VictorJuiz/thesis huggingface dataset:
Optimizing Distributed Computing Systems via Machine Learning

The prosperity of Big Data owes to the advances in distributed computing systems, which make it possible to process massive volumes of data in parallel efficiently. As distributed architectures enable scalable and parallel computation with thousands of servers, critical challenges---allocating resources, scheduling tasks, and optimizing computation algorithms across servers---also arise. The dynamic performance of distributed architectures makes it too volatile to address these challenges with deterministic algorithms. In this dissertation, we apply machine learning techniques to optimize distributed systems. Particularly, we contribute to the following two areas that drive the advance of distributed systems in resource provisioning, task scheduling, and architecture design. Optimizing large-scale data analytics systems. Large-scale data analytics---processing data across geographically distributed datacenters---suffers from fluctuating resource provisioning and heterogeneous demands. However, most of the existing solutions are based on simplified heuristics derived from prior experiences, assuming the network bandwidth is a bottleneck. However, we find that the performance bottleneck is alternating---disk I/O and memory can also become the bottleneck. We propose Lube, a new system that detects bottlenecks at runtime and minimizes job computation times by mitigating the bottlenecks. By examining the execution of analytic queries, we show that existing query optimizers choose the slowest execution plan due to the agnostic of bandwidth fluctuations. In this dissertation, we present Turbo, a system that dynamically optimizes execution plans in response to runtime resource variations. Accelerating distributed machine learning systems. Traditional machine learning collecting training data to a server-based cluster has introduced non-trivial overhead and data privacy issues. To address such problems, we propose to refactor distributed machine learning systems with new architectures. In this dissertation, Siren enables distributed machine learning with serverless architectures and simplifies the way of machine learning development and deployment by learning the optimal resource allocation for machine learning training. We then focus on optimizing federated learning---a new distributed machine learning paradigm---that performs training locally on devices to preserve data privacy. However, the statistical issues posed by the local data significantly slow down existing federated learning algorithms. We present Favor, a framework that optimizes federated learning by carefully selecting devices to address the statistical issues.

Keywords: Distributed Computing System
Machine Learning
Advisor: Li, Baochun
Tracing Developmental Origins of Pediatric Posterior Fossa Tumours

Study of the origin and development of cerebellar tumours has been hampered by the complexity and heterogeneity of cerebellar cells that change over the course of development. Here we use single-cell transcriptomics to study more than 60,000 cells from the developing mouse cerebellum and show that different molecular subgroups of childhood cerebellar tumours mirror the transcription of cells from distinct, temporally restricted cerebellar lineages. The Sonic Hedgehog medulloblastoma subgroup transcriptionally mirrors the granule cell hierarchy as expected, while Group 3 medulloblastoma resembles Nestin positive stem cells, Group 4 medulloblastoma resembles unipolar brush cells, and PFA/PFB ependymoma and cerebellar pilocytic astrocytoma resemble the prenatal gliogenic progenitor cells. Furthermore, single-cell transcriptomics of human childhood cerebellar tumours demonstrates that many bulk tumours contain a mixed population of cells with divergent differentiation potentials. Our data highlight cerebellar tumours as a disorder of early brain development and provide a proximate explanation for the peak incidence of cerebellar tumours in early childhood.

Advisor: Taylor, Michael D
Contaminated Environmentalism: The Visual Rhetoric of 1970s Ecocinema

