VictorJuiz/thesis huggingface dataset:
Recursive deep learning for natural language processing and computer vision [electronic resource]

As the amount of unstructured text data that humanity produces overall and on the Internet grows, so does the need to intelligently process it and extract different types of knowledge from it. My research goal in this thesis is to develop learning models that can automatically induce representations of human language, in particular its structure and meaning in order to solve multiple higher level language tasks. There has been great progress in delivering technologies in natural language processing such as extracting information, sentiment analysis or grammatical analysis. However, solutions are often based on different machine learning models. My goal is the development of general and scalable algorithms that can jointly solve such tasks and learn the necessary intermediate representations of the linguistic units involved. Furthermore, most standard approaches make strong simplifying language assumptions and require well designed feature representations. The models in this thesis address these two shortcomings. They provide effective and general representations for sentences without assuming word order independence. Furthermore, they provide state of the art performance with no, or few manually designed features. The new model family introduced in this thesis is summarized under the term Recursive Deep Learning. The models in this family are variations and extensions of unsupervised and supervised recursive neural networks which generalize deep and feature learning ideas to hierarchical structures. The RNN models of this thesis obtain state of the art performance on paraphrase detection, sentiment analysis, relation classification, parsing, image-sentence mapping and knowledge base completion, among other tasks.

Advisor: Manning Christopher D. primary advisor. Thesis advisor
Liang Percy advisor. Thesis advisor
Ng Andrew Y.
Reducing contact resistivity in Ge-rich SiGe modulators for optical interconnects

This thesis discusses reducing contact resistivity in Ge-like SiGe modulators through two methods: Dopant segregation and Metal-Insulator-Semiconductor (MIS) approach. We first discuss the challenges associated with implementing the dopant segregation technique because of the requirement of a high temperature anneal step.
We then discuss the techniques that were used to fabricate the MIS based SiGe modulators that used TiO2 as the insulator layer. Using this technique, we managed to almost completely depin the Fermi level and reduce the contact resistivity by 25x and two orders of magnitude.

Keywords: Optical interconnect
scaling
interconnect bottleneck
modulators
Silicon
Germanium
CMOS
SiGe
Silicon Germanium
contact resistivity
Tranfer Length Method
TLM
Titanium
Titanium Dioxide
TiO2
Depinning
Fermi level pinning
Quantum confined stark effect
MIS
MIGS
Dopant segregation
Quantum Wells
ALD
fabrication
nanotechnology
Thesis
Advisor: Harris Jr. James S.
Saraswat Krishna.
Reframing the Iraq war through erformance [electronic resource] : politics, rhetoric, and resistance

In 2003 the United States government launched a war against Iraq, a country that had not attacked it first. The Bush administration rallied support for this war using aesthetic, discursive, and performative devices that framed the war as necessary for national security and an ethical imperative for humanitarian intervention. At a time when the government relied on the tools of performance to justify and wage war, artists struggled to find new aesthetic and political approaches to theater, protest performance, and the media. Marked by a lack of formal innovation, performance during the war was variously a methodology for historicizing war as it happened, an embodied means of resistance, and an attempt to understand the effects and affects of the U.S. invasion and occupation of Iraq. Although trapped in the same political logic and capitalist systems they attempted to critique, performances about the Iraq War nonetheless reframed the war, enabling the public to see it differently. "Reframing the Iraq War through Performance: Politics, Rhetoric, and Resistance" argues that performance genres such as documentary, tragedy, and satire challenged the logic and emotional appeal of the government's call for war in order to create space for resistance. This project analyzes the relation between form and content in order to argue that particular modes of performance are uniquely positioned to reconceptualize specific frames of war. I examine the ways in which personal narratives in documentary plays reveal problems with the freedom agenda, adaptations of Greek tragedies to the Iraq war demonstrate contradictions embedded in American exceptionalism, and the satirical performances in The Daily Show and The Colbert Report challenge the manipulation of truth by the government and media.

