VictorJuiz/thesis huggingface dataset:
Tools and methods for large-scale convex optimization [electronic resource]

Convex optimization is widely used in many areas of engineering science such as control theory, statistics and machine learning, and image and signal processing. There are, however, several barriers to the use of convex optimization in everyday engineering: solvers for convex optimization in general require specialized knowledge to code, and in order to solve problems, users must typically perform tedious manual transformations before calling a solver. This problem is exacerbated when problem sizes become extremely large. In this thesis, we investigate tools and methods to address these two issues in the context of large-scale convex optimization. In particular, we develop technology to handle very large problems, including a large-scale solver and a tool to model potentially large optimization problems. This tool allows users to describe their problems with an intuitive model that is automatically transformed into a form handled by the large-scale solver, liberating users from performing tedious manual transformations. For the large-scale solver, we use the alternating direction method of multipliers (ADMM) and express conic optimization problems in consensus form, splitting the linear algebra from the generalized conic inequalities. For modeling optimization problems, we present the quadratic cone modeling language (QCML), which like CVX is a tool that automatically converts convex optimization problems into conic form and solves them with a standard cone solver. Unlike CVX, QCML can be used to analyze and generate code for entire problem families without requiring another analysis or generation phase when problem (instance) data or dimensions change.

Keywords: Electrical Engineering.
Advisor: Boyd Stephen P. primary advisor. Thesis advisor
Gorinevskiĭ D. M. advisor. Thesis advisor
Lall Sanjay advisor. Thesis advisor
Topics in two-sample testing [electronic resource]

Driven by recent advances in the collection of biological data, many such studies draw from heterogeneous datasources. We develop an idea of Jerome Friedman's to conduct two-sample testing using supervised learning procedures. In special cases, this technique generalizes the randomization t-test, for which an asymptotic normality result is known. Using Stein's method of exchangeable pairs, we produce Berry--Esseen-type bounds for the permutation t-statistic for the purpose of statistical inference. We demonstrate the use of kernel methods in two-sample testing on non-vectorial data (text and images), and apply multiple kernel learning (MKL) to the heterogeneous data domain. We show that these techniques can effectively synthesize signals from multiple datasources and produce interpretable weights that highlight the role of each component.

Keywords: Statistics.
Advisor: Friedman J. H. (Jerome H.) primary advisor. Thesis advisor
Holmes Susan
Diaconis Persi advisor. Thesis advisor
Efron Bradley advisor. Thesis advisor
Topology optimization of a MEMS device [electronic resource]

The mechanics of microelectromechanical systems (MEMS) are typically designed using a set of popular building blocks (rectangular cantilevers, folded flexure beams, crab legs etc.). Optimization of these structures or their variants is often performed using scaling laws, parametric optimization, or some insight gained from studying relationships between certain features and a device's behavior. Topology optimization is a more powerful tool that systematically generates the full topology of a design, including the size, shape, and location of features, and can satisfy several goals despite potentially complex relationships. The focus of this thesis is to answer the following question: Is it advantageous to design MEMS structures such as RF MEMS capacitive switches using topology optimization? This thesis takes the reader through a full design process. The problem setup and problem formulation are justified in depth. The mechanical behaviors of devices with stresses and stress gradients resulting from typical micro-fabrication processes are explained. The finite element simulations are described, and the modeling decisions that can be particularly relevant to other MEMS problems are highlighted. The topology optimization method is thoroughly explained, and the challenges and necessary adaptations to the method are exposed. Sets of topology optimized designs are presented; guidelines for future intuitive design are extracted from an examination of the resulting geometries. Experimental data is provided, justifying many of the decisions taken during the design process, and validating the finite element models and topology optimization results. The experimental results also provide supplemental understanding regarding capacitive switch mechanics. The new knowledge should be integrated into any future problem formulation. We conclude that topology optimization can be used for MEMS design, significantly increasing the design possibilities and solving complex, non-intuitive problems.

