VictorJuiz/thesis huggingface dataset:
Prior-informed machine learning for biomedical imaging and perception

Deepening our understanding of human health is more important than ever before for addressing real-world challenges in biomedicine and healthcare, especially with the recent pandemic. My research focuses on AI in medicine, to develop efficient ML models for biomedical imaging and perception for addressing clinically important problems. In this thesis, I will first explore the challenges in this emerging field and then present the two majors lines of my PhD research work. First, I will introduce my work on AI in biomedical imaging. Specifically, I will discuss how to integrate different kinds of prior knowledge to develop reliable data-efficient ML models, by exploiting the personalized priors, population priors and physics priors. With the prior-informed ML models, the proposed approaches can be applied to various applications including sparse-sampling CT and MRI image reconstruction, X-ray projection synthesis, and Cryo-EM imaging. These techniques show significant potential to impact cancer imaging and treatment. Second, I will introduce my work on AI in image perception. I will discuss how to develop ML-driven perception models that can adapt to the unique characteristics of biomedical data. Specifically, I will present a self-attention-guided ML model for quantitative image perception of fetal brain MRI images. This includes a cross-institute validation involving four U.S. clinical centers and a Turkish institute. This work demonstrates the ability of the developed ML model to characterize in utero neurodevelopment for anomaly detection in real-world clinical deployments

Keywords: Electrical Engineering.
Advisor: Pauly John (John M.)
Xing Lei
Wetzstein Gordon
Privacy in the COVID-19 Pandemic: Analyzing the Impact of the Length of Data Privacy Law Existence on Variation in COVID-19 Contact Tracing Apps

The rapid creation of contact tracing apps at the beginning of COVID-19 is unprecedented given that 109 countries adopted these apps in the span of just a few months. Governments turned to contact tracing apps to speed up the process of manual contact tracing, piloting a system that had never been used before. This was often presented as a solution to the pandemic, but these apps came with the innate drawback of collecting sensitive personal information. This data collection gave governments an opportunity to use contact tracing apps as a way to expand surveillance of their populations. There are many concerns that this surveillance will persist after the end of the pandemic, which poses a significant risk to privacy and civil liberties at large. In this thesis, I seek to understand how the length of time that a country has had a data privacy law impacts the implementation of its contact tracing app. I find that the duration of a data privacy law has no impact on a country’s contact tracing app implementation. Instead, country-specific factors play a role. I look at the cases of Australia and South Korea, as they both have had a data privacy law for a long period of time but implemented their contact tracing apps in very different ways. I argue that Australia’s previous mishandling of digital projects and South Korea’s experience with the 2015 MERS outbreak alongside the government’s skillful deployment of technology shaped how the two countries designed their contact tracing apps.

Keywords: Law
contact tracing apps
data privacy
Center on Democracy Development and the Rule of Law
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Thesis
Advisor: Fukuyama Francis
Private data analysis beyond the worst case

Differential Privacy (DP) provides strong guarantees on the risk of compromising a user's data in statistical and machine learning applications. However, privacy-preserving algorithms often suffer considerable loss in accuracy compared to non-private algorithms, both in theory and practice. In this thesis, we investigate and study several approaches towards improving the cost of private algorithms and closing the gap between private and non-private performance. While there exist many privacy-preserving algorithms with optimality certificates, most of these hold only in the worst case setting; that is, the performance of the algorithm is measured by it's performance on the worst-case input. Therefore a (worst-case) optimal algorithm may not be achieving the best possible performance for certain functions with more natural inputs. Building on this observation, we propose three general directions for designing algorithms that can improve the privacy cost and outperform existing (worst-case) optimal algorithms. In our first approach, we move beyond worst-case optimality and define a new notion of instance-optimality in differential privacy. Instance-optimal algorithms adapt to the difficulty of the underlying input and therefore result in improved performance for natural inputs. We develop an algorithm, namely the inverse sensitivity mechanism, which is nearly instance optimal and present several instantiations for statistical and machine learning applications such as median estimation, regression problems, and principal component analysis. As our instance-optimal algorithm may be computationally intractable in some settings, our second approach moves beyond worst-case optimality by identifying natural properties of the inputs that hold in practice. This will allow to (i) design efficient and optimal algorithms for these families, and (ii) improve the rates compared to worst-case inputs as these inputs do not satisfy the properties we consider. Our final approach builds on the observation that differential privacy may be too stringent for some use cases. To address this, we propose element level differential privacy, which extends differential privacy to provide protection against leaking information about any particular ``element'' a user has, allowing better utility and more robust results than classical DP. By carefully choosing these ``elements, '' it is possible to provide privacy protections at a desired granularity and result in better utility