Keywords: Theater and Performance Studies.
Advisor: Jakovljević Branislav primary advisor. Thesis advisor
Menon Jisha
Rayner Alice advisor. Thesis advisor
Regulation of hedgehog signaling by DLG5 modulation of smoothened activity [electronic resource]

Hedgehog (Hh) signaling during embryogenesis and adult tissue homeostasis involves the activation of the oncoprotein Smoothened (Smo), but little is known about its mode of regulation. We attempt to identify proteins which regulate Smo function by performing a large-scale proteomic screen using Smo as the bait. We identify Dlg5 as a novel Smo-interacting protein whose association with Smo is triggered by Hh. Depletion of Dlg5 leads to global destabilization of Smo protein and concomitant reduced ciliary accumulation. We find that that Dlg5 localizes to the basal bodies in cultured cells, and our evidence further suggests that a Dlg5-scaffolded protein complex at the basal body is required to regulate Smo prior to Smo entry into the primary cilia.

Advisor: Beachy Philip Arden primary advisor. Thesis advisor
Nelson William advisor. Thesis advisor
Oro Anthony
Talbot William
Regulation of Meiotic Division Numbers During Spermatogenesis by the COP9 Signalosome through a Cyclin/CDK Inhibitor

Strict control over meiotic division numbers is crucial for gamete generation and conservation of genetic material in sexually reproducing eukaryotes. Although much has been learned about how homologous chromosomes pair, recombine, and segregate in meiosis I, much less is known about the cell cycle regulatory events that lead to two rapid divisions without an intervening S-phase necessary for production of haploid gametes. This project focuses on cell cycle regulation of the two meiotic divisions in the male germ line of Drosophila melanogaster. Previous work in the lab discovered meiotic defects in germ cells lacking function of the COP9 signalosome (csn), which is involved in regulating activities of the Ubiquitin Proteasome System (UPS), which in turn marks proteins for degradation by the 26S proteasome. The failure to undergo meiosis II observed after loss of csn function in spermatocytes is reminiscent of the phenotype caused by over-expression of a previously reported cyclin/CDK inhibitor, roughex (rux), suggesting that csn might negatively regulate rux activity to allow progression of germ cells to meiosis II in the male germ line. Roughex had previously been shown to act as a dosage-dependent regulator of entry into meiosis II via inhibition of cyclin A and B activity. Here, I probed the regulatory relationship between csn and rux using genetic, cell biology, and biochemical approaches. Over-expression of cyclin A and cyclin B1 partially restored chromosome segregation in meiosis II to csn loss of function. Consistent with the hypothesis that csn allows meiosis II by inhibiting rux, I found that knock down of rux in csn mutants showed significant restoration of meiosis II as well. In addition, Western blot analysis showed visibly higher levels of rux protein in csn RNAi testis extracts compared to wild-type controls. My data suggest that csn may be required at a critical time during meiosis II for chromosome segregation by inhibition of rux activity to ensure sufficient cyclin activity.

Keywords:  Department of Biology
Developmental biology
csn
rux
chromosome segregation
meiosis
Biology
Thesis
Advisor: Fuller Margaret
Simon Michael
Regulation of the centriole life cycle by MDM1 [electronic resource]

Centrosomes are composed of microtubule based structures called centrioles surrounded by a proteinaceous pericentriolar material. They serve as the primary microtubule organizing center in mammalian cells and also nucleate cilia formation. Mutations in centrosome and cilium protein coding genes are implicated in ciliopathy-related diseases and cancer. Thus, understanding functions of these proteins can aid understanding the development of these diseases. Here we study Mdm1, which we previously identified as being transcriptionally upregulated in mouse tracheal epithelial cells (MTECs). We show that MDM1 is a centriole protein with microtubule binding and stabilizing properties that localizes to newly replicated procentrioles beginning in mitosis, coincident with the end of centriole duplication. Depletion and overexpression of MDM1 results in phenotypes consistent with the protein acting as a negative regulator of centriole duplication. We also examine the role of MDM1 in MTECs, showing that it does not appear to be deuterosome-associated, but does localize to centrioles upon their formation. We further show that MDM1 disperses from centrioles upon ciliation in mature multiciliated cells. MDM1 depletion in MTECs did not block entry into the multiciliated cell fate program, but did cause a ciliation defect, suggesting MDM1 depletion may cause a delay in the development pathway of these cells.