Keywords: Mechanical Engineering.
Advisor: Kenny Thomas William primary advisor. Thesis advisor
Lew Adrian advisor. Thesis advisor
Sheppard S. (Sheri) advisor. Thesis advisor
Towards 3D molecular movies [electronic resource] : electron orbital signatures in asymmetric tops

High-order harmonic generation in atoms or linear molecules offers valuable information about valence electrons. When combined with molecular alignment, high harmonic generation is sensitive to both Angstrom-scale structure and sub-femtosecond dynamics, and can even create very simple movies of molecules in motion. Extending these techniques to more complex molecules with three distinct dimensions is hindered, however, by the interference of radiation from random molecular orientations. In this dissertation, I demonstrate a solution to this dilemma by making use of the full-scale molecular revival pattern of a three-dimensional asymmetric top. I present an alignment-decomposition approach based on methods derived from rotational coherence spectroscopy and test them on the asymmetric-top molecule sulfur dioxide. I then apply this approach to experimental results from the full sulfur dioxide high-harmonic spectrum and show that prominent spectral features must be due to ionization and recombination from multiple molecular orbitals. These results simplify the task of spectral analysis and extend the usefulness of high harmonic generation to increasingly complicated molecules. They provide a first step towards constructing real, three-dimensional molecular movies.

Keywords: Applied Physics.
Advisor: Bucksbaum Philip H. primary advisor. Thesis advisor
Kasevich Mark A. advisor. Thesis advisor
Martinez Todd J. (Todd Joseph)
Towards a dynamic pragmatics [electronic resource]

This dissertation explores the interplay of conventional and interactional factors in the interpretation of natural language utterances. It develops a formal framework, dynamic pragmatics, in which pragmatic inferences arise as contextual entailments in a dynamic system in which information states are updated with information about the occurrence of utterance events (in contrast to dynamic semantics, where information states are updated with the content of linguistic expressions). In this way, the framework is able to faithfully model Gricean pragmatic inference as interlocutors' reasoning about each other's utterance choices. Linguistic utterances are analyzed as having essential facts of two distinct types: Epistemic effects (i.e., effects on the information states of the interlocutors) and normative effects (i.e., effects on the interlocutors' commitments). The latter effects are carried by extra-compositional, normative conventions of use that mediate the form-force mapping; the former arise largely due to the interlocutors' presumptions about each other's beliefs, preferences, and method of determining which (utterance) actions are best (i.e., practical reasoning). The framework of dynamic pragmatics allows us to consistently take a thoroughly Gricean perspective on language use, and allows us to explore how the interpretation of an utterance arises through the interplay of sentential force, content, and context. At the same time, the framework of dynamic pragmatics sheds a new light on the nature of conversational implicature, and language use in general.

Keywords: Linguistics.
Advisor: Condoravdi Cleo A.
Potts Christopher
Kiparsky Paul advisor. Thesis advisor
Towards a string theory model of de Sitter space and early universe cosmology [electronic resource]

String theory is arguably the best candidate for a theory of quantum gravity and unified interactions. Reconciling Einstein's theory of General Relativity with Quantum Mechanics. The theory however is best understood on Minkowski and Anti-de Sitter space-times, and not on exponentially expanding space-times with positive cosmological constant, like our own universe. There is still no satisfactory formulation of String Theory on these so called asymptotically de Sitter space times. In this thesis I will discuss certain avenues of progress towards a String Theory formulation of de Sitter space-times. Specifically, how understanding of the analytic continuations of Liouville Theory and how to gauge-fix it in the Timelike regime will aid in the understanding of the proposed FRW-CFT duality of de Sitter space. It is also discussed how non-trivial topology effects proposed Chern-Simons Matter duals of Vasiliev Higher Spin gravity theories which are important in the dS-CFT description of de Sitter Space.

Keywords: Physics.
Advisor: Susskind Leonard primary advisor. Thesis advisor
Kachru Shamit
Shenker Stephen Hart
Towards controlled nanostructure fabrication and characterization using combined scanning tunneling microscopy and atomic layer deposition [electronic resource]

Nanostructures play an increasingly important role in the design of a wide range of modern devices. Because of instrument limitations, major frontiers remain both in the systematic characterization of nanostructures and in the degree of control afforded in their fabrication. This thesis describes the design and realization of a new scientific instrument that combines a nanostructure fabrication technique - atomic layer deposition (ALD) - with a nanostructure characterization technique - scanning tunneling microscopy (STM) - in a single vacuum chamber. The instrument has the capability to monitor individual nanostructures in situ as they are grown with ALD, tracking changes in their physical and electronic structure as they develop. It can be used to monitor the natural growth of extremely thin ALD films with sub-nanometer resolution, providing information about materials which are candidates for thin film devices. In addition, the instrument is intended to be used to activate ALD growth locally through the influence of the STM tip, providing unprecedented control over the size, shape, and configuration of the created nanostructures and enabling their systematic study.