Keywords: Electrical Engineering.
Advisor: Duchi John
Feldman Vitaly 
Pilanci Mert
Weissman Tsachy
Probing extreme states of matter using high resolution inelastic X-ray scattering at hard X-ray free electron lasers

This dissertation focuses on the investigation of the stiffening of the interatomic potential of a gold lattice under intense optical irradiation. Even though this exotic behavior, predicted by theory, has been investigated experimentally using electron diffraction, its observation is still debated. Here, nanometer-thick foils of gold have been irradiated using a femtosecond optical laser pulse to energy densities higher than previously reported values and subsequently probed using X-rays. At these conditions, the response of laser-excited gold was found to be consistent with theoretical predictions. To go beyond the previous measurement, an experimental platform based on inelastic X-ray scattering at an X-ray Free Electron Laser is presented to circumvent the need for a theoretical model and thus bring an unambiguous observation of this exotic phenomena in laser-excited gold. Such observation would be important to deepen our understanding of the melting behavior of gold under extreme conditions such as the ones generated during ultrafast laser processing of materials

Keywords: Aeronautics and Astronautics.
Advisor: Glenzer S. H.
Senesky Debbie
Hastings Jerome
Lindenberg Aaron Michael
Probing molecular and cellular design principles in signaling : from Wnt biology to cytoskeletal mechanics

Most animals develop from a single-celled embryo into a morphologically complex adult form through a coordinated program of cell division, migration, death and differentiation. This developmental process is guided in large by mechanical and biochemical signals. The same signaling pathways are involved in the normal functioning of a grown adult, and their malfunction enables pathologies such as cancer and pathogenic infection. In this thesis, I focus on understanding how a subset of these pathways allow cells to communicate and interact with extracellular signals at a molecular and cellular level. In Chapter I, we investigated mechanisms by which the developmental signaling protein Wnt activates the canonical Wnt pathway, where the cell is instructed to turn off the "destruction complex" constitutively inhibiting the main co-transcriptional activator of the pathway. We find that upon Wnt activation, Dishevelled, the cytoplasmic transducer of the Wnt signal, is mostly present as oligomers of 1 to 10 molecules. The oligomers possess a double helical filamentous nature, and likely recruit and inhibit the destruction complex component protein Axin at the filament ends, thus enabling Wnt activation. In Chapter II, we study mechanisms by which epithelia respond to mechanical challenges, a critical part of their physiological role. In particular, we ask how cells recover when a wound forces them to detach from their adhesions. We find that branched actin polymerization-based lamellipodial membrane spreading helps recover the cell's original footprint within seconds, which is closely guided by membrane tethers extruded from adhesions during the detachment. Our experiments suggest that extruded tether-guided lamellipodia constitute a robust and general wound-healing response to cell detachment. In Chapter III, we focus on the cytoskeletal actin cortex beneath the cell membrane, which mechanically supports the cell but is able to drive processes such as cell migration through rapid remodeling. We ask how the cortex can be dynamic within the plane of the membrane, while simultaneously maintaining a stable attachment to the membrane through membrane-cortex linker proteins. By developing an optical trap assay, we show that the stereotypical membrane-cortex linker protein Ezrin forms a complex of 2-3 molecules that behave as a sliding anchor over micron distances while resisting orthogonal detachment forces. We propose that sliding anchors may constitute an overlooked yet essential element of the cell cortex

Advisor: Dunn Alexander Robert
Bryant Zev David
Fordyce Polly
Weis William I.
Processes that shape the avian gut microbiome

Animals harbor and maintain a diverse assemblage of bacteria, viruses, fungi, and other eukaryotic organisms that reside and interact at a particular body site. The net effect of these interactions, most notably in the gut, is responsible for mediating host health. The gut community consistently demonstrates its importance in animal hosts. However, most studies focus on humans or model organisms. As such, I applied the techniques developed in microbiology to wildlife, particularly avian hosts. In my dissertation, I independently developed research questions, acquired funding for projects, and established collaborations with experts in various fields to investigate: (1) how land-use change influences Neotropical passerine birds, (2) how dietary guild affects the gut microbiome of a diverse group of bird species, (3) how captivity changes the Brown Kiwi (Apteryx mantelli) gut microbial communities, and (4) how the gut microbiome assembles and changes throughout Brown Kiwi development. In the first chapter, I quantified the impact of land-use change on six species of Neotropical passerines and their gut microbiomes (San Juan et al. 2020). I found bacterial communities responded more strongly to host species identity than to the habitat type, where sites ranged from primary forests to intensified coffee farms. However, the microbiomes of two out of the six bird species were modified, suggesting some bird species may be more vulnerable to land-use change than others. In chapter 2, I assessed how host species and family, dietary guild, habitat, and migratory status contribute to the gut bacteria of 79 bird species. I found host species identity to be the strongest predictor of the gut microbiome, followed by dietary guild. Migratory status had little influence on the gut microbiota. In chapter 3, I investigated how captive rearing, a practice crucial in the recovery of endangered species, impacts Brown Kiwi gut bacteria and fungi. I found a significant drop in alpha diversity and shifts in community composition between wild and captive kiwi (San Juan et al. 2021). To further elucidate captivity's influence on the gut microbiome, I performed a comprehensive longitudinal study on captive kiwi to explore the temporal dynamics of their gut microbes. I found that the gut microbiome fluctuates day-to-day, especially early on in life. Age was a stronger predictor of gut microbiome variation compared to a common disease (coccidiosis). Overall, my research considers host identity, life history traits, and environmental factors including their habitat as explanatory variables of wildlife gut microbiomes. I generated datasets that emphasize the importance of the gut microbiome, an often neglected aspect in conservation practices. Understanding the factors that contribute to avian gut microbial communities may highlight areas we have not considered in other host species

