VictorJuiz/thesis huggingface dataset:
Learning from Subsampled Data: Active and Randomized Strategies

In modern statistical applications, we are often faced with situations/nwhere there is either too little or too much data. Both extremes can/nbe troublesome: Interesting models can only be learnt when sufficient/namounts of data are available, yet these models tend to become/nintractable when data is abundant. An important thread of research/naddresses these difficulties by subsampling the data prior to learning/na model. Subsampling can be active (i.e. active learning) or/nrandomized. While both of these techniques have a long history, a/ndirect application to novel situations is in many cases/nproblematic. This dissertation addresses some of these issues./nWe begin with an active learning strategy for spectral clustering when/nthe cost of assessing individual similarities is substantial or/nprohibitive. We give an active spectral clustering algorithm which/niteratively adds similarities based on information gleaned from a/npartial clustering and which improves over common alternatives./nNext, we consider active learning in Bayesian models. Complex Bayesian/nmodels often require an MCMC-based method for inference, which makes a/nnaive application of common active learning strategies/nintractable. We propose an approximate active learning method which/nreuses samples from an existing MCMC chain in order to speed up the/ncomputations./nOur third contribution looks at the effects of randomized subsampling/non Gaussian process models that make predictions about outliers and/nrare events. Randomized subsampling risks making outliers even/nrarer, which, in the context of Gaussian process models, can lead to/noverfitting. We show that Heavy-tailed stochastic processes can be/nused to improve robustness of regression and classification estimators/nto such outliers by selectively shrinking them more strongly in sparse/nregions than in dense regions./nFinally, we turn to a theoretical evaluation of randomized subsampling/nfor the purpose of inferring rankings of objects. We present two/nsimple algorithms that predict a total order over n objects from a/nrandomized subsample of binary comparisons. In expectation, the/nalgorithms match an &Omega(n) lower bound on the sample complexity/nfor predicting a permutation with fixed expected Kendall tau/ndistance. Furthermore, we show that given O(nlog(n)) samples, one/nalgorithm recovers the true ranking with uniform quality, while the/nother predicts the ranking more accurately near the top than the/nbottom. Due to their simple form, the algorithms can be easily/nextended to online and distributed settings.

Advisor: Jordan, Michael I
Femtosecond laser processing of photovoltaic and transparent materials

The photovoltaic semiconducting and transparent dielectric materials are of high interest in current industry. Femtosecond laser processing can be an effective technique to fabricate such materials since non-linear photochemical mechanisms predominantly occur. In this series of studies, femtosecond (fs) laser processing techniques that include laser drilling on Si wafer, laser scribing on CIGS thin film, laser ablation on Lithium Niobate (LN) crystal, and fabrication of 3D structures in fused silica were studied./nThe fs laser drilling on Si wafer was performed to fabricate via holes for wrap-through PV devices. For reduction of the number of shots in fs laser drilling process, self-action of laser light in the air was initiated. To understand physical phenomena during laser drilling, scanning electron microscopy (SEM), emission, and shadowgraph images were studied. The result indicated the presence of two mechanisms that include fabrication by self-guided beam and wall-guided beam. Based on our study, we could fabricate ~16 micrometer circular-shaped via holes with ~200 laser pulses on 160-170 micrometer thick c- and mc-Si wafer./nFor the fs laser scribing on ink jet printed CIGS thin film solar cell, the effect of various parameters that include pulse accumulation, wavelength, pulse energy, and overlapping were elucidated. In our processing regime, the effect of wavelength could be diminished due to compensation between beam size, pulse accumulation, energy fluence, and the absorption coefficient. On the other hand, for high PRF fs laser processing, pulse accumulation effect cannot be ignored, while it can be negligible in low PRF fs laser processing. The result indicated the presence of a critical energy fluence for initiating delamination of CIGS layer. To avoid delamination and fabricate fine isolation lines, the overlapping method can be applied. With this method, ~1 micrometer width isolation lines were fabricated./nThe fs laser ablation on LN wafer was studied. The ablation thresholds and laser induced periodic surface structure (LIPSS) patterns according to the angle between laser polarization and crystal orientation were elucidated via SEM images. We could observe that both the ablation threshold and the LIPSS patterns were affected by the angle between laser polarization and crystal orientation. Additionally, we could fabricate ~45 nm dots on z-cut LN wafer surface along the x-axis./nFinally, 3D helical microchannel was fabricated in fused silica and utilized for protein mixing. The channel of ~50 micrometer diameter was fabricated by the femtosecond laser irradiation and chemical etching (FLICE) technique. For understanding of fluidic motions, numerical analysis was performed. The numerical analysis indicates the existence of an effective mixing condition due to compensation between residence time of the flow in the channel and the transverse flow patterns. Experiments supported the numerical analysis and we could achieve 90% mixing within ~400 micrometer distance from the confluence of two streams.