Keywords: Physics.
Advisor: Prinz F. B. primary advisor. Thesis advisor
Goldhaber-Gordon David
Moler Kathryn A. advisor. Thesis advisor
Towards internal wave resolving simulations of the ocean [electronic resource]

Most ocean models solve the hydrostatic primitive equations. Small-scale processes such as nonlinear internal solitary waves, however, require computationally expensive nonhydrostatic simulations to be well-resolved because the balance of nonlinearity and dispersion is responsible for the wave's shape. The main goal of this dissertation is to inform the practice of nonhydrostatic ocean modeling. To this end, I have examined the accuracy and stability of poplar methods used in nonhydrostatic modeling. Most ocean models are second-order accurate, inducing numerical dispersion generated from odd-order terms in the truncation error. Numerical dispersion is problematic because it mimics physical dispersion due to nonhydrostasy. To ensure relative dominance of physical over numerical effects, simulations require the horizontal grid spacing ([Delta] x) to be less than the depth of the internal interface (h1). When this condition is not satisfied, numerical dispersion overwhelms physical dispersion, and modeled internal waves exist with a dynamical balance between nonlinearity and numerical dispersion. Satisfaction of this condition may be a significant additional resolution requirement beyond the current state-of-the-art in ocean modeling. To cope with this high horizontal resolution requirement, it becomes necessary to find other means of reducing resolution requirements and computational cost. To this end, I suggest a specific framework which has been implemented as a prototype for a next-generation ocean model. The new model is a nonhydrostatic, isopycnal-coordinate ocean model, which to my knowledge is the first of its kind. Isopycnal coordinates provide a natural representation of the problem physics which in turn reduces the number of vertical grid points and thus improves efficiency. Existing isopycnal-coordinate models are purely hydrostatic owing to the nearly hydrostatic scaling of most oceanic processes and the belief that nonhydrostatic effects are only associated with overturning motions which cannot be represented in isopycnal coordinates. However, processes such as nonlinear internal solitary waves are clearly nonhydrostatic and not associated with overturning motions. Thus a nonhydrostatic isopycnal coordinate model may be well-suited to simulating nonlinear internal solitary waves. Ideally, when the internal wave structure is predominantly mode-1, an isopycnal model with only two layers may suffice. I demonstrate that the new model is capable of simulating a variety of nonhydrostatic processes in idealized test cases with a reduced number of vertical layers.

Keywords: Civil and Environmental Engineering.
Advisor: Fringer Oliver B. (Oliver Bartlett) primary advisor. Thesis advisor
Koseff Jeffrey Russell advisor. Thesis advisor
Monismith Stephen Gene advisor. Thesis advisor
Tracheal progenitor outgrowth from the niche during Drosophila melanogaster metamorphosis [electronic resource]

While there has been great progress in identifying stem and progenitor cells and the signals that control their proliferation and differentiation, how stem/progenitor cells exit their niche and how they form new tissue is not well understood. Unlike in the embryo, tissue formation in an adult animal faces new challenges such as longer distances to migrate and a complex milieu of differentiated tissue to migrate around and/or coordinate with. To restore function to a tissue, stem/progenitor cells must also integrate into healthy tissue and coordinate growth with decaying tissue. In this thesis, I examine how tracheal progenitor cells exit their niche to form tracheal tissue during Drosophila melanogaster metamorphosis. Tracheal progenitors exit the niche in two waves. During the first wave, progenitors migrate onto the basal surface of larval tracheal branches destined for destruction, and track along the decaying branches. Progenitor outgrowth requires the embryonic tracheal branch inducer, Breathless FGFR, and surprisingly, the Branchless FGF ligand is expressed in larval branches along which progenitors crawl. In this way, outgrowth is coordinated with tissue decay. Progenitors that remain within the niche during the first wave exit later. However, instead of moving onto the basal surface of larval branches, progenitors exiting the niche during this second wave move along the apical surface, displacing larval cells, and repopulating the tracheal branch. This latter process does not resemble branching morphogenesis in the embryo and does not require Bnl/Btl FGF signaling, demonstrating that progenitor outgrowth does not always require embryonic guidance cues.

