VictorJuiz/thesis huggingface dataset:
WYSIWYG computational photography via viewfinder editing [electronic resource]

The past decade witnessed a rise in the ubiquity and capability of digital photography, paced by the advances in embedded devices, image processing and social media. Along with it, the popularity of computational photography also grew. Many computational photography techniques work by first capturing a coded representation of the scene---a stack of photographs with different settings, an image obtained via a modified optical path, et cetera---and then computationally decoding it later as a post-process according to the user's specification. However, the coded representation, available to the user at the time of capture, is often not sufficiently indicative of the decoded output that will be produced later. Depending on the type of the computational photography technique involved, the coded representation may appear to be a distorted image, or may not even be an image at all. Consequently, these techniques discard one of the most significant attractions of digital photography: the what-you-see-is-what-you-get (WYSIWYG) experience. In response, this dissertation explores a new kind of interface for manipulating images in computational photography applications, called viewfinder editing. With viewfinder editing, the viewfinder more accurately reflects the final image the user intends to create, by allowing the user to alter the local or global appearance of the photograph via stroke-based input on a touch-enabled digital viewfinder, and propagating the edits spatiotemporally. Furthermore, the user specifies via the interface how the coded representation should be decoded in computational photography applications, guiding the acquisition and composition of photographs and giving immediate visual feedback to the user. Thus, the WYSIWYG aspect is reclaimed, enriching the user's photographing experience and helping him make artistic decisions before or during capture, instead of after capture. This dissertation realizes and presents a real-time implementation of viewfinder editing on a mobile platform, constituting the first of its kind. This implementation is enabled by a new spatiotemporal edit propagation method that meaningfully combines and improves existing algorithms, achieving an order-of-magnitude speed-up over existing methods. The new method trades away spatial locality for efficiency and robustness against camera or scene motion. Finally, several applications of the framework are demonstrated, such as high-dynamic-range (HDR) multi-exposure photography, focal stack composition, selective colorization, and general tonal editing. In particular, new camera control algorithms for stack metering and focusing are presented, which takes advantage of the knowledge of the user's intent indicated via the viewfinder editing interface and optimizes the camera parameters accordingly.

Advisor: Levoy Marc primary advisor. Thesis advisor
Horowitz Mark (Mark Alan) advisor. Thesis advisor
Pulli Kari
An X-ray CT study of multidimensional imbibition in dual porosity carbonates [electronic resource]

Recovering oil from fractured systems is very challenging. Implementing a waterflood recovers oil in the fractures but not much of the oil in the matrix. To mitigate low recovery, one option is to increase the viscosity of the injected water using polymers or foam. This work investigates another option that involves injecting surfactant solutions. Surfactants reduce interfacial tension (IFT) and consequently capillary forces that are responsible for trapping oil within the matrix. Our claim is that if capillary forces are low enough, gravity lifts the oil by buoyancy towards the fracture network then to the producers. To investigate this claim, core-flood experiments are conducted vertically to account for gravity forces. A horizontal experiment, however, is initially performed to allow for evaluating the improvement of oil recovery when the experiments are conducted vertically. All experiments are monitored by X-ray computed tomography (CT) scanning to quantify fluid saturations and monitor front movements. There are two phases for each experiment: a saturation phase and an imbibition phase. In the saturation phase, the core is confined by a core sleeve and initial oil and water saturations are obtained. The confining pressure is released, in the imbibition phase, allowing for a fracture-like space between the core and the sleeve. Injected fluids now selectively channel through the fractures towards the outlet and oil recovery from the matrix becomes mainly governed by spontaneous imbibition. Both phases need to be performed in one core holder to minimize positioning errors while X-ray CT scanning. Therefore, a novel core holder was designed and fabricated that allows for saturating the core and then conducting the imbibition experiment. Two types of carbonate cores were used: Texas cream from an outcrop and oil field cores. For the oil phase, decane was initially used for to focus the study on fluid-fluid interactions and crude oil was later used for other experiments to account for fluid-fluid interactions and rock-fluid interactions. Experiments show that gravity has the potential to improve oil recovery when IFT is reduced. Even for small reduction of IFT, recovery factor (RF) increased by more than 4% of original oil in place (OOIP) when the experiments were conducted vertically. Moreover, the surfactant flood mode was found to impact the ultimate RF. The ultimate recovery factor (URF) for a secondary surfactant flood was greater by about 7% of OOIP than a tertiary surfactant flood.

