VictorJuiz/thesis huggingface dataset:
Techniques for Machine Understanding of Live Drum Performances

This dissertation covers machine listening techniques for the automated real-time analysis of live drum performances. Onset detection, drum detection, beat tracking, and drum pattern analysis are combined into a system that provides rhythmic information useful in performance analysis, synchronization, and retrieval. The techniques are designed with real-time use in mind but can easily be adapted for offline batch use for large scale rhythm analysis./n/nAt the front end of the system, onset and drum detection provide the locations, types, and amplitudes of percussive events. The onset detector uses an adaptive, causal threshold in order to remain robust to large dynamic swings./nFor drum detection, a gamma mixture model is used to compute multiple spectral templates per drum onto which onset events can be decomposed using a technique based on non-negative matrix factorization. Unlike classification-based approaches to drum detection, this approach provides amplitude information which is invaluable in the analysis of rhythm. In addition, the decay of drum events are modeled using "tail" templates , which when used with multiple spectral templates per drum, reduce detection errors by 42%./n/nThe beat tracking component uses multiple period hypotheses and an ambiguity measure in order to choose a reliable pulse estimate. Results show that using multiple hypotheses significantly improves tracking accuracy compared to a single period model./n/nThe drum pattern analysis component uses the amplitudes of the detected drum onsets and the metric grid defined by the beat tracker as inputs to a generatively pre-trained deep neural network in order to estimate high-level rhythmic information. The network is tested with beat alignment tasks, including downbeat detection, and reduces alignment errors compared to a simple template correlation approach by up to 59%.

Advisor: Morgan, Nelson
Wessel, David
Dynamic IR Peak Coalescence and Ultrafast Chemical Exchange Reactions Studied by Two Dimensional Infrared Spectroscopy

Vibrational spectroscopy is one of the most powerful techniques in chemistry due to its ability to report direct information on the geometries and nuclear motions of complex molecules. At thermal equilibrium, rearrangements between different, or equivalent, molecular structures help to define the reactivity of the system. On the ultrafast timescale, these chemical exchange reactions may cause features in the vibrational spectrum to become averaged. The Bloch equations have been used previously to quantitatively predict the rates of such reactions. This approach has been quite successful in NMR spectroscopy where exchange on the microsecond timescale is often sufficient to cause peak coalescence. The application of the Bloch equations to IR spectroscopy has been debated due to the presence of other contributions to the vibrational lineshape that may prevent an accurate description of the relevant dynamics. Two dimensional infrared spectroscopy (2D-IR) is a time resolved ultrafast technique that is capable of directly measuring the kinetics of chemical exchange at thermal equilibrium where there is no net change in the populations of reactants and products. This work examines two model systems that display dynamic IR peak coalescence. A group of mixed valence dimers of trinuclear ruthenium clusters have exhibited a wide range of IR coalescence that is sensitive to solvent, temperature, and ligand substitution. No electron exchange was observed by 2D-IR during the timescale required for peak coalescence. The two isomers of a square pyramidal ruthenium dithiolene compound also result in highly coalesced spectra. The equilibrium populations, as well as the extent of peak coalescence, are strongly dependent on temperature and solvent. The experimental results of this second project were largely inconconclusive; however, future work with density functional theory calculations looks promising for revealing more information on these dynamics. Ultimately, the application of the Bloch equations to IR spectra is not generally reliable. While this type of analysis may still yield accurate results in some special cases, it is very difficult to distinguish legitimate exchange induced coalescence from similar broadened lineshape features, and this approach should be avoided.

