VictorJuiz/thesis huggingface dataset:
Optimization and high-dimensional loss landscapes in deep learning

Despite deep learning's impressive success, many questions remain concerning how training such high-dimensional models behaves in practice and why it reliably produces useful networks. We employ an empirical approach, performing experiments guided by theoretical predictions, to study the following through the lens of the loss landscape. (1) How do loss landscape properties affect the success or failure of weight pruning methods? Recent work on two fronts -- the lottery tickets hypothesis and training restricted to random subspaces -- has demonstrated that deep neural networks can be successfully optimized using far fewer degrees of freedom than the total number of parameters. In particular, lottery tickets, or sparse subnetworks capable of matching the full model's accuracy, can be identified via iterative pruning and retraining of the weights. We first provide a framework for the success of low-dimensional training in terms of the high-dimensional geometry of the loss landscape. We then leverage this framework both to better understand the success of lottery tickets and to predict how aggressively we can prune the weights at each iteration. (2) What are the algorithmic advantages of recurrent connections in neural networks? One of the brain's most striking anatomical features is the ubiquity of lateral and recurrent connections. Yet while the strong computational abilities of feedforward networks have been extensively studied, our understanding of the role of recurrent computations that might explain their prevalence remains an important open challenge. We demonstrate that recurrent connections are efficient for performing tasks that can be solved via repeated, local propagation of information and propose that they can be combined with feedforward architectures for efficient computation across timescales

Keywords: Physics.
Advisor: Druckmann Shaul
Ganguli Surya
Goldhaber-Gordon David
Optimization of food-energy-water infrastructure in remote microgrids

Over a billion people in the world lack access to clean, reliable, and affordable electricity. Microgrids with renewable energy, or renewable microgrids, can reduce operating costs by decreasing dependence on diesel fuel and its expensive supply lines, and by reducing air pollution health damage and its associated costs. However, high penetrations of renewable energy, if not integrated properly, can affect microgrid stability. The goal of this dissertation is to inform remote communities that are food-energy-water (FEW) insecure how to optimally integrate FEW infrastructures with renewable energy. A new modeling framework is developed to optimize energy supply and demand in three remote microgrids in the Arctic and sub-Artic. Findings demonstrate that demand-side management (DSM) of FEW infrastructures can decrease dependence on battery energy storage, improve utilization of intermittent renewables in remote microgrids, and reduce diesel fuel consumption. Modeling and site validation in the sub-Arctic have demonstrated potential diesel fuel savings of up to 55% while operating at 100% renewable energy for several days at a time

Advisor: Jacobson Mark Z. (Mark Zachary)
Jain Rishee
Wies Richard
Optimization of ion acceleration from high-intensity laser-plasma interactions

High-energy (100s MeV), high spectral quality ion beams are important for many applications like radiography of plasmas, isochoric heating of materials, and tumor therapy. Advances in the development of intense short pulse lasers, recognized with the 2018 Nobel Prize in physics, have been seen as a very promising route to drive compact ion beam sources. However, despite signficant progress over the past two decades, the control of the ion beam properties remains an outstanding challenge. In this Thesis, we discuss two approaches for controlling and optimizing these laser-driven ion beams, using particle-in-cell simulations and theoretical analysis. First, we show that in laser radiation pressure acceleration, the spectral quality of the ion beam is determined by electron heating, which is dictated by the growth of a surface instability. We show that its growth rate imposes an upper limit on the laser pulse duration, and can limit the maximum peak ion beam energy. Next, we explore the development of a hybrid accelerator that combines the advantages of laser-driven beams (compact, high-charge, 10s MeV) with high-gradient RF acceleration in a meter-scale linac, eliminating the large and expensive radio frequency quadrupoles for bunching. Our one-to-one simulations show that the space-charge field plays a critical role in the acceleration effectiveness, and that by tuning the distance at which the laser-driven beam enters the RF, the space-charge field can be controlled such that it actually increases the beam capture. These are important in guiding future experimental developments, for example for the ultrashort laser pulses at state-of-the-art laser facilities and high-gradient linacs, for which we showcase the possibility of a compact (4.5 m) hybrid accelerator that produces a high-quality, high-charge 250 MeV proton beam