Keywords: Energy Resources Engineering.
Advisor: Kovscek Anthony R. (Anthony Robert) primary advisor. Thesis advisor
Castanier Louis M. advisor. Thesis advisor
Horne Roland N. advisor. Thesis advisor
Zigzag coarsenings, mapper stability and gene-network analyses [electronic resource]

This thesis extends the theory and applications of two standard tools of applied algebraic topology, namely zigzag persistence and the MAPPER algorithm. On the theory side, we provide new stability results that support the application of these tools to point-cloud data. On the applications side, we apply these tools toward efficient shape matching of point clouds and for a novel analysis of gene-interaction networks. The levelset zigzag is a special case of zigzag persistence and is a powerful summary of a real-valued function. The stability of the levelset zigzag is one of its most important properties, since it provides justification for its usage in a continuous setting. We extend this stability of levelset zigzags to both zigzags that are in and not in the so-called pyramid family. The latter class are the coarsened levelset zigzags that are developed in this work, primarily to ease the application of levelset zigzags to point cloud data. MAPPER is the standard algorithm to calculate Reeb graphs from point-cloud data. Reeb graphs are graph-based summaries of topological spaces equipped with functions and have extensive applications in shape matching, surface compression and reconstruction, cancer sub-population discovery etc. As such, MAPPER has been successfully used in many applications. However, a missing piece till date is that there have been no guarantees on the stability of or error bounds on MAPPER. In the current work, we propose one notion of what it means for a Reeb graph calculation algorithm to be stable. Using the language of zigzag persistence, we are able to succinctly formalize the difference between calculated and ideal Reeb graphs. A worst case bound on the Reeb graph reconstruction error is then derived under fairly general conditions. A direct application of this result toward shape matching is demonstrated. We also demonstrate how Reeb graphs summarize vital information about datasets, beyond just point clouds. We apply MAPPER to gene expression networks constructed on cancer datasets. This gives us valuable insights about the structure of these networks. We compare our approach favorably to other state of the art methodologies. We outline the various biological insights that stem from our analysis.

Advisor: Carlsson Gunnar
Intermont Michele advisor. Thesis advisor
Plevritis Sylvia advisor. Thesis advisor
Activation of the calcium release-activated calcium channel by STIM1 [electronic resource]

In excitable and non-excitable cells store-operated Ca2+ entry (SOCE) is a ubiquitous cellular mechanism that is critical for numerous processes such as gene expression, exocytosis, and metabolism. SOC channels are activated when stimulation of cell surface receptors initiates a signaling cascade leading to Ca2+ release from the endoplasmic reticulum (ER). ER Ca2+ release triggers activation of SOC channels in the plasma membrane (PM), the best characterized of which is the Ca2+ release-activated Ca2+ (CRAC) channel. An ER embedded protein, STIM1, acts as the ER Ca2+ sensor, and a tetramer of Orai1 subunits forms the pore of the active CRAC channel. After store depletion, STIM1 and Orai1 redistribute to sites of close apposition between the ER and the PM known as ER-PM junctions where they interact to produce Ca2+ entry. However, the fundamental question of how they interact to elicit Ca2+ entry was unknown. In our first line of inquiry, we show that the C-terminal polybasic domain of STIM1 targets STIM1 to ER-PM junctions independently of Orai1, that a cytosolic region of STIM1--CRAC activation domain (CAD)--binds directly to Orai1, that CAD is necessary and sufficient to cluster and activate CRAC channels, and that clustering and activation are functionally separable events. These results support a two-part diffusion trap mechanism for SOCE. After store depletion, STIM1 forms puncta independently of Orai1 underneath the PM where CAD is positioned to trap diffusing CRAC channels in the PM and induce a conformational change to activate channels. In the second line of inquiry we address the stoichiometric requirements for CRAC channel trapping and activation at ER-PM junctions. For this we developed a novel technique in single cells to control and measure the STIM1-Orai1 stoichiometry at ER-PM junctions while simultaneously recording channel activity. We find that binding of 1-2 STIM1s is sufficient to immobilize the tetrameric CRAC channel at ER-PM junctions but this fails to evoke significant activation, while binding of 8 STIM1s causes maximal CRAC channel activity. We also find that the extent of fast Ca2+-dependent inactivation parallels STIM1-CRAC channel stoichiometry. The data are well described by a modified Monod-Wyman-Changeux model where STIM1 binds to Orai1 with negative cooperativity and channels open with positive cooperativity due to stabilization of the open state by STIM1. These results suggest a highly nonlinear dependence of CRAC channel activation on STIM:Orai stoichiometry.

