VictorJuiz/thesis huggingface dataset:
Predictable Processors for Mixed-Criticality Systems and Precision-Timed I/O

In cyber-physical systems, where embedded computation interacts with physical processes, correctness depends on timing behavior, not just functionality. For high confidence in the timing behavior of real-time embedded software, the underlying hardware must support predictable and isolated task execution. These properties are sacrificed in many conventional processors that use frequent interrupts and hardware prediction mechanisms to improve average-case performance. Mixed-criticality systems—where tasks with different levels of safety criticality are integrated on a single hardware platform to share resources and reduce costs—facilitate complex functionality but further complicate design and verification. The challenge is designing processor architectures that provide high confidence in software functionality and timing behavior without sacrificing processor throughput./nThis dissertation presents architectural techniques for task-level trade-offs between predictability, hardware-based isolation, and overall instruction throughput—facilitating the verification of safety-critical tasks and allowing software to meet precise timing constraints. Our processor design, named FlexPRET, uses fine-grained multithreading with flexible hard- ware thread scheduling and integrated timers to evaluate these techniques. With no restrictions on thread interleaving, the hardware thread scheduler executes hard real-time threads (HRTTs) at specific cycles for isolated and predictable behavior and allows soft real-time threads (SRTTs) to use both specific and spare cycles for efficient operation./nA configurable version of FlexPRET is implemented in simulation and on FPGA using Chisel, a hardware construction language that generates both C++ and Verilog code. For a given program path at a constant thread scheduling frequency, the latency of every instruction is constant and known, and the precision of input/output (I/O) instruction timing is bounded. The comparison of FlexPRET with two baseline processors provides the FPGA resource costs of FlexPRET’s microarchitectural features. Using two example applications, we demonstrate a mixed-criticality deployment methodology that provides hardware-based isolation to critical tasks and improves overall instruction throughput by using spare cycles and software scheduling for less critical tasks. FlexPRET can also use software to perform multiple independent I/O operations instead of requiring hardware peripherals.

Advisor: Lee, Edward A
Refinements in Syntactic Parsing

Syntactic parsing is one of the core tasks of natural language processing, with many appli- cations in downstream NLP tasks, from machine translation and summarization to relation extraction and coreference resolution. Parsing performance on English texts, particularly well-edited newswire text, is generally regarded as quite good. However, state-of-the-art constituency parsers produce incorrect parses for more than half of sentences. Moreover, parsing performance on other genres or in other languages is still quite hit-or-miss, mostly miss./nMany approaches have been developed for building constituency parsers over the years, in- cluding lexicalization (Collins 1997; Charniak 2000), structural annotation (Johnson 1998a; Klein and Manning 2003), and latent variable annotation (Matsuzaki, Miyao, and Tsujii 2005; Petrov et al. 2006). Each of these kinds of models have different strengths and weak- nesses./nIn this thesis, we develop a model of constituency parsing that attempts to unify these earlier parsing models. This approach centers around the idea of refinement of a simple underlying grammar. We show how latent variable modeling, structural annotation, and lexicalization can all be expressed as grammar refinements./nThese kinds of refinements capture different phenomena, but systems have generally chosen one kind or another. This is because grammars can grow exponentially as additional refinements are added. We present an approach where multiple refinements coexist, but in a factored manner that avoids this combinatorial explosion. Our method works with linguistically-motivated annotations, induced latent structure, lexicalization, or any mix of the three. By using the approximate inference algorithm expectation propagation (Minka 2001), we are able to use many refinements at the same time, without incurring substantial overhead in terms of parsing speed. With this system in hand, we examine the extent to which using many kinds of refinements can improve performance./nFrom there, we question whether grammar refinements are necessary at all. We present a parser that largely eschews refinements in favor of simple surface configurations. We show that it works quite well on ten different languages from several different language families./nFinally, we show how to take advantage of the refinement structure of latent variable grammars to double the speed of an already extremely fast parser for graphics processing units (GPUs). Our resulting GPU parser is around 40 times faster than the original CPU implementation, parsing over 400 sentences per second on a commodity consumer-grade GPU.