Keywords: Biology.
Advisor: Stearns Tim primary advisor. Thesis advisor
Cyert Martha S.
Nelson W. J. (W. James)
Rohatgi Rajat
RegulomeDB: An Updated Resource for Annotating Regulatory Regions of Personal Genomes

Genome-wide association studies have uncovered thousands of single nucleotide polymorphisms (SNPs) that are statistically associated with diseases or phenotypes of interest.  Most efforts to understand these results have focused on SNPs that disrupt coding regions of the genome, despite the fact that a majority of variants are found in noncoding areas. To address this imbalance, we previously developed the RegulomeDB database, which allows for the improved identification and characterization of regulatory SNPs.   RegulomeDB annotates SNPs provided by the user, indicating how likely each is to have a functional effect on gene regulation based on experimental evidence from the Encyclopedia of DNA Elements (ENCODE) Consortium, Gene Expression Omnibus (GEO), and other sources.  However, the scoring system is entirely heuristic, making it difficult to interpret and use the results.  To improve this system, we develop a machine learning based approach to determine whether a SNP without direct experimental evidence is likely to affect transcription factor binding. This work is the first in a series of steps to improve RegulomeDB as a tool for annotating potentially damaging regulatory SNPs in personal genomes.

Keywords:  Department of Biology
Stanford University Biology Department
personal genomics
computational biology
SNPs
Thesis
Advisor: Snyder Michael
Petrov Dmitri
Reliable functional composition of a recombinase device family [electronic resource]

This dissertation describes design principles and demonstrates applications of a recombinase device family to provide examples for how to compose reliable synthetic gene systems. I begin by introducing the functional composition challenges in building a cell cycle counter, a theoretical example of complex synthetic gene systems requiring hundreds of genetic parts. I develop novel designs for combinatorial counters that could store exponentially more states than existing examples. Using numerical simulation, I demonstrate the feasibility and limits of each design; the lack of reliably rewritable binary state devices for use in genetic counting systems is also highlighted. I then focus on experimental proof-of-concepts, failure analyses and design principles for a Recombinase Addressable Data (RAD) device built from bacteriophage integrases and excisionases. RAD devices based on Bxb1 integrase-excisionase are capable of storing state over one hundred cell generations and can be switched repeatedly without performance degradation. The tedious process of engineering a first RAD device raises the question of whether it is practical to scale such devices beyond a single bit, to implement other logical operations beyond set-reset, and to couple such devices to application-specific control signals. To address these questions, I reconfigure RAD devices to operate entirely from genomic DNA, generalize rewritable RAD principles to three other integrase-excisionase pairs, and implement single-use two input logics, buffer gates and integrase-excisionase cascades. I also demonstrate the feasibility of using competitive binding to multiplex the control of different recombination sites via the same recombinase. Finally, I show that the outcomes of composing recombinase devices with novel transcription sources can be predicted, leading to an implementation of autonomous switches driven by growth-phase dependent promoters. Taken together, the work developed here comprises an initial framework for composing complex yet reliable genetic systems using recombinase enzymes.

Keywords: Bioengineering.
Advisor: Endy Andrew D. primary advisor. Thesis advisor
Calos Michele P. advisor. Thesis advisor
Covert Markus advisor. Thesis advisor
Horowitz Mark (Mark Alan) advisor. Thesis advisor
Representation and realism in Descartes's meditations [electronic resource]

Recent scholarship regarding Descartes's theory of ideas as presented in his Meditations makes a case for regarding Descartes as a direct realist: someone who believes in the existence of extra-mental objects, and who believes our cognitive activity involves the direct apprehension of those objects. On this view, we have direct cognitive access to those objects through ideas, but such ideas are conceived simply as acts, or operations, of the mind, not as mental objects before the mind. This contrasts with a long-standing view of Descartes as a representational realist: someone who believes in the existence of extra-mental objects, and who believes our cognitive activity involves a mediated relationship with those objects. On this view, we have direct cognitive access only to mediating mental objects, called ideas. In this dissertation, I generally defend a representational realist interpretation of Descartes against several direct realist interpretations. I reject John Yolton's sign-signifier, direct realist interpretation, Deborah Brown's Thomistic direct realist view, and John Carriero's quasi-Aristotelian direct realist view. I also reject the view that we ought to interpret Descartes as a direct realist because the concepts involved in his theory of ideas are owed to direct realist, Scholastic predecessors.