During the 1970s a spate of ecologically-themed science fiction films were produced in North America. Films like The Planet of the Apes (1968), Silent Running (1972), Soylent Green (1973), and Logan’s Run (1976) transformed the concerns of the rapidly expanding modern environmental movement into dystopian narratives and imagery. This dissertation reads examples of science fiction ecocinema from the 1970s alongside the key environmental texts that inspired their production, such as Rachel Carson’s Silent Spring (1962) and Paul Ehrlich’s The Population Bomb (1968). This comparative reading strategy uses science fiction film as a prism through which to view North American environmental history. By placing these films, which may at first seem derivative, alongside the books that inspired the modern environmental movement it becomes possible to expose rhetorical patterns that shape how we think about nonhuman nature. By crystallizing the environmental rhetoric of authors like Carson and Ehrlich into cinematic narrative, essentially turning their doomsday predictions into future worlds, these films put so much pressure on the tropes of the environmental movement that cracks in their logic become visible. This dissertation explores these cracks, demonstrating that the contradictions they reveal lie deep within the environmental movement, continuing to plague it into the present. One such contradiction, or crack, is so prevalent that it structures the dissertation. It is the nearly ubiquitous tension between the environmentalist desire to contain and control nonhuman nature in order to preserve it on the one hand, and the fear of a contaminated environment on the other. While containing, preserving, and archiving the environment may at first seem the best way to protect nonhuman nature from devastating anthropogenic effects, it perpetuates the myth of mastery that placed nonhumans in danger in the first place. An emphasis on contamination, which seems like the opposite of an environmentalist policy, is a more effective way of representing the always chaotic and interconnected environment. The cinema is the perfect medium for exploring this ecological contradiction as it simultaneously contains, and is contaminated by, the profilmic environment.

Keywords: 1970s Environmentalism
Ecocinema
Ecocriticism
Film Philosophy
Rhetoric
Science Fiction
Advisor: Price, Brian
Passive Demand but Active Pay: The Effect of ETFFlows on CEO Stock Option Compensation

The rising prominence of exchange-traded funds (ETFs) over the past decade has resulted in a non-fundamentals driven demand for stocks held in ETF baskets. Prior research on ETFs finds both ETF-related stock price mis-valuation and ETF-related increases in the co-movement of stock prices. Separately, prior research on CEO compensation suggests that firms should use less stock option compensation when stock prices are less informative about firm performance as it becomes more difficult to mitigate the moral hazard problem, but more stock option compensation when there is increased co-movement, as stock options become a more effective tool for retention. Motivated by the fact that stock prices play a key role in CEO compensation decisions, this study tests the effect of ETF flows on CEO stock option compensation. I find that stock option compensation is increasing with ETF flows. Further, I find that the positive relation between stock option compensation and ETF flows is prominent in cross-sections where there is an ex ante motivation to compensate executives with options for retention purposes. Additionally, I do not find a positive relationship between risk-taking or firm performance with ETF flows, but do find a decrease in CEO turnover with increased ETF flows. The combined results suggest that: 1.) ETF flows may have affected firm incentives to compensate managers with stock options for retention purposes, and 2.) incentive alignment does not appear to be a prominent factor in awarding CEO stock options.

Keywords: CEO compensation
ETFs
governance
Stock Options
stock price informativeness
stock return co-movement
Advisor: Bova, Francesco
Mohanram, Partha
Utilization of CRISPR/Cas9-mediated Gene Editing for Correction of Deletion Mutations in DMD

Duchenne muscular dystrophy (DMD) is an X-linked recessive neuromuscular disorder that affects 1 in 5000 boys. DMD is caused by the absence of dystrophin due to mutations in the DMD gene, leading to compromised muscle fiber integrity and progressive muscle deterioration. Deletion mutations account for almost 70% of the DMD mutation spectrum, where the DMD open reading frame (ORF) is disrupted, resulting in the absence of dystrophin expression. In developing a mouse model representative of the DMD disease progression, the first mouse model carrying a Dmd deletion of exons 52-54 (Dmd D52-54) was generated. Dmd D52-54 lacks dystrophin, resulting in dystrophic pathophysiology, cardiac hypertrophy and tachycardia. Removal of exon 55 in the Dmd D52-54 model is expected to yield an in-frame deletion of Dmd exons 52-55 (Dmd D52-55), which is representative of the milder Becker muscular dystrophy (BMD). Through phenotypic characterization, the Dmd D52-55 mouse model validates that the in-frame deletion produces a functional dystrophin protein which improves disease manifestation. To reproduce the Dmd D52- 55 mutational outcome in Dmd D52-54, CRISPR/Cas9 was used to restore the Dmd ORF by either deleting exon 55 or disrupting exon 55 inclusion by targeting a splice site. The strategy was further improved by increasing the dosage of sgRNAs, which led to the recovery of truncated dystrophin protein in the heart and skeletal muscle as well as mild functional improvement. Optimization in sgRNA dosage will be implemented to enhance the efficiency of dystrophin restoration using CRISPR-mediated single sgRNA exon skipping, providing a potential new therapeutic avenue for DMD caused by deletion mutations.