Keywords: Physics.
Advisor: Fiuza Frederico
Glenzer S. H.
Abel Tom G.
Huang Zhirong
Optimized community layouts incorporating heat pump technology in large commercial buildings

The global focus on reducing carbon emissions is becoming more pressing to meet Intergovernmental Panel on Climate Change (IPCC) and the 26th United Nations Climate Change conference (COP26) targets. As such, energy demands within the building sector, which account for more than one third of the world's emissions, must be reduced. Here, an urban energy co-optimization model was used to evaluate the effectiveness of energy efficient heat pumps to replace traditional heating, ventilation, and air conditioning (HVAC) systems in large commercial building archetypes at the community scale. This work looks at the effects of such a transition to more energy efficient HVAC systems within a community cogeneration network layout, using a neighborhood in San Francisco, CA as a case study. The model uses a Genetic Algorithm to generate and optimize sustainability performance for over 100,000 community designs, using 21 commercial building archetypes, 32 combined heating and power engines, and 16 chillers. The results of the study show that there are significant reductions in the social cost of carbon (SCC), lifecycle cost of equipment (LCC), and total energy demand in an optimized community design when heat pumps are installed within community cogeneration settings. The results also share insights into the optimal mix of cogeneration equipment needed to reduce SCC and LCC at the community scale. However, on a broader solution space scale, the average community designs within the top-performing SCC did not show any statistically significant improvements in carbon emissions for community designs with heat pumps. The replacement of traditional HVAC with heat pumps in a subset of large commercial buildings therefore produces a small set of design options for urban and energy planners to choose from when using this type of model, and suggests that if heat pumps are pursued for energy and carbon savings goals, it needs to be designed optimally for the building's conditions to produce positive outcomes. The findings also suggest leveraging the use of such a model for carbon reduction goals through the model's ability to quantify the SCC when examining building level changes to HVAC systems. Together, the results provide planners and policy makers with insight on the importance of the technological design considerations of heat pumps when advancing their use in net zero energy and building electrification goals for carbon reductions

Advisor: Lepech Michael
Optimizing application of wastewater-based epidemiology for SARS-CoV-2 at various scales of operation

The COVID-19 pandemic has accelerated the development of wastewater-based epidemiology focused on SARS-CoV-2 and has proven to be a valuable supplement to clinical data. Many researchers have successfully detected and quantified SARS-CoV-2 in a variety of wastewater samples, leading now to the establishment of formalized wastewater monitoring programs not only for SARS-CoV-2 but for other pathogens relevant to human health as well. At present, however, there is no clear consensus on the best method for processing of wastewater samples or the many ways that detection and quantification can be optimized. Through a combination of data analysis, simulations, and a pilot study, this dissertation investigates different ways to optimize domestic wastewater surveillance at various scales. Chapter 2 analyzes data from multiple wastewater monitoring programs for comparison of SARS-CoV-2 RNA concentration from solid and liquid samples obtained from publicly owned treatment works (POTWs). Chapter 3 investigates how digital droplet PCR sensitivity to SARS-CoV-2 affects wastewater surveillance detection limits for COVID-19. Finally, Chapter 4 is a pilot study conducted at two K-12 schools in California to verify the usefulness of wastewater surveillance for smaller communities like schools where individuals only spend a portion of their time. Taken together, the contents of this dissertation will help public health officials in their development of wastewater-based surveillance methods to aid with assessment of community health for a comprehensive surveillance system tailored to local needs

Advisor: Criddle Craig
Boehm Alexandria
Luby Stephen
Order parameter texture of unconventional superconductors