Keywords: Biology.
Advisor: Fukami Tadashi
Daily Gretchen C.
Peay Kabir
The production, retention, and measurement of teachers

This dissertation is comprised of three papers relating to the American public school teacher work force. I use large scale records covering millions of teachers to ask: 1) How many teachers are quitting their jobs, and can we use public records to better answer this question? I assemble public records to create a database that includes individual teacher records from 13 states covering roughly 35\% of American public school teachers. I find that across states between 10 and 15 percent of teachers stop teaching in their district in a given year, and also that there is substantial variation across districts in that rate. I discuss implications for future research from the widespread availability of individual level, longitudinally linked, teacher employment data. 2) When Oklahoma boosted teachers' salaries by \$6,000, did their retention rates improve? Descriptive time series analyses in Oklahoma find no noticeable change in trend for turnover rates. I use a difference in difference analysis to compare district turnover rates in Oklahoma to Texas and Kansas, and can rule out a change as small as 0.72 percentage points. This lack of effect is robust across multiple specifications and comparison groups. 3) If we change the passing standards on a teacher licensure exam, will that change who attempts to take the test? Given the current concerns about increasing the number and diversity of new teachers, policy makers are re-examining the role of teacher licensure tests. I use difference in difference techniques to compare who shows up to take a teacher licensure exam before and after the passing "cut score" is changed. I find suggestive evidence that when standards are lowered from high levels, the share of Black candidates and candidates from alternative preparation programs increases. However, an analysis of 32 cut score change events, most of which were small changes, did not find a consistent relationship between the cut score change and changes in the composition of test takers

Keywords: Education.
Advisor: Domingue Ben
Dee Thomas S. (Thomas Sean)
Loeb Susanna
Progress on the practical integration of cryogenics to gravitational-wave detectors

The success of the LIGO and Virgo observatories has launched a new era of gravitational-wave astronomy. Despite their achievements, there is still plenty of room for improving the technologies that have made gravitational-wave detection possible. One avenue for improvement comes in the form of using silicon masses cooled to 124 Kelvin to reduce the thermally driven noise in the midband of the observatories. This idea, while promising, carries a lot of technical challenges that must be overcome before it can be put to practice. This work covers investigations on some practical aspects of integrating cryogenics to gravitational-wave interferometers, including estimation of technical noises introduced by cryogenic equipment---such as Newtonian or scattered light noises---selection of a proper cryogen, and adequate procedures for faster iteration times for research and development of the cryocooled interferometer technologies

Keywords: Physics.
Advisor: Byer R. L. (Robert L.)
Fejer Martin M. (Martin Michael)
Hollberg Leo (Leo William)
Promoting Nutrition Security in Diverse Low-Income Communities: Methods to Comprehensively Assess Food Access

It is well understood that what we eat is intimately connected with our health. Traditional health promotion strategies rely heavily on individual behavioral interventions, but not all individuals have equitable access to the nutritious foods needed to live a healthy and disease-free life. Moreover, quantifying and addressing food access is difficult because of the multitude of complex factors involved. In response to this challenge, this study evaluates how a mixed multi-method approach of characterizing the food environment 1) addresses the conceptual definitions of food access; and 2) identifies assets and areas for community activation to increase access to nutritious foods. In particular, a food environment map using geographic information systems (GIS) will be discussed as a method to assess food access surrounding four independently owned mid-sized grocers and corner stores in San Jose, California. The GIS food environment map in this study is a supplemental piece of a larger project with the Our Voice initiative and The Food Trust which utilizes citizen science to promote nutrition security in the community. The map revealed a high prevalence of food outlets with processed food options as compared to food outlets with fresh produce options. It also revealed there were numerous opportunities to obtain food that were not acknowledged by the USDA Food Access Research Atlas. An accurate understanding of food access in the local environment, inclusive of community member insights, essential for developing and implementing solutions (interventions, policies, programs) to promote nutrition security in a community.