Advisor: Cohn, Ronald D
The Politics of the Middle Class and the Left in Uruguay: Feelings of Insecurity, Solidarity, and Support for Redistribution

This dissertation explores the relationships between the middle class and the Left with a specific focus on attitudes towards redistributive policies. The work is based on an examination of the social attitudes and political propensities of the Uruguayan middle class during the Left governments of the Frente Amplio (FA) (2005-2014) including the lead up to their re-election in 2014. In investigating the attitudes and political proclivities of members of the Uruguayan middle class, I incorporate a consideration of the significant political and economic changes that occurred from the middle of the twentieth century onward. The work combines historical analysis and analysis of in-depth interviews conducted by the author. I argue that the presence of two sets of factors that shape individual’s senses of insecurity and solidarity help to explain middle class support for, or opposition to, redistributive policies. One set involves the presence or absence of a complex of insecurity mitigating factors; the second involves socialization processes that inculcate support for the social norms of equality and collective responsibility. I argue that a combination of insecurity mitigating factors and exposure to socialization processes that inculcate norms of equality and collective responsibility, producing social solidarity, tends to contribute to middle class support for the Left and the redistributive measures it stands for. On the other hand, the absence of these two sets of factors increases feelings of insecurity and erodes social solidarity. Particularly when combined with economic and political uncertainly, this tends to result in middle class resistance to redistributive measures. This complex of factors is therefore important in contributing to the necessary cross-class coalition of support required for the election of Left governments and ensuing redistributive measures.

Keywords: Insecurity
Middle Class
Political Left
Politics of Inequality and Redistribution
Solidarity
Uruguay
Advisor: Teichman, Judith
Effect of Sulfur Chemical Potentials on Identities and Involvements of Hydrogen Species in Hydrogenation of Heteroarenes and Carbonyl Compounds on Sulfided Transition Metal Clusters

Hydrogenation mechanisms of heteroarenes and aliphatic carbonyls on transition metal or metal sulfide catalysts depend on metal chemical states, reactive hydrogen species, and thermochemical properties of hydrocarbons. This thesis examines the structures of Ru/SiO2, Pd/SiO2, and Pt/SiO2 catalysts in the presence of H2S (1.44 × 10-3–2.64 × 10-2 H2S:H2 ratio), where Ru nanoparticles transform into metallic cores covered with one monolayer of S-deficient RuS2, whereas Pd and Pt nanoparticles retain their metallic states with surfaces covered with reversible and irreversible sulfur. On Ru sulfides, the Run+-(Hδ–)-S2–-(Hδ+) proton-hydride pairs and Run+-(SH2)-S2– protons are the reactive hydrogen species. Pyridine has a high proton affinity; its hydrogenation is initiated by a proton addition from either Run+-(Hδ–)-S2–-(Hδ+) or Run+-(SH2)-S2– at its N, followed by a kinetically relevant hydride addition from Run+-(Hδ–)-S2–-(Hδ+) at the α-C. Pyrrole has a lower proton affinity; its hydrogenation is initiated by a kinetically relevant attack of a S2–-(Hδ+) proton from Run+-(Hδ–)-S2–-(Hδ+) at β-C, followed by an addition of a Run+-(Hδ–) hydride at α-C. On Pd and Pt, the protonic, reversible HSr* species and hydridic H* adatoms are the reactive hydrogen species. Pyridine adsorbs on metallic sites either via σ-interaction through the N lone electron pair, or via π-interaction through its aromatic ring. Hydrogenation of both σ- and π-bonded pyridine requires five H* additions at C atoms and one HSr* addition at N, where the third or fourth H* addition at C limits the rates for σ-bonded pyridine, and the third or fourth HSr* attack to N limits the rates for π-bonded pyridine. The comparison of Ru sulfides, S-covered Pd and Pt shows that both hydrogenation and C-N bond hydrogenolysis reactivities have volcano dependences on metal-sulfur binding strengths, and the hydrogenolysis-to-hydrogenation rate constant ratio increases with the decreasing metal-sulfur binding strength. Finally, this thesis establishes the reactivity trends of heteroarenes and aliphatic carbonyls on Ru sulfides. For heteroarenes, the hydrogenation reactivities relate to proton affinities, because the initial proton addition limits the rates. For aliphatic carbonyls, the reactivities relate to hydride affinities, because the initial hydride addition limits the rates.