Advisor: Grigoropoulos, Costas P
Tools for engineering biology: methods for designing, building, and testing

Genetic engineering remains a difficult task and the design, build, test cycle may take months or years to complete. Currently, all three aspects are laborious, expensive, and mostly handle volumes of tens of units. The typical process of reaching a proof of concept genetic prototype involves an intensive survey of literature, synthesizing or acquiring genes, and testing their function. Here I outline tools to address bottlenecks in the genetic engineering workflow. First, I describe the Engineered DNA Sequence Syntax Inspector (EDSSI). This software pipeline checks protein-coding DNAs for syntax errors, which are incorrect or missing elements in the DNA. By using EDSSI, researchers are able to avoid the simple but costly mistakes of point errors, misannotated gene structure, or unintended extraneous ORFs. Second, I describe Multiplex Ortholog Library Synthesis and Expression Testing (MOLSET), a method to build genes and test their expression in E. coli. MOLSET enables the multiplex synthesis and expression testing of up to a hundred genes directly from a microarray oligo pool. data generated by MOLSET is incorporated into a design synthesis algorithm called Act Synthesizer that employs this information to improve predictions of pathways. Finally, we show the usefulness of the Act synthesizer by designing and testing a pathway for product of the household painkiller, acetaminophen, in E. coli.

Advisor: Anderson, John C
Bringing the Public into Policymaking: National Participatory Institutions in Latin America

Participatory experiments have been adopted throughout Latin America in an attempt to reinvent democracy to be more responsive to all citizens - not just an elite few. Participatory policymaking institutions are formal, institutional spaces that engage civil society groups in policy debates and decision-making processes. Participatory policymaking is particularly strong in Latin America, where 12 countries require subnational governments to incorporate civil society organizations into the policymaking process in policy sectors ranging from health to the environment to agriculture policy. Yet there is great variation in what happens after participatory institutions are created: some participatory institutions develop a major role in policymaking, while others only exist on paper. This project seeks to explain under what conditions national participatory experiments become institutionalized./nIn the late 1980s and early 1990s, Brazil and Colombia established the region's most expansive national participatory frameworks, requiring dozens of participatory institutions across a range of policy sectors. Facing major legitimacy crises, both countries created participatory institutions as part of democratizing reforms that sought to amplify the voices of excluded groups and enhance accountability. Despite their shared origins, participatory institutions followed very different trajectories in the two countries. Why has participatory policymaking become institutionalized in Brazil, yet decayed over time in Colombia?/nWhile national participatory institutions were created with the goal of deepening democracy, this democratizing impulse is insufficient to secure institutionalization, which requires ongoing material, human, and political investments from the government. Governments will only sustain these investments when pressured to do so by a reform coalition of diverse stakeholders. I show that such a broad coalition only arises when councils are created alongside the introduction of substantive policy changes, and when elite stakeholder groups mobilize other stakeholders in support of the councils. The broad reform coalition will unite to advocate for council implementation as a means to ensure overall reform implementation, as happened in Brazil. In contrast, participatory institutions are doomed when adopted as part of reforms that seek to deepen democracy but do not shift the substance of policy. This was the case in Colombia, where the councils only attracted those stakeholders directly interested in participatory policymaking. The narrowness of this reform coalition hampered its ability to apply pressure on the government, ultimately resulting in failed institutionalization.

Advisor: Collier, Ruth Berins
Three Political Philosophers Debate Social Science: Leo Strauss, Alasdair MacIntyre, and Charles Taylor

This dissertation analyzes the emergence of an alternative form of inquiry to that which has dominated the Anglophone social sciences for over half a century. Examining the philosophies of Leo Strauss, Alasdair MacIntyre, and Charles Taylor, it ultimately seeks to vindicate a humanistic and interpretive approach to the study of politics against the ongoing tendency towards mechanistic and pseudo-scientific forms of explanation./nAn introduction gives readers the necessary background context for understanding the importance of these controversies. The contributions of Strauss, MacIntyre, and Taylor are to be understood in light of an intellectual, cultural, and political movement which I describe as "positivism." Because this form of positivism continues to be of great influence today, the contributions of these three political philosophers also remain relevant./nThe first part of the dissertation treats the work of Strauss. Chapters 1 and 2 argue that Strauss's critique of social science, while marking an important first wave of resistance against positivism, nevertheless falls short. Although Strauss identifies some of the key problems with mainstream social scientific inquiry, his alternative remains inadequate./nThe second part of the dissertation examines MacIntyre's and Taylor's respective critiques of social science. Chapters 3 through 6 argue that these two philosophers have successfully criticized modern social science, while also proposing a viable, interpretive alternative. These chapters also argue that MacIntyre and Taylor provide us with an approach to social science that overcomes the supposed dichotomy between facts and values. Rather than dichotomizing empirical and normative inquiry, MacIntyre and Taylor each devise novel ways of joining empirical research with moral and political reflection.