A variety of unconventional superconductors have shown closely competitive tendencies towards different orderings. This leads to a rich phase diagram as a function of external tuning parameters, including magnetic fields and disorder. Under proper conditions, these perturbations can lead to inhomogeneous superconducting states, which become particularly important near phase transitions. The consequent inhomogeneity can affect the shape of the phase boundary, and the nature of phase transitions can be significantly altered. This thesis will illustrate these points under three circumstances. The first part of the thesis is about the competition between superconductivity and charge density wave (CDW) order. As local disorder suppresses charge ordering, it effectively enhances superconductivity. In the core of a dislocation of the CDW, local superconducting states can emerge. These superconducting puddles can develop long-range order at low temperatures. Chapter one will describe experimental signatures of this fragile superconducting state. The second part of the thesis is about the effect of inhomogeneous strain. In a clean system, the superconducting critical temperature of a chiral p-wave superconductor is a linear function of the uniaxial strain, and the phase diagram can host a tetracritical point. The shape of the superconducting phase boundaries near this critical point is significantly altered by the local variations of the uniaxial strain. The last part of the thesis is about the effect of quenched disorder near a first-order phase transition between two superconducting orderings. As the local ordering preference is disturbed by the disorder, superconducting inhomogeneity proliferates. The effect of thermal fluctuation is enhanced by inhomogeneity, which reduces the superconducting critical temperature near the first-order phase transition. This eventually leads to a non-monotonic phase boundary. The first-order phase transition itself may be destroyed under proper conditions

Keywords: Physics.
Advisor: Kivelson Steven
Raghu Srinivas
Hwang Harold Yoonsung
Kapitulnik Aharon
Organic mixed ionic electronic conductors for electrochemical devices

The development of wearable devices for continuous health monitoring of biomarkers requires materials that are mechanically compliant, biocompatible, and are sensitive to biochemical molecules. One class of materials that show promise are Organic Mixed Ionic Electronic Conductors (OMIECs), commonly semiconducting polymers, which are redox-active and can simultaneously conduct ions and electrons. Electronic charges accumulated on the conjugated polymer backbone result in secondary property changes in electrochemical potential and electronic conductivity, allowing OMIECs to be implemented in a variety of devices such as chemical sensors, organic electrochemical transistors, and energy storage electrodes. Additionally, the mechanical flexibility and biocompatibility of these polymers enable conformable and seamless integration with biological interfaces, enabling bio-interfacing devices for continuous health monitoring. My PhD research investigates how OMIECs can be designed, characterized, and implemented in 1) polymer-based batteries for energy storage, 2) electrochemical sensors for the detection of biological analytes, 3) organic electrochemical transistors that amplify biosensing signals, and 4) tunable antennas for wireless signal transmission in microwave frequencies compatible with consumer electronics. Leveraging fundamental materials characterization to drive the understanding of device physics, these OMIEC-based technologies are integrated into a fully self-powered and wireless glucose sensor

Keywords: Materials Science and Engineering.
Advisor: Salleo Alberto
Bao Zhenan
Chueh William
Organizing for violence : the politics of militant group formation and fragmentation in armed conflict

Non-state armed groups fuel much of the world's ongoing armed conflict. Though often weaker than their government adversaries and forced to operate in secret, many armed groups have shown a surprising ability to emerge, survive, and even thrive in challenging environments. What explains the strength and durability of these groups? Drawing on several sources of original data, I show that armed groups and their leaders gain strength from the founding support of international actors and from the consolidation of organizational control. These internal and external sources of strength enable armed groups to emerge and endure in environments where group formation is difficult and organizational fragmentation is likely. In the first paper, I show that a primary threat to the survival of armed groups is leadership transition. To thwart internal challenges to group cohesion, group leaders must actively employ managerial tools to discourage splintering within their organizations. In the second and third papers, I show that international actors play a central role in creating highly violent armed groups. Seeking trustworthy and capable proxies, foreign states can facilitate the formation of new armed groups to serve as their partners. I argue that states engage in this behavior as a way to mitigate the principal-agent problems that often plague sponsor-proxy relationships. I find that states are more likely to employ "founding" support under certain conditions, particularly when the menu of potential partners in a target state is small. Sponsors may perceive their "foreign founded" proxies as more trustworthy and thus may be willing to invest significantly in the military capabilities of these groups. I find that foreign founded groups conduct more attacks in civil war compared to armed groups receiving other types of non-founding state support. Overall, the findings of this dissertation demonstrate that international and organizational politics directly influence the emergence and strength of armed groups and patterns of violence in civil war

