Battery Management Systems for a pack must take these non-uniformities or peculiarities into account while developing algorithms for modeling, estimation, and control. To that end, this dissertation adopts a bottom-up approach by developing modeling and estimation tools at the cell-level, and then extending it to the module/pack-level for efficient control. An experimentally validated electrochemical model at the single cell-level forms the basis to develop a model-based observer to estimate "non-measurable" internal battery health variables. The cell-level electrochemical model is extended to a high-fidelity module-level model by incorporating the thermal, electrical, and aging interactions between cells to analytically and quantitatively understand the effect of heterogeneities and gradients on the behavior of battery modules. Subsequently, the model is utilized to develop an optimization-based control strategy to minimize the non-uniformities, thereby improving the safety and lifespan of battery modules. The outcome of this research will open up opportunities to advance knowledge of cell- and module-level dynamics, accurate real-time prognostic algorithms, and health-conscious module-level control. This research is primarily targeted towards the transportation sector (electric vehicles), but it can be extended to stationary grid storage applications, and more importantly used to determine the feasibility of using end-of-life lithium-ion cells in "second-use" applications
Holomorphic curve invariants of open contact manifolds
Keywords: Mathematics.

Contact homology is a well-established tool for studying contact manifolds. It was originally defined for closed manifolds, and variants have been produced for a certain class of open manifolds, but these depend on certain extra structure at infinity, and hence do not provide an invariant for the manifold itself. In this thesis, we introduce a variant of contact homology which is defined for certain ("convex") open manifolds. This provides the first tool for distinguishing tight contact structures on euclidean space and, as an application, we prove the existence of exotic tight contact structures on (4m+1)-dimensional euclidean space for every m> 0. In addition, we give a preliminary version of a general framework for defining algebraic invariants based on holomorphic curves
Homeworking in Italy during the COVID-19 Pandemic: An Analysis of Preliminary European Labour Force Survey Results
Keywords:  Department of Communication
italy
homeworking
smart working
internet
pandemic
covid-19
Thesis

This paper explores how the Italian homeworking landscape transformed during the 2020 pandemic in relation to the broader European context. After providing an overview of the history of homeworking in pre-pandemic Italy and Europe, I analyze 2020 homeworking data from national statistics institutes of individual countries collected as part of the European Union Labour Force Survey. I frame my study of homeworking within the three-element scheme proposed by Lutz Gschwind and Oscar Vargas in Telework in the 21st Century. While fluctuations in 2020 homeworking trends in Italy can be attributed to the unstable nature of the pandemic, I argue that the country’s volatile and short-term adoption of flexible working arrangements stems from barriers posed by employment regulation, working culture, and information and communication technology (ICT) infrastructure. My analysis takes into consideration the historical territorial divides on the Italian peninsula, as well as the “teleworkability” of–or the feasibility of implementing homeworking arrangements in–different economic sectors.
Homo musicus : he musical instrument as a model of life and mind in early modern Europe
Keywords: History.

My dissertation examines the ways in which early modern physicians and natural philosophers employed musical metaphors and models in order to conceptualize human vital function and cognition. Almost every early modern investigation of the body, whether medical, physiological, or psychological, had to confront in some way the central tension between the faculties of the soul and the activities of the body. In music, musical instruments, and musical ideas, philosophers from across western Europe found conceptual tools with which they attempted to bridge this gap, by connecting the physical and even mechanical processes of the body with the more abstract phenomena of thought, cognition, health, and pleasure. Musical instruments were material and mechanical, and thus could describe the basic physical attributes of human bodies. But they were also affective, emotional, rational - in both their symbolism and their operation. By the middle of the 18th century, what I have dubbed homo musicus, or the musical human being, had become one of the most wide-spread metaphors of the human body, and indeed human experience. My dissertation thus tells an alternative history of mechanism, one which did not reject, but rather embraced, the soul and its faculties. Homo musicus was both an elaboration and a complication of cartesian dualism: it was a mechanism with soul
How CS 184, Bridging Policy & Tech Through Design, Came to Be: Luck, Persistence + Strong marketing
Keywords: Design and technology
Public policy
Text
Report
Thesis

Constanza Hasselmann’s capstone project detailed the inception, implementation, and success of the “CS 184- Bridging Policy & Technology through Design” course at Stanford University. Originally starting out as an independent study course inspired by her interest in public technology and design, Constanza notes how this quickly pivoted from an independent study structure to a student lab titled Public Interest Technology (PIT) @ Stanford. Through adamant community and academic support, the PIT Lab fully launched CS 184 in Spring 2020. Partnering up with various organizations, project mentors, and faculty, CS 184 served as a project-based course meant to engage with the emerging topic of public interest technology and serve as a space where students from different academic backgrounds worked with external partner organizations at the nexus of digital technology and public policy. The goal of the class and the Lab is to ultimately reach new student audiences, engage with additional faculty and offer a project incubator. CS 184 remains an active Stanford course that aims to create an environment for a vibrant and interdisciplinary community of students, faculty, and external partners.
How many shades of brown? - Excremental rhetoric in modern Japanese literature
Keywords: East Asian Languages and Cultures.