Advisor: Bevir, Mark
Characterization of Seizure Suppression in Drosophila

Epilepsy and seizure disorders affect a large portion of the population. These disorders are complex in both cause and in phenotypic manifestation. Genetic factors have been shown to play a role in seizure sensitivity. Much research has been focused on the genetics underlying the mechanisms of seizure sensitivity and the development of/ntreatments for seizure disorders. Despite this, many questions remain unanswered. Using Drosophila as a genetic model for epilepsy and seizure disorders has given us some insight into the mechanisms of seizure susceptibility, particularly in suppression of/nseizures. The following dissertation, details a forward genetics screen for suppressors of seizures in parabss1 and identification of gilgamesh (gish) as a voltage-gated sodium channel specific seizure suppressor mutant. Additionally, the utility of dorsal vessel injection of antiepileptic drugs is discussed in detail. Following discussion of these findings, future plans for the use of Drosophila as a genetic model for intractable epilepsies and discovery of additional seizure suppressor mutants are laid out. While many questions regarding the mechanisms of seizure suppression remain, this work and any future work from this point will help to unravel the complexities of epilepsy and seizure disorders.

Advisor: Tanouye, Mark A
Vanadium Oxide Electrochemical Capacitors: An Investigation into Aqueous Capacitive Degradation, Alternate Electrolyte-Solvent Systems, Whole Cell Performance and Graphene Oxide Composite Electrodes

Vanadium oxide has emerged as a potential electrochemical capacitor material due to its attractive pseudocapacitive performance; however, it is known to suffer from capacitive degradation upon sustained cycling. In this work, the electrochemical cycling behavior of anodically electrodeposited vanadium oxide films with various surface treatments in aqueous solutions is investigated at different pH. Quantitative compositional analysis and morphological studies provide additional insight into the mechanism responsible for capacitive degradation. Furthermore, the capacitance and impedance behavior of vanadium oxide electrochemical capacitor electrodes is compared for both aqueous and nonaqueous electrolyte-solvent systems. Alkali metal chloride and bromide electrolytes were studied in aqueous systems, and nonaqueous systems containing alkali metal bromides were studied in polar aprotic propylene carbonate (PC) or dimethyl sulfoxide (DMSO) solvents. The preferred aqueous and nonaqueous systems identified in the half-cell studies were utilized in symmetric vanadium oxide whole-cells. An aqueous system utilizing a 3.0 M NaCl electrolyte at pH 3.0 exhibited an excellent 96% capacitance retention over 3000 cycles at 10 mV s-1. An equivalent system tested at 500 mV s-1 displayed an increase in capacitance over the first several thousands of cycles, and eventually stabilized over 50,000 cycles. Electrodes cycled in nonaqueous 1.0 M LiBr in PC exhibited mostly non-capacitive charge-storage, and electrodes cycled in LiBr-DMSO exhibited a gradual capacitive decay over 10,000 cycles at 500 mV s-1. Morphological and compositional analyses, as well as electrochemical impedance modeling, provide additional insight into the cause of the cycing behavior. Lastly, reduced graphene oxide and vanadium oxide nanowire composites have been successfully synthesized using electrophoretic deposition for electrochemical capacitor electrodes. The composite material was found to perform with a higher capacitance than electrodes containing only vanadium oxide nanowires by a factor of 4.0 at 10 mV s-1 and 7.5 at 500 mV s-1. The thermally reduced composite material was examined in both symmetric and asymmetric whole cell electrochemical capacitor devices, and although the asymmetric cell achieved both higher energy and power density, the symmetric cell retained a higher capacitance over 50,000 cycles at 200 mV s-1.

Advisor: Doyle, Fiona M
Papers on Indirect Mortality Estimation & Analysis in Low-Resource Settings