Keywords: Molecular and Cellular Physiology.
Advisor: Lewis Richard (Richard Sheridan) primary advisor. Thesis advisor
Dolmetsch Ricardo E. advisor. Thesis advisor
Nachury Maxence
Tsien R. W. (Richard W.) advisor. Thesis advisor
Active messages for speed, scalability, and efficiency [electronic resource]

Integrating active messages onto many-core chip multiprocessors (CMPs) increases the speed, efficiency, and scalability of parallel programs. In traditional shared-memory CMPs, communication is handled implicitly and inefficiently by the hardware cache coherency protocol. Active messages, those that trigger remote atomic execution of custom handlers, give the programmer explicit control of communication and computation location. This dissertation describes the implementation, enumerates five usage idioms, and quantifies the benefits of on-chip active messages. Full programs run 63% faster, have 2.2x less network traffic, and consume 11% less energy on a 256 core CMP when using active messages.

Keywords: Electrical Engineering
Advisor: Dally William
Horowitz Mark (Mark Alan) advisor. Thesis advisor
Kozyrakis Christoforos
Adaptive design of clinical trials with interim selection of treatment arms [electronic resource]

When developing new drugs, Phase I and II trials are commonly conducted to determine the dose of the new treatment in preparation for the subsequent confirmatory Phase III trial. However, because these early-phase trials usually do not have large enough sample sizes to decide which dosage level or treatment regimen is the best, several of them may arise as candidates for the confirmatory Phase III trial. Conventional fixed sample size designs that carry out all the treatment arms of interest are obviously expensive. Therefore, the pharmaceutical industry is increasingly interested in adaptive designs that can use information acquired during the course of the trial to update certain of the design features. In this thesis we explore several existing designs and discuss their pros and cons. We then propose one that shares the flexibility of Bayesian adaptive designs, while still being able to maintain the frequentist type I error probability. We develop an asymptotic theory for efficient outcome-adaptive randomization schemes and optimal stopping rules. Our approach consists of developing asymptotic lower bounds for the expected sample sizes from the treatment arms and the control arm, and using generalized sequential likelihood ratio procedures to achieve these bounds. These allow us to allocate patients and study resources efficiently by using outcome-adaptive randomization schemes, or by arm suspension/selection if fixed randomization is used. We also derive an adaptive test with a p-value that can be evaluated by Monte Carlo simulation based on an ordering scheme of the sample space. We then show that the approach can also be applied to the closely related problem of multi-stage testing of multiple hypotheses.

Keywords: Statistics
Advisor: Lai T. L. primary advisor. Thesis advisor
Lavori Philip W.
Shih Mei-Chiung advisor. Thesis advisor
Agency in its many guises [electronic resource]

This dissertation defends a contextualist approach to the problem of human agency. Its central thesis is that human behaviors are conferred agential status in the context of specific social practices, and, consequently, that the standards in virtue of which agency ascriptions are made exhibit practice-dependent variation. Qua status conferrals, agency ascriptions take the form of tacit or explicit modalities of interpersonal regard that sanction agents' behavioral interventions as adequate to sustain a specific shared practice. As such, I contend, substantive conceptions of value that animate these forms of interpersonal recognition become inextricably linked to our understandings of agency. In developing this view I am arguing against what is nowadays the mainstream approach in the field of action theory. This approach assumes that the nature of agency can be illumined by specifying forms of psychological structuring that ensure human agents' active participation in their thought and behavior. I argue that the theories deploying this approach are wrongheaded insofar they attempt to account for human agency by extricating the putatively relevant psychological capacities constitutive of it from the values-imbued human ways of life that make possible their individuation.

Keywords: Philosophy
Advisor: Hills David James
Anderson R. Lanier advisor. Thesis advisor
Lawlor Krista advisor. Thesis advisor
Aircraft design with active load alleviation and natural laminar flow [electronic resource]

In this thesis we incorporate maneuver load alleviation (MLA), gust load alleviation (GLA), and natural laminar flow (NLF) into aircraft conceptual design. Existing conceptual design frameworks tend to reduce the impact of these technologies to empirical weight and drag corrections. The present work use physics-based methods to capture the dynamic interplay among natural laminar flow, load alleviation and structure design. The results demonstrate that the simultaneous application of MLA and GLA can tilt the balance of the transonic Mach-sweep-thickness trade in favor of a high aspect ratio, low-sweep natural laminar flow wings. A minimum cost turbulent aircraft designed concurrently with MLA and GLA control systems can a achieve a significant 10% reduction in fuel burn and 3.4% reduction in cost relative to a baseline design without load control. The fuel and cost savings grow to 15% and 5% respectively when we introduce natural laminar flow into the design process. Sensitivity studies confirm that the control and actuator requirements of effective active load alleviation are consistent with the performance parameters of modern aircraft. Comparisons with idealized high-sweep NLF wing further suggest that the combination of active load control and low-sweep NLF wing is a potential alternative to more sophisticated 3-D NLF wing design or complex active laminar flow control (LFC) systems. The aeroservoelastic conceptual design framework developed in this thesis can serve as a platform for assessing future aircraft configurations and operational paradigms aimed at reducing aircraft fuel consumption and environmental impact.