Advisor: Klein, Dan
Visioning a Transit City: Citizen Participation and Transit Planning in Quito, Ecuador

This study investigates the intersections of local democratic experimentation and transit planning in Quito, Ecuador between 1972-2015 to better understand how transit planning outcomes take shape. It shows that while current national transformation promotes a participatory democracy and a desired future of different economic and social realities, this has resulted in alternative logics that take place through transit planning./nWithin this context, on the one hand, I reveal that when transit planning institutions apply institutional practices of citizen participation these engagements not only fail to incorporate concepts of justice or equity, at the same time, they are also deeply entrenched by social, political, and cultural meaning that provoke new possibilities. On the other hand, I show how transit planning occurs through the performance of different transit visions. I trace transit visions to understand how transit planning outcomes emerge through the repetition of social relations./nMy investigation treats transit planning as an unstable object of analysis in order to reveal the ensemble of visible and invisible dynamics behind transit outcomes. I show that transit decisions are made between a variety of positions that are not just shaped by traditional tools of prediction and behavior. Instead, I use four guiding transit visions: (1) unstable (2) mayors (3) institutions and (4) infrastructures to indicate how transit planning is accomplished through reiteration. I triangulate multiple sources—social media, archives, participant observation, interviews and two survey instruments—to write about transit planning from an ethnographic point of view to comprehend how transit outcomes are done. The study documents how these visions coalesce through the experiences of public transit users. I subsequently analyze data gathered from urban cyclists, who are at the margins of transit infrastructure, to provoke new ways of researching and analyzing transit problems.

Advisor: Roy, Ananya
Using Chemoproteomic and Metabolomic Platforms to Identify Nodal Metabolic Pathways Important to Inflammation

There are an increasing number of human pathologies that have been associated with altered metabolism, including obesity, diabetes, cancer, atherosclerosis, and neurodegenerative diseases. Most attention on metabolism has been focused on well-understood metabolic pathways and has largely ignored most of the biochemical pathways that operate in physiological and pathophysiological settings. This is, in part, because of the vast landscape of uncharacterized and yet-undiscovered enzymes and metabolites that operate in metabolism. One technology that has arisen to address this challenge is activity-based protein profiling (ABPP). ABPP uses activity-based chemical probes to broadly assess the functional states of characterized and uncharacterized enzymes alike across entire enzyme classes. ABPP, when coupled with inhibitor discovery platforms and functional metabolomic technologies has led to discoveries that increase our definition of known biochemical pathways to expand our knowledge of metabolism in human health and disease./nBeing able to identify key nodal metabolic pathways will undoubtedly lead to new therapeutic strategies for combating diseases associated with metabolism. We are particularly interested in studying inflammatory metabolism, because chronic, low-grade inflammation is increasingly associated with many human pathologies. Although there are several successfully marketed small molecule anti-inflammatory drugs such as cyclooxygenase inhibitors and glucocorticoids, many of these compounds are also associated with various adverse cardiovascular or immunosuppressive effects. Thus, identifying novel anti-inflammatory small molecules and their biological targets is critical for developing safer and more effective treatment strategies for inflammatory diseases. We conducted a chemical genetics screen to identify small molecules that suppress the release of the pro-inflammatory cytokine TNFα from stimulated macrophages. We have used an enzyme class-directed chemical library for our screening efforts to facilitate subsequent target identification using ABPP. Using this strategy, we have found that KIAA1363 is a novel target for lowering certain pro-inflammatory cytokines through affecting key ether lipid metabolism pathways. This study highlights the application of combining chemical genetics with chemoproteomic and metabolomic approaches toward identifying and characterizing anti-inflammatory small molecules and their targets.

Advisor: Nomura, Daniel
The Measurement and Application of Electric Effects in Combustion