Keywords: Nutrition
Food security
Nutrition security
Community-engaged
Geographic information systems
Citizen science
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Thesis
Proof systems for scaling blockchains

The integrity of record-keeping is essential to a functioning society. Our dependence on digital records has become absolute, from our personal wealth, commerce, and identities to sources of knowledge and news. In recent years, blockchains have arisen as a new form of digital record-keeping that is operated by decentralized sets of participating computers. While traditional record-keeping places trust in a centralized service, blockchains remain secure so long as the number of corrupt computers does not exceed a large threshold, an assumption that can also be strengthened via economic incentives. However, this robustness comes at a cost. Blockchains struggle to process updates at the same rate as standard transactional systems. As a result, rising demand has led to congestion and soaring transaction fees. In this dissertation, we construct several cryptographic proof systems that help scale the throughput of blockchains. The first set of tools we construct are authenticated data-structures (ADSs) and succinct non-interactive arguments of knowledge (SNARKs) that leverage new techniques based on groups of unknown order (GUOs) to achieve significantly lower communication than prior methods, without relying on a so-called trusted setup. These tools can be used to reduce the required bandwidth, computation, and storage of nodes participating in the blockchain protocol. However, it is challenging to apply these tools on their own to scale the throughput of blockchains while maintaining the guarantee that critical public data recorded in the blockchain remains available to users. To address this challenge we construct a new type of proof system called proofs of replication (PoReps), which help to ensure data is redundantly stored and available

Advisor: Boneh Dan
Reingold Omer
Tan Li-Yang
Wootters Mary
Proteomic Profiling of Purkinje Cell Surface Reveals the Critical Role of Armadillo-like helical domain containing protein 4 in Mammalian Dendrite Morphogenesis

Improper dendrite development is exhibited in a range of human neurodevelopmental disorders and neurodegenerative diseases, such as autism spectrum disorder and schizophrenia. Yet, the underlying molecular mechanisms of dendrite morphogenesis are not well characterized. During neuronal development, highly conserved, precisely timed protein interactions at the cell surface mediate dendrite morphogenesis; therefore, cell surface protein identification and characterization may provide key insights to the intricate molecular processes essential to proper dendrite development. Using cell surface proteomic datasets attained by a novel spatiotemporally resolved proteomic profiling technique in situ, we instructed a loss-of-function candidate screen of 13 cell surface proteins to observe their impacts on dendrite morphology. We found that in vivo disruption of the transmembrane protein Armadillo-like helical domain-containing protein 4 (Armh4) engendered a striking dendrite morphological phenotype in transfected cerebellar Purkinje cells. Armh4 disrupted cells exhibited significant height deficiency, decreased total dendrite length and branching, and growth of additional primary dendrites. Here, we present the critical cell-autonomous function and characterization of the signaling mechanisms of the Purkinje cell surface protein Armadillo-like helical domain containing protein 4 (Armh4) during dendrite morphogenesis. We demonstrate that dendrite morphogenesis is sensitive to Armh4 cell surface levels and that endocytosis is required for Armh4 signaling downregulation in proper dendrite development.

Keywords:  Department of Biology
Biology
Molecular biology
Genetics
Proteomics
Morphogenesis
Developmental biology
Neurodevelopment
Dendrites
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Thesis
Advisor: McConnell Susan K
Luo Liqun
The protestant road to state bureaucracy

After the seventeenth century, rulers across Europe attempted reforms to replace amateur administrators with professional bureaucrats. The success of administrative reforms hinged on whether rulers could compensate entrenched patrimonial office-holders and recruit talented employees for a wage. I show that the degree to which these two administrative conditions were met at the time of state reforms depended on whether states experienced a Protestant Reformation in the sixteenth century. I argue that the Reformation, which involved the expropriation of the Catholic Church's assets, set in motion two processes. First, to finance their wars, Protestant rulers used confiscated assets instead of selling offices, leading to smaller stocks of venal office-holders who resisted administrative reforms. Second, expropriations made churches poorer and reduced the number of plum jobs in the clergy, and this incentivized a reallocation of educational investments from religious to "secular" skills that were more useful for state administration. This distinctive Protestant developmental path hastened the demise of the patrimonial state, and by 1789 the only major territorial states that were bureaucratic were Protestant, while all Catholic states remained patrimonial

Keywords: Political Science.
Advisor: Cox Gary W.
Acharya Avidit
Fouka Vasiliki