Advisor: Harris, Charles B
Nuances of Climate Change Mitigation: Four Different Goals and Approaches in the Climate Boxes Framework

The Climate Boxes Framework presented in this dissertation provides a structure to discuss and improve the alignment between policy positions and climate goals. I explore the differences in mitigation paths implied by four different mitigation goals ("boxes"): 1) delaying climate change, 2) avoiding a global temperature increase of 1.5-2°C above pre-industrial levels, 3) avoiding a global temperature increase of 3-4°C above pre-industrial levels, or 4) no delay or avoidance of climate change. The topic of delay is particularly under-explored in the literature, and I devote several chapters to calculations of its potential, possible benefits, and arguments for and against different means of achieving it./nThroughout the dissertation, the focus is on identifying the physical and technical constraints that set the bounds on the climate goals that can be achieved via different types of mitigation. For Box 1 (Delay), I calculate that maximum technically feasible reductions of short- and medium-lived pollutants have the potential to delay a given temperature increase by 15 years relative to the current trajectory. Elimination of deforestation would delay a 2°C temperature increase by 20 years relative to the current trajectory. There are many pragmatic reasons for delay, but more research is needed to determine whether there would be lasting climate system benefits from a lower rate of temperature change./nFor Box 2 (Avoid 1.5-2°C), I present a broad range of emission trajectories (peak year, target reduction, plateau year) that would avoid 2°C with various likelihoods, demonstrating the option to leverage an early emissions peak to make relatively smaller reductions for the period through 2050. For both Box 2 (Avoid 1.5-2°C) and Box 3 (Avoid 3-4°C), I calculate the cumulative CO2 budgets that would avoid each temperature increase in the transient and equilibrium time periods. I also highlight the limitations of the carbon budget theory and identify future research needed to make the theory more robust. I find that if CO2 emissions are consistent with an equilibrium goal of avoiding 2°C, then a transient temperature peak above 2°C is unlikely (25-40% likelihood even with elimination of cooling sulfates). Maximum technically feasible reductions of short- and medium-lived warming pollutants could further improve the likelihood of avoiding a transient temperature peak by 8-11 percentage points. For Box 3 (Avoid 3-4°C), I propose a novel policy approach (the Point One Approach) that would be based on the increments of 0.1°C temperature increase that are currently experienced every 7-8 years./nOverall, I demonstrate that whether policies are consistent with "addressing climate change" depends materially on which mitigation goal is being pursued; most policy choices are only consistent with a sub-set of the boxes. This applies particularly to policies related to CO2 targets, short- and medium-lived pollutants, offsets, geo-engineering, fossil fuel expansion, forests, and developing world infrastructure.

Advisor: Harte, John
Torn, Margaret
Anti-Constitutionalism: Frontiers sans Frontiers

Anti-Constitutionalism: Frontiers sans Frontiers maps and critiques a revitalized “rule-of-law” discourse in contemporary American politics, a discourse that cuts across and binds traditional ideological differences. I argue that this discourse generates a logic whereby the “law” is rendered a per se good threatened by two primary antagonists: lawlessness and politicization. All territories and persons, according to this vision, must be brought within the bounds of the rule-of-law and simultaneously the law must resist the temptations of politics. Drawing upon a variety of critical political and theoretical traditions that have witnessed the law as something other than synonymous with “justice” or “freedom,” including feminist legal theory and critical race studies, the dissertation argues that law void of political attachments is an impossibility. Thus, the desire for a depoliticized legality is always a desire tethered to and through a particular political ordering of things. In advancing this argument, I look to several recent events in U.S. law and political life that have incited this flight of hope to legality: the Supreme Court decision in Bush v. Gore, the emergency “culture of life” legislation aimed at Terri Schiavo, and the “Torture Memos” authorizing torture as method for imperial governance. Each of these cases suffers from being neither lawless nor political but rather from a radical singularity that undercuts the very possibility of a constitutive political ground. This thesis engages with contemporary political theorists on the question of “lawlessness” in the present and with theorists of the Early Republic (particularly Thomas Paine, James Madison and Alexis de Tocqueville) on the “politics” of law at constitutional inception.