Keywords: Aeronautics and Astronautics
Advisor: Kroo Ilan primary advisor. Thesis advisor
Alonso Juan José
Jameson Antony
Algorithms for analyzing collections of trajectories [electronic resource]

Large scale collections of trajectory data, such as GPS traces, are becoming widely available, and there are many emerging applications that involve understanding and extracting information from such data. Much of this data is noisy, contains outliers, and has missing parts — raising many difficult statistical, geometric, and algorithmic problems. In this thesis, we study methods to extract structure from such data and to organize the data in a fashion that facilitates further analysis. We start by presenting a data-driven framework for smoothing trajectory data. Our framework, which can be viewed of as a generalization of the classical moving average technique, naturally leads to practical algorithms for various smoothing objectives. The second part of this thesis is about understanding the essential structure underlying the collections of trajectories. This topic is similar in spirit to dimension reduction or manifold learning in classical data analysis. Under reasonable similarity measures, collections of trajectories have significantly different structure than that of traditional data sets. In particular, simplifying assumptions such as the belief that the data lies on a low-dimensional manifold are no longer reasonable. Instead, it is often the case that the underlying space of the trajectories has a one dimensional stratified (or branching) structure. Our goal is then to reconstruct such a branching structure from a collection of input trajectories. Using sampling assumptions modeled after previous geometric reconstruction work in the computational geometry community, we formulate a new algorithm for reconstructing branching structures with guarantees. To make such a structure useful, we study the problem of map matching, which enables the branching structure to be used efficiently as a coordinate system. In particular, we extend recent results for Fréchet distance computation to obtain an algorithm for map matching with respect to the Fréchet distance that runs in near-linear time under reasonable models for the input trajectory and the map, which improves on previous near-quadratic running times. Finally, we also study a version of our reconstruction problem in a more general setting with weaker assumptions and develop an algorithm that is oblivious to ordering information of the individual trajectories in the data set, and even to the embedding of the data. Here, we explore a new model of reconstruction we call "metric reconstruction" that lies somewhere between geometric and topological reconstruction. In this model, we reconstruct the topology and distances of the underlying structure, while being somewhat oblivious to its extrinsic embedding. This algorithm allows the reconstruction of branching structures to be extended to settings where ordering information may not be reliable, or even to more abstract instances where an embedding is not available.

Advisor: Guibas Leonidas J. primary advisor. Thesis advisor
Goel Ashish advisor. Thesis advisor
Roughgarden Tim advisor. Thesis advisor
All-epitaxial orientation-patterned III-V semiconductors for nonlinear optics [electronic resource]

Applications such as airborne countermeasures, chemical spectroscopy, and imaging require high-power, compact, and tunable light sources in the infrared (IR) and terahertz (THz) spectral ranges. While laser sources exist at certain frequencies in this range, they are bulky and require low temperature operation. An alternative solution is to generate the desired IR and THz frequencies through nonlinear optical frequency conversion in orientation-patterned III-V semiconductors using readily available, and room temperature operating high-power semiconductor lasers in the near-IR. Orientation-patterning is an all-epitaxial technique in which we fabricate quasi-phasematched semiconductor structures by the following steps: growth by molecular beam epitaxy (MBE), lithography, etching, and regrowth by MBE. Previous work on orientation-patterned GaAs has led to the demonstration of a variety of nonlinear optical devices; however, there is a push to develop orientation-patterned GaP (OP-GaP) to overcome inherent material limitations GaAs. This thesis work has been focused on the development of OP-GaP, including MBE growth and characterization of GaP films on Si and processing of OP-GaP structures. Improvements in material quality have been made through the course of studying the nucleation and growth conditions of GaP on Si to control the formation and annihilation of antiphase domain defects. Understanding the growth of GaP on Si has not only enabled the development of OP-GaP as a platform for nonlinear optical devices, but also enabled the initial investigation of III-V epitaxial mirrors on Si substrates for high performance optical coatings.

Keywords: Materials Science and Engineering
Advisor: Harris J. S. (James Stewart)
McIntyre Paul Cameron primary advisor. Thesis advisor
Fejer Martin M. (Martin Michael) advisor. Thesis advisor