Keywords: Genetics.
Advisor: Krasnow Mark
Fuller Margaret
Kim Stuart
Lipsick Joseph Steven
Trading volume reactions to earnings announcements and future firm performance [electronic resource]

I investigate whether firms with higher abnormal trading volume (ATV) around earnings announcements (EAs) outperform those with lower ATV over the short and long terms following the EA. In addition, I address whether any positive relation between ATV around EAs and future firm performance is weaker for firms with a higher proportion of shares held by sophisticated investors. Consistent with theories that attribute ATV around public announcements primarily to differing investor interpretations of the news and that link differential interpretation to future returns, I find that, for several years after an EA, firms in the highest decile of ATV significantly outperform those in the lowest decile. Further, I find that ATV and earnings surprises explain future returns incremental to the three Fama and French (1993) and momentum risk-factors. Next, consistent with the proportion of ATV driven by lack of consensus regarding the price being lower when the presence of rational investors is higher, I document that the level of investor sophistication−a proxy for investor rationality−attenuates the positive relation between ATV and future returns. Taken together, my study lends support to and links two streams of theories from financial economics, and demonstrates that trading volume reactions to EAs provide information about future returns and firm financial performance that cannot be deduced from the price reactions or the magnitudes of earnings surprises. My study also documents that the positive relation between ATV and future firm performance is sensitive to the level of security holdings of sophisticated investors.

Keywords: Business.
Advisor: Barth Mary E. primary advisor. Thesis advisor
Kasznik Ron advisor. Thesis advisor
Lee Charles M. advisor. Thesis advisor
Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines [electronic resource]

The human genome's nucleotide sequence contains a small amount of information relative to the complexity of the organism. The diversity of developmental programs and stimulus responses is instead enabled by a vast regulatory network of chemical modifications and protein interactions that determine the activity level of each genome element dynamically. Recent advances in molecular profiling techniques have led to the creation of large data sets that assay each regulatory interaction across the entire genome at once, with high sensitivity and precision. Here I introduce a new computational method, UniPeak, that synthesizes the output from any number of these experiments into a single straightforward analysis with rigorous quantitative measures. I then apply this method to the largest available data sets of genome regulation experiments, and integrate them with parallel experiments on genome activity. I discover and characterize novel regulatory interactions, and model how these interactions regulate the activity of genes.

Keywords: Genetics
Advisor: Sidow Arend primary advisor. Thesis advisor
Baker Julie (Professor of genetics) advisor. Thesis advisor
Fire Andrew Zachary advisor. Thesis advisor
Sherlock Gavin advisor. Thesis advisor
Transformer array power combining and stacking for CMOS RF power amplifiers [electronic resource]

CMOS technology scaling has enabled the integration of RF transceivers on a single chip for various applications. However, as the feature sizes of the transistors scale, their breakdown voltages are reduced. Lower breakdown voltages lower the maximum voltage swings across the transistors and necessitate operation from a lower supply voltage. These factors, in turn, impose significant limitations on RF power amplifier design: (1) the low voltage swings limit the maximum power that can be delivered to the load, and (2) the DC-DC converter needed to generate a low supply voltage for the power amplifier from typical battery voltages increases the power consumption, size, and cost of the design. To address the first challenge, transistor stacking and transformer-based power combining are investigated as means of increasing the output power, while to address the second issue, transistor stacking and amplifier stacking are considered. Two CMOS RF power amplifier architectures serve as vehicles for exploring these concepts, each leading to the design and implementation of an experimental prototype. The first design is based on a stacked amplifier architecture with an off-chip matching network. Transistor stacking is used to increase the output power and supply voltage of the power amplifier, and a bias circuit is designed to enable operation of the power amplifier from a large supply voltage without exceeding the transistor breakdown limitations. The second design is an array RF PA architecture that employs (1) series-parallel transformers, (2) transistor stacking, and (3) amplifier stacking. This array RF PA uses series-parallel combinations of transformers to provide simultaneous impedance transformation and power combining. The proposed scalable transformer array architecture offers the possibility of designing a power amplifier to meet given specifications of output power and load impedance over a wide bandwidth. Stacking transistors in the array RF PA increases the output power provided by each of the unit PA stages comprising the array. In addition, the PA stages are themselves stacked. The two stacking methods increase the operating supply voltage. To demonstrate the proposed concept, a 2-by-4 amplifier array has been integrated in a 65-nm CMOS technology.

Keywords: Electrical Engineering
Advisor: Lee Thomas primary advisor. Thesis advisor
Wooley Bruce A.
Su David (David Kuochieh) advisor. Thesis advisor