Policy makers in the health and development fields have established important goals and benchmarks for development progress, as showcased in the Declaration of Alma Ata (in 1978) and the Millennium Declaration (in 2000). Within these frameworks a clear and verifiable set of benchmarks were developed as a means of advancing transparency and accountability. Yet, often the data that are required to inform such evaluations, even for basic indicators such as child mortality, are lacking in low-income countries. This dissertation reviews the state of vital registration data systems in low-income countries, and then explores interim methods for measuring mortality when comprehensive civil registration systems are lacking. In particular, I evaluate the reliability of indirect methods to measure mortality rates under the age of 5 years by drawing on available data from Demographic and Health Surveys and from UNICEF's Multiple Indicator Cluster Surveys. I also carry out a validation study of indirect adult mortality estimation methods using historical population registers from northeast China, and assess the quality of mortality data collected at a demographic surveillance site in South Africa. The analysis demonstrates that indirect estimates, especially when adjustments are made to address simplifying assumptions, are generally consistent with adjusted direct estimates (in the case of child mortality) and life table estimates (in the case of adult mortality estimates). These results suggest that indirect estimates have a limited use in low-income countries, namely for populations that have experienced either smooth mortality declines or only short periods of excess mortality in their recent past. When examining data quality at the Agincourt demographic surveillance site, I found that such data provide a strong basis for the examination of health and mortality transitions in low-income countries given that they are less vulnerable to many of the data errors found in household surveys and population censuses in low-income countries. These findings underline the limitations of indirect methods, the promise of demographic surveillance systems as a valuable data source, and the critical importance of sustained improvements to civil registration systems.

Advisor: Wilmoth, John R
The Relations Among Multiple Risks, Parenting Styles, and Chinese American Children's Internalizing and Externalizing Problems

This study examined the prospective effects of multiple risks on the internalizing and externalizing problems of 258 1st and 2nd generation Chinese American school-aged children, as well as the mediating and moderating roles of parenting styles. When examining the relations between risk domains and children's behavioral adjustment, children's low self-regulation and negative emotionality, single-parent family structure, and gaps in parent-child cultural orientations were found to be unique predictors of adjustment outcomes two years later. The multiple risk index, which represented the joint effects of uniquely predictive risk variables, was related to higher levels of child-reported internalizing and externalizing problems. Similarly, the cumulative risk index, which represented the number of risk factor exposures, was also associated with increased internalizing and externalizing problems as reported by children. Though we did not find support for parenting styles as mediators, results did indicate that authoritarian parenting interacted with the multiple and cumulative risk indexes. High authoritarian parenting had a tendency to strengthen the relation between the multiple risk index and increased teacher-reported internalizing problems, while low authoritarian parenting had a tendency to attenuate the relation between cumulative risk and parent-reported internalizing problems.

Advisor: Zhou, Qing
The Complexity of Optimal Auction Design

This dissertation provides a complexity-theoretic critique of Myerson's theorem, one of Mechanism Design's crown jewels, for which Myerson was awarded the 2007 Nobel Memorial Prize in Economic Sciences. This theorem gives a remarkably crisp solution to the problem faced by a monopolist wishing to sell a single item to a number of interested, rational bidders, whose valuations for the item are distributed independently according to some given distributions; the monopolist's goal is to design an auction that will maximize her expected revenue, while at the same time incentivizing the bidders to bid their true value for the item. Myerson solves this problem of designing the revenue-maximizing auction, through an elegant transformation of the valuation space, and a reduction to the problem of designing the social welfare-maximizing auction (i.e. allocating the item to the bidder who values it the most). This latter problem is well understood, and it admits a deterministic (i.e. the auctioneer does not have to flip any coins) and simple solution: the Vickrey (or second-price) auction. In the present dissertation we explore the trade-offs between the plausibility of this result and its tractability:/nFirst, we consider what happens as we shift away from the simple setting of Myerson to more complex settings, and, in particular, to the case of bidders with arbitrarily correlated valuations. Is a characterization as crisp and elegant as Myerson's still possible? In Chapter 2 we provide a negative answer: we show that, for three or more bidders, the problem of computing a deterministic, ex-post incentive compatible and individually rational auction that maximizes revenue is NP-complete --in fact, inapproximable. Even for the case of two bidders, where, as we show, the revenue-maximizing auction is easy to compute, it admits nonetheless no obvious natural interpretation a-la Myerson./nThen, motivated by the subtle interplay between social welfare- and revenue-maximizing auctions implied by Myerson's theorem, we study the trade-off between those two objectives for various types of auctions. We show that, as one moves from the least plausible auction format to the most plausible one, the problem of reconciling revenue and welfare becomes less and less tractable. Indeed, if one is willing to settle for randomized solutions, then auctions that fare well with respect to both objectives simultaneously are possible, as shown by Myerson and Satterthwaite. For deterministic auctions on the other hand, we show in Chapter 3 that it is NP-hard to exactly compute the optimal trade-off (Pareto) curve between those two objectives. On the positive side, we show how this curve can be approximated within arbitrary precision for some settings of interest. Finally, when one is only allowed to use variants of the simple Vickrey auction, we show in Chapter 4 that there exist auctions that achieve constant factor approximations of the optimal revenue and social welfare simultaneously.

Advisor: Papadimitriou, Christos H