Keywords: Political Science.
Advisor: Fearon James D.
Schultz Kenneth A.
Weinstein Jeremy M.
The origins of a sixteenth-century "in-between" generation and the long shadow of early twentieth-century German historiography

This dissertation takes as its point of departure a problematic historiographical tradition. Even while recognizing that the death of the famous composer Josquin des Prez (1450--1521) marked a stylistic turning point, scholars working in Germany in the early twentieth century characterized the decades that followed, ca. 1520--50, as an aesthetic retrenchment, overstating Josquin's influence and unwittingly lumping into the same generation sixteenth-century musicians who in fact worked at different times and in different stylistic idioms. Relying on research in approximately thirty archives, this study reveals how a problematic narrative arose owing to nationalism, religious politics, interpersonal politics, the state of the field at the time, and the inaccessibility of primary source materials. The dissertation revisits composer biographies and the datings of central musical sources. And it uses comparative stylistic analyses of sacred polyphony to pinpoint how, when, and where a new style emerged ca. 1520. Placing writings that launched the modern historiographical tradition in dialogue with musical repertories central to the early history of musicology, the dissertation aims to give appropriate weight to a decisive shift in the history of music while also revealing the enduring influence of early German scholarship on the discipline as a whole

Keywords: Music.
Advisor: Rodin Jesse
Berger Karol
Schiltz Katelijne
Outcomes of Hispanic and non-Hispanic White pediatric and young adult patients with B-cell acute lymphoblastic leukemia after commercial tisagenlecleucel

Population-level data show significantly inferior outcomes for Hispanic children, adolescents, and young adults (CAYA) diagnosed with acute lymphoblastic leukemia (ALL) relative to non-Hispanic White (NHW) patients, even after adjusting for disease prognosticators and socioeconomic status. Here, we compare outcomes between Hispanic and NHW CAYA patients with relapsed and/or refractory (R/R) B-cell ALL (B-ALL) receiving tisagenlecleucel, a CD19-specific chimeric antigen receptor (CAR) T cell therapy. We used data from the Pediatric Real World CAR Consortium (PRWCC) retrospective cohort of 200 patients who underwent cell shipment to Novartis for standard-of-care tisagenlecleucel between August 2017 and March 2020 at 15 US institutions. Baseline factors, efficacy outcomes, and safety outcomes were characterized for Hispanic and NHW infused patients. With respect to baseline factors, Hispanic patients were significantly older at diagnosis and had significantly shorter time from diagnosis to infusion. Hispanic and NHW patients did not significantly differ across sex, age at CAR infusion, leukemia type, number of prior lines of therapy, receipt of prior CD19-directed therapy, disease burden pre-infusion, number of relapses pre-infusion, or initial cytogenetic risk. With respect to efficacy outcomes, Hispanic and NHW patients did not significantly differ across day 28 complete response (CR) rate, 6-month overall survival (OS), 1-year OS, 18-month OS, 6-month event-free survival (EFS), 1-year EFS, 18-month EFS, 6-month duration of response (DOR), 1-year DOR, 6-month duration of B-cell aplasia (DBA), or 1-year DBA. Univariate and multivariate analyses did not associate Hispanic ethnicity with a change in OS, EFS, DOR, or DBA. With respect to safety outcomes, Hispanic and NHW patients did not significantly differ across cytokine release syndrome (CRS), maximum CRS grade, tocilizumab use, steroid use, neurotoxicity, maximum neurotoxicity grade, grade 4 neutropenia, tumor lysis syndrome, number of infections post-infusion, or length of pediatric intensive care unit (PICU) stay. Both efficacy and safety outcomes were similar between Hispanic and NHW CAYA R/R B-ALL patients receiving tisagenlecleucel in the real-world setting. Increasing access to CAR therapy among Hispanic patients could help mitigate population-level disparities in outcomes.