Keywords: carbonyl compound
heteroarene
hydrogenation
mechanism
sulfur chemical potential
transition metal
Advisor: Chin, Ya-Huei (Cathy)
Understanding and Supporting Anticipatory Driving in Automated Vehicles

With state-of-the-art driving automation technology available to the public (i.e., SAE Level 2 driving automation), drivers no longer need to control the vehicle continuously, but are still required to monitor the road and the automation, and take over control or adjust the automation’s setting when necessary. Thus, many driving skills, such as anticipatory driving, which can allow drivers to predict potential traffic changes and respond to them in advance, can still enhance driving safety in automated vehicles. Anticipatory driving has already been found to be more prevalent among experienced drivers in non-automated vehicles. However, the factors influencing anticipatory driving in automated vehicles has not yet been investigated. Thus, this dissertation aims to understand anticipatory driving behaviors in automated vehicles and investigate displays that can support it. Three driving simulator experiments were conducted. The first experiment investigated the relationships between anticipatory driving, distraction engagement, driving experience, and visual attention allocation in non-automated vehicles. The second experiment re-investigated the factors mentioned above in a simulated automated vehicle equipped with adaptive cruise control and lane keeping assistance. The third experiment investigated the effectiveness of two displays in supporting anticipatory driving among experienced and novice drivers in automated vehicles, i.e., a TORAC display with takeover request (TOR) and automation capability (AC) information, and a STTORAC display with surrounding traffic (ST) information in addition to the TORAC display. Results show that in both automated and non-automated vehicles, experienced drivers exhibited more anticipatory driving behaviors, and distraction engagement impeded anticipatory driving for both novice and experienced drivers. Further, allocating more visual attention toward cues indicating upcoming events increased the odds of exhibiting anticipatory driving behaviors in non-automated vehicles. For automated vehicles, it was found that drivers’ reliance on automation might have a larger impact on the performance of anticipatory driving compared with visual attention to cues. The TORAC display led to less anticipatory driving in automated vehicles, possibly because it led to over-reliance on automation. Providing additional context information in the STTORAC display presumably supported drivers’ anticipation of potential traffic conflicts.