The existence of interactions between flames and electric fields has been known for quite some time and has received experimental and theoretical study over the years but remain an active topic of research in the combustion community. The present work specifically investigates the sensitivity of premixed flames electric fields. Prior work has demonstrated that electric fields may be used to enhance and control combustion, but full potential and range of applications for this effect have not been explored. Multiple theories have been presented to explain the process, but there is not yet a truly complete understanding of how electric fields fundamentally change the process of combustion. This work serves to explore new applications of electric-flame interactions and to provide experimental measurements to support the development of detailed theoretical models./nThermo-diffusive and acoustic instabilities in freely propagating flames can trigger the formation of wrinkled flames and turbulence, which may or may not be desirable in different scenarios. Electric fields present a means to interact with such instabilities either by generating direct hydrodynamic forces ('ionic wind') or by modifying the rate of combustion. Experiments performed on downward-propagating hydrocarbon flames have demonstrated that electric fields can be applied to excite or suppress existing instabilities and control the onset of turbulence. Numerical models following from these experiments indicate that subtle spatial variations in chemical reactivity can achieve similar control of inherently unstable flames./nA practical limitation of combustion is the phenomenon of quenching, where heat losses to the surroundings extinguish a flame. The enhancement achieved by electric fields is shown to dramatically increase flame propagation speed and reduce quenching in methane-air flames, which may permit the miniaturization of combustion-based power generation systems. In the course of these experiments, flames were found to exhibit different behavior depending on the direction of the applied field. This result is consistent with a proposed model of ion transport in laminar flames, although the experiments have shown a greater degree of enhancement than predicted./nUltimately, modeling the electrical aspects of combustion should be based on detailed accounting of the ion species present in flames. To support the ongoing development of detailed ion-chemistry mechanisms, a non-intrusive microwave interferometer for use in shock tube studies of combustion kinetics was developed. This was used to measure the formation and consumption of free electrons in shock-induced combustion. The range of equivalence ratios tested and the variety of hydrocarbon fuels used provide a rich dataset. Comparison of these results to complementary chemical kinetics simulations have been used to validate proposed improvements to existing mechanisms.

Advisor: Fernandez-Pello, Carlos
Microfluidic Chips for Structural and Functional Investigations of Biological Macromolecules

Microfluidic chips allow researchers to perform complex chemical and biological assays with less volume and in less time than comparable benchtop experimental formats. To date, many microfluidic chip designs have been developed that replicate macro-scale experimental techniques while increasing sensitivity and measurements density. Biochemical assays investigating the function of biological macromolecules have particularly benefitted from the ability to perform complex, micro-scale experiments that use expensive, often precious reagents in microfluidic devices; structural investigations of biological macromolecules also have benefitted from microfluidic approaches. For my doctoral work, I designed and fabricated microfluidic chips to carry out functional investigations of macromolecular interactions and for X-ray diffraction studies of microcrystalline samples. In the first phase of this work, microdroplet-based microfluidic devices were used to study the reaction kinetics of the protein DnaA with various DNA substrates. Despite successful device fabrication and calibration, attempts to study the rates at which DnaA can extend a single-stranded DNA substrate ultimately were unsuccessful due to technical issues involving poor sample behavior in-chip. These challenges led me to focus on a different problem; namely, how to deliver microcrystals to microfocus synchrotron and X-ray free electron laser beam sources. Using the knowledge of microfluidic technologies gained through designing microdroplet-based chips, I helped design a PDMS-based flow trap array for microcrystal capture and positioning, and I independently designed, fabricated, and tested a silicon nitride-based device for microcrystal harvesting and delivery to X-ray beam line endstations. Both chip designs provide a powerful new means for allowing data collection from challenging structural targets.

Advisor: Berger, James M.
Martin, Andreas
Communication-Avoiding Krylov Subspace Methods in Theory and Practice

Advancements in the field of high-performance scientific computing are necessary to address the most important challenges we face in the 21st century. From physical modeling to large-scale data analysis, engineering efficient code at the extreme scale requires a critical focus on reducing communication -- the movement of data between levels of memory hierarchy or between processors over a network -- which is the most expensive operation in terms of both time and energy at all scales of computing. Achieving scalable performance thus requires a dramatic shift in the field of algorithm design, with a key area of innovation being the development of communication-avoiding algorithms./nSolvers for sparse linear algebra problems, ubiquitous throughout scientific and mathematical applications, often limit application performance due to a low computation/communication ratio. Among iterative methods, Krylov subspace methods are the most general and widely-used. To alleviate performance bottlenecks, much prior work has focused on the development of communication-avoiding Krylov subspace methods, which can offer asymptotic performance improvements over a set number of iterations./nIn finite precision, the convergence and stability properties of classical Krylov methods are not necessarily maintained by communication-avoiding Krylov methods. Depending on the parameters used and the numerical properties of the problem, these communication-avoiding variants can exhibit slower convergence and decreased accuracy compared to their classical counterparts, making it unclear when communication-avoiding Krylov subspace methods are suitable for use in practice./nUntil now, the literature on communication-avoiding Krylov methods lacked a detailed numerical stability analysis, as well as both theoretical and practical comparisons with the stability and convergence properties of standard implementations. In this thesis, we address this major challenge to the practical use of communication-avoiding Krylov subspace methods. We extend a number of theoretical results and algorithmic techniques developed for classical Krylov subspace methods to communication-avoiding Krylov subspace methods and identify constraints under which these methods are competitive in terms of both achieving asymptotic speedups and meeting application-specific numerical requirements.