Keywords: Cellular therapy
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Thesis
Advisor: Kurian Allison
Schultz Liora
Outpatient Gastroenterology follow-up reduces GI-specific readmissions among patients with acute severe ulcerative colitis

Ulcerative colitis (UC) is a form of inflammatory bowel disease (IBD) that is characterized by pathologic inflammation and ulcerations in the colon resulting in bloody bowel movements, anemia and malnutrition with a relapsing and remitting course. Hospitalization for disease flares is common in cases with a severe phenotype and requires intensive monitoring and intravenous therapies; readmission within 30 days occurs in up to 18% of patients, for which the most common indication is disease flare. Readmissions are associated with increased morbidity, mortality, as well as costs, but the importance of post-discharge follow-up with a gastroenterology specialist as well as the optimal interval are unknown. We conducted a retrospective cohort study of 223 patients with medically-managed ulcerative colitis who were admitted to the Stanford University Hospital between 2010 and 2020. We included adult patients with UC who were admitted for a UC flare. Patients with a colectomy by time of discharge or who were diagnosed with Clostridium difficile infection at the index hospitalization were excluded. The primary outcome was time to readmission for a GI-related indication, and the primary predictor of interest was follow-up with a gastroenterology provider. Patients were censored 180 days after discharge. At the index hospitalization, 60.9% had pan-colitis, and 87.9% had moderate-to-severely active endoscopic disease. Follow-up occurred within 7 days in 65 patients (29%), within 30 days in 153 patients (68.7%), and within 180 days in 198 patients (89%). Readmission occurred in 57 patients (25%); 31 happened within 30 days for a 30-day readmission rate of 13.9%. In the Cox proportional hazards model adjusted for age, sex, and albumin level using follow-up with a gastroenterology provider as a time-dependent predictor, follow-up was associated with fewer readmissions (hazard ratio 0.42, 95% confidence interval 0.22-0.81, p=0.009). In particular, follow-up within 7 days after discharge (occurred in 65 patients) was strongly associated with reduced risk of subsequent readmission (HR 0.24, 95% CI 0.09-0.69, p-0.008). Via the log-rank test for trend, earlier follow-up was found to be associated with fewer less readmissions (p<0.0001). Our analysis demonstrates the benefits of early post-discharge follow-up in patient, which may represent an important approach to reduce the burdens of readmissions in this patient group.

Keywords: Inflammatory bowel diseases
Ulcerative colitis
readmission
follow-up
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Thesis
Overexposed? The Effects of Prenatal Pesticide Exposure on Educational Outcomes

This thesis aimed to investigate the potential connection between prenatal exposure to two specific types of pesticides (organophosphates and proposition 65 chemicals) and academic outcomes, including both standardized test scores and behavioral measures. The sample was drawn from students enrolled in the Fresno Unified School District in the 2015–16 school year who were born in the state of California. The sample was majority Hispanic (n = 16686) and included slightly more females (n = 14855) than males. Organophosphate exposure had a significant negative effect on standardized test scores (but notably not on behavioral outcomes) in unadjusted analyses, but these effects disappeared after adjusting for sociodemographic factors. Proposition 65 chemical exposure did not have a significant effect on any of the outcomes of interest in either the unadjusted or adjusted analyses. In conclusion, it seems unlikely that prenatal pesticide exposure (at the level it currently exists in California) has a significant effect on school-aged children beyond the effects of the demographic factors it is associated with.

Keywords: Prenatal influences
Pesticides
Academic achievement
School attendance
Special education
Fresno Unified School District
organophosphate
Proposition 65
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Thesis
Advisor: Sanders Lee
Yeatman Jason