Advisor: Brown, Wendy
A CMOS Magnetic Sensor Chip for Biomedical Applications

The growing need for point-of-care applications in global health and personalized medicine motivates a significant reduction in the size and cost of present technologies. Current solutions use fluorescent or enzymatic labels with complex optical instrumentation that has proven difficult to miniaturize. Recently, magnetic bead labeling has emerged as an alternative solution enabling portable and low-cost platforms./n/nA compact and robust magnetic label detector for biomedical assays is implemented in 0.18-μm CMOS. No external magnet, reference sensor or baseline calibration is required. Detection relies on the magnetic relaxation signature of a microbead label for improved tolerance to environmental variations and relaxed dynamic range requirement. Correlated double sampling combined with offset servo loops and magnetic field modulation, suppresses the detector offset to sub-μT. Single 4.5-μm magnetic beads are detected in 16 ms with a probability of error < 0.1%. Magnetic imaging and bead differentiation based on relaxation are demonstrated which could potentially lead to new applications.

Advisor: Boser, Bernhard E
Causal Inference and Prediction in Health Studies: Environmental Exposures and Schistosomiasis, HIV-1 Genotypic Susceptibility Scores and Virologic Suppression, and Risk of Hospital Readmission for Heart Failure Patients

Causal inference-inspired semi-parametric methods of measuring variable importance are well designed to answer questions of interest in health settings. Unlike traditional regression approaches, such variable importance measures are based on causal parameters that have straightforward real-world definitions, regardless of the approach used to estimate them. Parameters of regression models, in contrast, are not at all straightforward to interpret in real-world settings, because their definition relies completely on the correctness of the pre-specified model. Prediction-focused machine learning methods can avoid the issues of model pre-specification, but still do not provide estimates of variable importance that can be easily interpreted; the set of predictors chosen can also be highly variable. Semi-parametric methods combine the best of both approaches, and are able to utilize data-adaptive estimation algorithms while still returning a parameter estimate that is meaningful and can be simply understood./n/nIn this dissertation, semi-parametric methods to assess variable importance are applied to three real-world health applications: the relationship between types of water contact and the prevalence of schistosomiasis infection in rural China; HIV-1 treatment regimen genotype susceptibility scores and their relationship with the rate of virologic suppression; and the impact of a telemanagement program on and the association of multiple risk factors with the rates of hospital readmission for heart failure patients. Emphasized are (1) the choice of parameter of interest as motivated by the research question, (2) estimator choice based on a consideration of theoretical properties and performance under non-ideal conditions, and (3) the use during the estimation process of machine learning algorithms and algorithms that utilize multiple candidate models. Four different causal parameters are defined and described, and multiple estimators are considered./nEach data analysis presents different opportunities to investigate aspects of causal inference-based semi-parametric methods. In the schistosomiasis analysis, a traditional regression approach is compared with semi-parametric methods. Estimator performance is compared in the HIV analysis, particularly in the context of the observed extreme violations of the experimental treatment assignment (ETA) assumption. The G-computation estimator, the inverse-probability-of-censoring-weighted (IPCW), its double-robust counterpart (DR-IPCW), and the targeted maximum likelihood estimator (TMLE), are included in this comparison. The heart failure analysis addresses differences in causal parameter definition for a community-level treatment, and the related assumptions that must be added to the typical theoretical framework. Also included in this analysis is a comparison of super learning with traditional regression in terms of predictive performance.

Advisor: Hubbard, Alan E
Nano-Electro-Mechanical (NEM) Relay Devices and Technology for Ultra-Low Energy Digital Integrated Circuits