Abstract This dissertation examines excrement as a literary and rhetorical device of imaginative discursive possibilities in modern Japanese literature. Given the ambivalent status of excrement as both stigmatized as well as a source of fascination, excremental rhetoric has the unique potential to illuminate the multiplicity of discourses -- aesthetics, body politics, ideology, and diachronic socio-cultural conditions -- that play out within Japanese literary production over the course of the twentieth century. Challenging the dominant tendency in both Western and Japanese scholarship to read the excremental through a given theoretical perspective, my work proposes a multifocal mode of reading that recognizes the plurality of excremental rhetoric by attending to excremental modalities, or the states in which excrement exists or is experienced and/or expressed. I show that reading for the modalities of the literary excremental within the text shifts emphasis from an "unveiling of truth" to an exploration of various sections of a pluri-discursive "sewage system" in modern Japanese literature, including those examined in these chapters related to toilets, gastrointestinal disorders, and copro-philia and -phagia. Chapter 1, "Toilet and Excrement Collectors: Tanizaki and Other Aesthetes" investigates Tanizaki's prolific literary excremental output against the backdrop of the aesthetic and scientific discourses of his time and in conversation with the literary production of others with comparable interests in the aesthetic excremental. Bringing to the fore the changing configurations of private and shared space, Tanizaki's toilet and excrement collection offers a theoretical model for how a variety of discourses related to modernization and modernity interconnect in the subterranean Japanese literary sewage system. Chapter 2, "Shit(ty) Wars or Battlefield Excrementalism: Hayashi Fumiko, Hino Ashihei, and Others from the Warfront" explores the aesthetics and ideology of what I designate as "battlefield excrementalism" or the excremental rhetoric employed in war narratives. The chapter revolves around Hayashi Fumiko's accounts from the Fifteen Years' War (1931-45). I examine Hayashi's works in conversation with other wartime narratives, most notably those by Hino Ashihei, and show how the constructedness of literary battlefield excrementalism engages with various types of colonizing and colonized bodies. Chapter 3, "Enema Stories and Queer Shit: From Kitan Club to Murakami Ryū" examines narratives dedicated to non-normative sexualities related to anal sexual practices and the predilection toward enema, in particular, in post-World War II and then Bubble/post-Bubble Japan. Enema in these two contexts demonstrates the waste potential of commodity and the commodity potential of waste, revealing itself as (literary) commodity
How the Asian Infrastructure Investment Bank is Advancing Chinese Foreign Policy Goals
Keywords:  Program in International Relations
AIIB
BRI
Asian Infrastructure Investment Bank
Belt and Road Initiative
China
Stanford
International Relations
Stanford International Relations Honors Program
Thesis

The Chinese-led Asian Infrastructure Investment Bank (AIIB) was launched in 2016 as a “lean, clean, and green” development bank focused specifically on Asia. In this thesis, I examine the effects of the AIIB on Chinese lending across Asia, specifically through the Belt and Road
Initiative (BRI). Using data from the AIIB and the American Enterprise Institute’s BRI database, I compare and assess AIIB and BRI policy in regional spending, environmental safeguards, and project specifics. Through this analysis, I argue that the AIIB and BRI reflect different patterns lending and serve different goals for China. In particular, while the BRI allows China to spread influence and create access to new markets through bilateral cooperation, the AIIB serves as an effective means for China to reform global development norms in their favor.
How the internet and online interaction strengthen social movements
Keywords: Sociology.

In recent years, it has become increasingly apparent that the internet and online interaction plays a role in the mobilization of social movement participants and in potential movement success. Social movement scholars have long debated whether such technological affordances enable similar or different mechanisms compared to traditional offline "in person" social movements and what this means for outcomes. These three papers that serve as dissertation chapters broadly seek to understand how the internet strengthens and influences contemporary social movements. Here I show how computer technologies augment and change traditional pathways for social movement emergence, specifically highlighting these key differences: 1. Secrecy and pseudonymity enabled by social computing platforms can increase trust between online activists and serve as a movement resource; 2. Tie formation over the internet widens the potential pool of activists and reach of movement activity; and 3: Activists can use social media to spread visual matter such as photographs and videos that encourage greater bystander support through more effective framing. I use the case of LGBT military inclusion in the United States from research conducted between 2009 and 2019 of social movement tactics and mobilization among LGBT military service members working to repeal "Don't Ask, Don't Tell" and transgender exclusion laws in the recent social movements for LGBT military inclusion. The contributions provide deeper understanding for how contemporary social movements are created, maintained, and changed in an era of online connectivity, showing the power that new computer technologies can have on society
Identification and characterization of neutralizing HIV antibodies targeting the gp41 trimer-of-hairpins structure
Keywords: Microbiology and Immunology.