Keywords: Driver behavior
Driver distraction
Driving automation
Driving simulator
Experience
Visual attention
Advisor: Donmez, Birsen
Handheld Microfluidic Bioprinter for In Situ Delivery of Skin Tissue Constructs

Full-thickness burns where both the epidermal and dermal layer of the skin are destroyed lead to high patient mortality due to complications like dehydration, infection, and shock. The current standard of care involves isolating healthy skin from uninjured regions, followed by meshing and grafting onto the debrided wound site. However, this approach is not appropriate for patients with large area burns covering over 40% of the total burn surface area as insufficient quantities of healthy skin remain. Although many bioprinting approaches have been developed to meet this demand by converting biopolymer solutions, or “bioinks”, into three-dimensional tissue structures, current bioprinters are primarily designed for laboratory use and allow only small, centimeter-sized tissues to be prepared. Here, a novel handheld bioprinting system for in situ delivery of cell-containing biomaterial constructs was designed to deliver a variety of cell types embedded in alginates, collagens, or fibrins, accounting for unique physical properties and gelation mechanisms of each biomaterial. This technology was shown to be compatible with primary keratinocytes, dermal fibroblasts, and mesenchymal stem cells, allowing cell organization into distinct patterns such as stripes, spots, and bilayers using a microfluidic printhead. To enable conformal and consistent biomaterial construct delivery onto physiological substrates, a two degree-of-freedom rotational printhead and a compliant silicone wheel was integrated into the printhead setup. A fibrin-hyaluronic acid bioink composition was optimized to promote the formation of tissue constructs on tilted surfaces, balancing appropriate enzymatic gelation times with resistance to material drainage. In a case study to determine the utility of this approach, mesenchymal stromal cells delivered using the handheld bioprinter were shown to improve wound healing outcomes on four porcine models of full-thickness burn. Lastly, the capabilities of the instrument were further developed by implementing active and passive temperature control to allow consistent deposition of collagen-based bioinks, and by integrating disposable thermoplastic printheads fabricated using silicon wafer-based thermal embossing to enable sterile operation in a clinical setting. Taken together, this handheld bioprinter enables the conformal delivery of cell-containing extracellular matrix bioinks in situ and lays the foundation for future human clinical trials for the treatment of large-area, full-thickness burns.

Keywords: Biomaterials
Bioprinting
Medical Devices
Microfluidics
Tissue engineering
Advisor: Guenther, Axel
Three Essays on Empirical Asset Pricing

This dissertation contains three essays on empirical asset pricing. In the first essay, I study the relationship between idiosyncratic volatility and expected returns of risky assets. I find that when the true asset pricing model cannot be identified, the idiosyncratic volatility obtained from a misspecified model contains information regarding the hedge portfolio in Merton’s (1973) ICAPM. Empirically, I find that from 1815 to 2018, a combination of equal-weighted idiosyncratic volatility (EWIV) and value-weighted idiosyncratic volatility (VWIV) can strongly forecast stock market returns over short- and long-term horizons. Furthermore, EWIV and VWIV jointly can explain the cross-section of average stock returns. I show that the combination of EWIV and VWIV is a proxy for the conditional covariance risk in the ICAPM. The deduction also provides new insights concerning the tail risk measure proposed by Kelly and Jiang (2014). The second essay is a joint work with Bing Han. We propose a new and robust predictor of stock market returns and real economic activities based on information from equity options. We aggregate the difference in implied volatilities of at-the-money call and put options across stocks and find that the aggregate implied volatility spread (IVS) is significantly and positively related to future stock market returns. We attribute the predictive power to common informed trading in equity options instead of time-varying risk premium. The third essay, coauthored with Yoontae Jeon and Raymond Kan, studies the expected option return under an extended Black-Scholes model that incorporates the presence of stock return autocorrelation. We show that expected returns of both call and put options are increasing functions of return autocorrelation coefficient of the underlying stock. We find strong empirical evidence from the cross-section of average returns of equity options to support this prediction. Average returns of calls and puts as well as straddle returns all show monotonically increasing relationship with the degree of underlying stock’s return autocorrelation coefficient. We also examine how the information on stock return autocorrelation helps investors to improve the out-of-sample performance of their portfolios.

Keywords: cross-section of stock returns
idiosyncratic volatility
implied volatility spread
option returns
stock return autocorrelation
time-series stock return predictability
Advisor: Han, Bing
Kan, Raymond