Complementary-Metal-Oxide-Semiconductor (CMOS) technology scaling has brought about an integrated circuits (IC) revolution over the past 40+ years, due to dramatic increases in IC functionality and performance, concomitant with reductions in cost per function. In the last decade, increasing power density has emerged to be the primary barrier to continued rapid advancement in IC technology, fundamentally due to non-zero transistor off-state leakage. While innovations in materials, transistor structures, and circuit/system architecture have enabled the semiconductor industry to continue to push the boundaries, a fundamental lower limit in energy per operation will eventually be reached. A more ideal switching device with zero off-state leakage becomes necessary./nThis dissertation proposes a solution to the CMOS power crisis via mechanical computing. Specifically, robust electro-mechanical relay technologies are developed for digital circuit application. A 4-Terminal (4T) relay design is firstly developed. Key technology features include tungsten contacts for high endurance; low-thermal-budget p+-poly-Si0.4Ge0.6 structure for post-CMOS process compatibility; Al2O3 as a reliable insulation material; dry release step to mitigate stiction; and folded-flexure design to mitigate the impact of residual stress. Fabricated relays show good conductance (RON < 10 kΩ), abrupt switching behavior (sub-threshold swing below 0.1 mV/dec), and virtually zero leakage (IOFF ~ 10-14 A). Switching delay in the 100 ns range and endurance exceeding 109 on/off cycles is achieved with excellent device yield (> 95%). With relay design and process optimizations, pull-in voltage below 10 V with less than 1 V hysteresis is achieved. Miniaturization reduces the device footprint to 35μm×50μm, ~10% of the first generation device footprint (120μm×150μm). Relays with multiple source/drain electrodes and multiple gate electrodes are proposed for increased circuit functionality and reduced device count./nFinally, simple relay-based logic circuits are demonstrated to show pathways to relay-based digital integrated circuits. The complementary inverter is the basis for all digital logic circuits and is investigated in depth. Relay-based logic gates are demonstrated using CMOS-like and relay-specific design approaches. Multi-input/multi-output relays are proposed to enable any complex logic function to be implemented compactly with only two relays.

Advisor: King Liu, Tsu-Jae
Visionary Mimesis: Imitation and Transformation in the German Enlightenment and Russian Realism

The dissertation examines the intersection and conflict of two aesthetic imperatives, one mimetic and the other didactic, in the literary culture of early eighteenth-century Germany and mid-nineteenth-century Russia. Describing a structure that I call "visionary mimesis" or "progressive realism," I show how texts struggle to bridge the gap between imitation and transformation, the present and the future, or what is and what ought to be. I present this underlying contradiction as a defining dynamic of both Enlightenment and Realist literature./nFirst I analyze J. C. Gottsched's Critical Poetics (1729), showing how the text deploys multiple shifting understandings of literary mimesis in order to reconcile the "imitation of nature" with the demand for morally instructive portrayals. Then I examine how this conflict is worked out in a fictional text, C. M. Wieland's novel The History of Agathon (1766-67). After tracing Wieland's turn toward a more "earthly" aesthetic in his earliest writings, I demonstrate that his novel pushes apart the very antinomies that it ostensibly seeks to combine. I then examine how the contradictions of "visionary mimesis" are reworked in the cultural context of the "1860s" in Russia. I describe the strained yet wonderfully ingenious interpretations put forth by the radical realist critic N. A. Dobroliubov in his desperate attempt to find the revolutionary hero within Russian reality. I then examine how F. M. Dostoevsky pursues a religious version of the radical project. After turning to his correspondence and his Diary of a Writer for background, I show how The Brothers Karamazov (1879-80) creates a path from ordinary experience to spiritual transcendence./nThe comparative angle of the dissertation places nineteenth-century Russian literature in a broader European context. Texts of this period are often viewed as precursors of twentieth-century socialist realism; I argue that they continue an Enlightenment project and, with the German texts, belong to the larger literary configuration of "visionary mimesis." An awareness of this configuration helps explain the complexity and instability of "progressive realist" texts. Because these texts often fail to span the contradictions of imitation and transformation, they mirror the perennial cultural gap between our objective perceptions and our subjective visions.