Despite the extensive amount of time and resources that have been put into HIV research over the past 40 years, the production of an effective preventative vaccine has remained elusive. More recently, vaccine efforts have been reinvigorated with the identification of more broadly neutralizing antibodies (bNAbs) that give hope to the success of B cell focused vaccine approaches. Neutralizing antibodies target the envelope protein (env), which is the only protein expressed on the outside of the HIV membrane. Env is composed of two subunits: gp120, which is responsible for binding to cellular receptors, and gp41, which contains the membrane fusion machinery. Although several broadly neutralizing epitopes have been identified, attempts to generate bNAbs in a vaccine setting have been underwhelming. We therefore set out to characterize new bNAbs against highly conserved regions of the gp41 subunit that are exposed in the pre-hairpin intermediate structure during viral fusion. Since few neutralizing epitopes have previously been characterized for gp41, we first explored HIV patient antibody responses to the N-heptad repeat (NHR) and C-heptad repeat (CHR) regions of gp41. After identifying individuals that produced antibodies against these structures, we single cell sorted their B cells and sequenced the heavy and light chains of their antibody genes, leading to the discovery of three novel anti-CHR neutralizing antibodies. A 3.5 Å crystal structure of the most potent neutralizing antibody, 1CB6, determined that these antibodies targeted the immunodominant cluster II epitope, previously regarded as a non-neutralizing epitope. Similarly to other cluster II antibodies, we observed that the three neutralizing antibodies targeted the CHR as exposed in the gp41 trimer-of-hairpins structure, which is thought to form at the fusion of viral and host membranes. Finally, by utilizing FcγRI on TZM-bl cells and the fusion inhibitor sensitive L565Q env mutation, we demonstrate that cluster II antibodies neutralize during the fusion pathway. These experiments definitively demonstrate that neutralizing antibodies target the cluster II epitope. Additionally, these experiments influence our understanding of gp41 collapse and the fusion process. Exposure of the cluster II epitope on the gp41 trimer-of-hairpins and the high affinity of these antibodies for this structure suggest the formation of a late stage fusion intermediate that can be targeted for the neutralization of HIV
Identification of E. coli amyloid assembly inhibitors, modes of action, and influence on biofilm formation
Keywords: Chemistry.

Biofilms are multicellular communities of cells surrounded in a self-produced extracellular matrix (ECM), a complex mixture of polymeric substances. This matrix is associated with several beneficial functions for bacteria, depending upon the type of biofilm. These can include resistance to antibiotics and host defenses. Biofilm formation in the human host can contribute to the persistence and recurrence of infection. Uropathogenic E. coli is the most common causative agent of urinary tract infection and can assemble unique biofilms through the production of functional amyloid fibers termed curli and a modified form of cellulose -- phosphoethanolamine (pEtN) cellulose. Curli play a vital role in bacterial adhesion to biotic and abiotic surfaces as well as promoting multicellular biofilm formation. Curli fibers are assembled from CsgA protein subunits that non-covalently polymerize into the fibril form through the nucleation-precipitation pathway. Herein, we describe the characterization of the natural product NDGA and the salicylanilide closantel as inhibitors of curli formation. We demonstrate the effects of inhibitors on bacterial curli production, bacterial adhesion, bacterial biofilm formation as well as protein polymerization in vitro. Molecular analyses are accompanied by the evaluation of curli gene transcription to consider compound effects on gene expression. NDGA exhibits curlicide activity, preventing CsgA polymerization, and does not bind to intact curli. These results are consistent with the inhibition of early steps in curli biogenesis, e.g. amyloid nucleation, transport through CsgG, or CsgA-CsgF interactions. Closantel exhibits curlicide activity at very low concentrations and also binds to intact curli fibers. Thus, closantel is able to bind CsgA in its polymerized amyloid form and may also recognize early amyloidogenic conformations of CsgA or additionally recognize the soluble and unstructured form of CsgA preceding nucleation and polymerization. This comprehensive and mechanistic approach in the full cellular context of bacteria provides an avenue to identify and develop curli-specific amyloid inhibitors and may hold promise in identifying the best inhibitors of amyloidogenesis and assembly of amyloid oligomers and fibers associated with human diseases. Finally, we expanded our understanding of the functions and contributions of both curli and cellulose in uropathogenic E. coli biofilm formation through comparisons of curli and pEtN cellulose gene mutants in the uropathogenic E. coli clinical isolate UTI89. We examined biofilm formation at the agar-air and air-liquid interfaces. We also examined mixed cultures of mutants lacking either curli or modified cellulose and discovered that they could recapitulate the formation of a biofilm similar to wild-type UTI89. This work breaks new ground in understanding the contributions of complex and insoluble biopolymers to the assembly of architectures that extend beyond the surface of single bacteria and that are built for community behaviors