Advisor: Demmel, James W
The evolutionary origins of neural crest and placodes

The sudden appearance of neural crest and neurogenic placodes in early branching vertebrates has puzzled biologists for over a century. These embryonic tissues contribute to the development of the cranium and associated sensory organs, which were crucial for the evolution of the vertebrate head. The evolution of neural crest and neurogenic placodes has been postulated as a key event leading to the appearance of new cell types that fostered the transition from filter feeding to active predation in ancestral vertebrates. However, the evolutionary origin of neural crest and neurogenic placodes has remained obscure due to the lack of embryonic data from tunicates, the closest living relative to the vertebrates. We provide evidence that the tunicate Ciona intestinalis possesses a cephalic melanocyte lineage (a9.49) similar to neural crest that can be reprogrammed into migrating ectomesenchyme by the targeted misexpression of Twist. Our results suggest that the neural crest melanocyte regulatory network predated the divergence of tunicates and vertebrates. We propose that the co-option of mesenchyme determinants, such as Twist, into the neural plate ectoderm was crucial for the emergence of the vertebrate “new head”./nFurthermore, we show that Ciona intestinalis possesses a preplacodal ectoderm (PPE) that is specified by a BMP antagonist and expresses the key regulatory determinant Six1/2, a developmental program conserved across vertebrates. The Ciona PPE is shown to produce ciliated neurons that express gonadotropin-releasing hormone (GnRH), a G protein-coupled receptor for relaxin-3 (RXFP3), and a functional cyclic nucleotide gated channel (CNGA), suggestive of dual chemosensory and neurosecretory activities. These observations provide the first evidence that Ciona possesses a neurogenic placode, which produces multifunctional sensory and neurosecretory cells related to those derived from olfactory placodes of vertebrates. In vertebrates, GnRH neuroblasts are first formed in the olfactory placode and use the axon tracts of chemosensory neurons to guide them to their final destination in the hypothalamus. Tracing experiments have shown that olfactory and GnRH neurons form a direct neuronal circuit. We speculate that the PPE-derived neurons in Ciona resemble an ancestral cell type, a progenitor to the complex neuronal circuit that integrates sensory information and neuroendocrine control in vertebrates.

Advisor: Levine, Michael S
In the Name of Humanity: Britain and the Rise of Global Humanitarianism

This study examines how a new humanitarian community emerged in the late 1960s/nand why it came to act in the name of “humanity.” To realize the nature of this/ntransformation, the study focuses on Britain and its relationship to more global forms of/nhumanitarianism. In post-imperial Britain a new set of actors beyond the British state/ncame to adopt humanitarian ethics. In a series of case studies, the study examines how/nhumanitarianism mobilized a range of new historical actors who came to replace the/nimperial state, beginning with non-governmental activists and former military experts and/nexpanding to include multinational corporations and ordinary people./nInitially, post-imperial aid relied on imperial infrastructure and knowledge. In the/n1960s, organizations such as Oxfam used former Imperial experts to manage and/ndistribute global relief in places like Nigeria. Older imperial institutions like the British/nmilitary became major respondents to disasters in the Sahel and South Asia. But the postimperial landscape also included new, more business-minded actors. In the mid-1970,/nmultinational corporations and private businesses began developing their own solutions/nto humanitarian suffering through agribusiness projects. Through charity shops, rock/nconcerts, and boycotts, ordinary people, consumers, and youth groups joined such/nmultinationals in acting for the cause of humanity. By the 1980s, humanitarian/norganizations operated as a profitable business, generating substantial revenues that were/nmobilized to care for, rescue, and intervene in response to natural and man-made/ndisasters such as famines, civil wars, and earthquakes./nDrawing on extensive archival work in Britain, the United States, and Switzerland,/nthis study shows that British humanitarianism was shaped by both the legacies of the end/nof empire and the tensions brought by new forces of globalization in the 1970s. The end/nof empires created the globalization of markets and goods as well as the rise of/nnongovernmental and commercial actors. In a period of economic globalization and mass/nconsumption, I argue, a new humanitarian culture came to commodify aid. As such, I/nargue, British humanitarianism became part of the new, increasingly market-driven,/npolitical economy of the 1970s. In doing so, Britons were integrated into affective and/neconomic communities of aid, as well as the project of global governance.

Advisor: Laqueur, Thomas W
Vernon, James