Advisor: Naiman, Eric
Investigating genetic determinants of phenotypic variation in natural isolates of Saccharomyces cerevisiae

The causal link between genotype and phenotype is one of the fundamental principles of modern biology; yet there remain significant challenges to successfully identifying and validating the effect of a specific genetic variant on an organism. Much of the tremendous diversity observed in nature, even among individuals of the same species, remains unexplained. Here, we used the model eukaryote, Saccharomyces cerevisiae, to investigate naturally occurring variation and employ a candidate gene approach, through a combination of genome sequence analysis and mining functional gene annotations, to identify genetic determinants of the phenotypes observed. First, we took a look at morphological variation, a major source of biological diversity, in an environmental isolate of S. cerevisiae and found that its allele of CDC28 underlies multiple phenotypes: linearly arranged spores after meiosis, elongated cell shape during mitosis, and branching filaments during filamentous growth. Second, we studied a wild yeast population, using a comparative transcriptomics approach, which revealed divergence in iron metabolism that exhibited itself as slow growth in a high iron environment. We again identified two of the genetic determinants, YAP5 and CCC1, both essential for resistance to iron toxicity, that contribute to the phenotype and show evidence that genes involved in iron homeostasis have undergone non-neutral evolution. Our work illustrates the viability of using genomic data to successfully predict the genes responsible for phenotypes of interest as well as the power of yeast a model system for investigating natural variation.

Advisor: Brem, Rachel B.
Speculative Modern: Urban Forms and the Politics of Property in Colonial Hong Kong

This dissertation traces the genealogy of property development and emergence of an urban milieu in Hong Kong between the 1870s and mid 1930s. This is a period that saw the transition of colonial rule from one that relied heavily on coercion to one that was increasingly "civil," in the sense that a growing number of native Chinese came to willingly abide by, if not whole-heartedly accept, the rules and regulations of the colonial state whilst becoming more assertive in exercising their rights under the rule of law. Long hailed for its laissez-faire credentials and market freedom, Hong Kong offers a unique context to study what I call "speculative urbanism," wherein the colonial government's heavy reliance on generating revenue from private property supported a lucrative housing market that enriched a large number of native property owners. Although resenting the discrimination they encountered in the colonial territory, they were able to accumulate economic and social capital by working within and around the colonial regulatory system. Meanwhile, the growing stake of Chinese capital in Hong Kong's economy was perceived as a threat by local British and European residents, who tried to maintain their privileges via discriminatory legislation./nA central goal of this study is to elucidate how particular forms of urban development predicated on opportunism and a "liberal governmentality" came to be consolidated within a racially divided, highly unequal, but nevertheless upwardly mobile, "modernizing" colonial city. By focusing on speculative building practices and the changing administrative framework that sought to regulate urban forms and social norms, this dissertation aims to illustrate some of the inherent contradictions in colonial development between the liberal, laissez-faire ideology that propelled capitalist expansion and the exclusionary impulses that clung to a hierarchical spatial order. Although this bifurcated milieu helped legitimized different rules for different peoples, it also opened up new channels for cultural and political negotiations. The examination of the competing discourses about the city and its development in Hong Kong's early period also provides a crucial explanatory framework for the so-called "Hong Kong economic miracle" in the postwar era and the prevalence of speculative property activities that continues to the postcolonial present.

Advisor: AlSayyad, Nezar
Synthesis of Pharmaceutically Relevant Nitrogen Heterocycles via Rhodium Catalyzed C-H Bond Functionalization

Recently in the Ellman and Bergman groups a method was discovered for preparing 1,2-dihydropyridines via rhodium-catalyzed coupling of α,β-unsaturated imines and alkynes. Subsequent in situ oxidation provides access to the corresponding pyridines. This method was expanded to include terminal alkynes, challenging substrates for transition-metal mediated transformations. In contrast formal reduction of the dihydropyridine intermediates through Diels-Alder reaction with alkenes provides access to isoquinuclidines, an important class of piperidines, in excellent diastereoselectivities.

Advisor: Bergman, Robert G