Keywords: Philosophy.
Advisor: De Pierris Graciela Teresa primary advisor. Thesis advisor
Findlen Paula advisor. Thesis advisor
Lawlor Krista advisor. Thesis advisor
Resonances [electronic resource] : for wind instruments

This dissertation is comprised of a single work, Resonances, which was written and premiered by Elision Ensemble. The compositional motivation behind Resonances was driven by the following two questions pertaining to the acoustic peculiarities of wind instruments: (1) Is it possible to design an algorithmic system to formulate various degrees of polyphonic correlations, which would yield multiple formal relations as a function of acoustic distinctiveness?; (2) If so, how perceptible would the resulting polyphony be? Focusing on the deviation degrees of acoustic properties, Resonances views the instruments as complex acoustic mechanisms. I represent the complexity of each instrument in a matrix, the inputs of which are various acoustic measurements of a wind instrument. An algorithm operates on these matrices to generate new matrices. Then, the output matrices are plotted in a multidimensional space through which various geometric relations (in terms of deviational scaling) are devised to formulate formal structures.

Keywords: Music.
Advisor: Ferneyhough Brian
Applebaum Mark advisor. Thesis advisor
Chafe Chris advisor. Thesis advisor
Ulman Erik
Resource utilization and discovery for wireless media streaming [electronic resource]

We study the issues governing user experience for media streaming in next-generation wireless networks by investigating problems in access point utilization and discovery. When there are many potential points of attachment to the network, a mobile station must be able to retrieve content from the best access point via handoff control before user mobility or a fluctuating wireless environment causes service interruption. With the aim to develop efficient yet effective control algorithms, we formulate models to study the implications of optimal control policies and their tractable approximations in various relevant settings. By analyzing and characterizing the factors affecting their performance, we arrive at many insights about practical system design.

Keywords: Management Science and Engineering.
Advisor: Bambos Nicholas primary advisor. Thesis advisor
Singh Jatinder
Ye Yinyu advisor. Thesis advisor
Response of regional climate to global forcing [electronic resource] : the dynamics of climate change in West Africa

There is now unequivocal evidence that the Earth's climate is changing as a result of human activities. These changes pose a number of potential risks for human and natural systems. Within the Sahel, a semi-arid region of northern Africa that is home to over 50 million people, climate-related stresses on human systems are exacerbated by a limited capacity for climate adaptation and persistent uncertainty in projections of future climate. In this dissertation I utilize a suite of numerical modeling techniques in conjunction with observational data to study the multi-scale interactions that shape rainfall and atmospheric circulation in northern West Africa. This dissertation consists of three chapters. In the first chapter, I use an ensemble of general circulation model experiments to examine the relative roles of different global drivers in shaping projected changes in West African climate. Specifically, I assess the response of precipitation and atmospheric circulation in West Africa to the individual influences of direct atmospheric radiative forcing from projected increases in greenhouse gas concentrations and greenhouse gas-induced sea surface temperature forcing. In the second chapter, I evaluate the simulation of synoptic-scale weather disturbances, known as African easterly waves, in the latest generation of global climate models. African easterly waves serve as an important source of Sahel rainfall and play a critical role in Saharan dust transport and the initiation of the most intense Atlantic basin hurricanes. In this work I identify key reasons for biases in the simulation of African easterly waves, and offer several new insights for improved climate modeling efforts in West Africa. In the third chapter, I explore the response of atmospheric circulation in West Africa to projected increases in greenhouse gas concentrations. Models exhibit a robust increase in monsoon strength and African easterly wave activity in response to the pattern of future warming in West Africa. These results suggest the possibility of a number of future climate-related impacts on human and natural systems in West Africa and the greater Atlantic basin.

Keywords: Environmental Earth System Science.
Advisor: Diffenbaugh Noah S. primary advisor. Thesis advisor
Caldeira K. (Ken)
Lambin Eric F. advisor. Thesis advisor
Thomas Leif N. advisor. Thesis advisor
Rethinking sanitation [electronic resource] : quantifying and capturing resource flows in "waste" across geographic and economic contexts

Sanitation, or the effective management of human excreta, is a basic societal function without which it is virtually impossible to preserve public health, human dignity, or the environment. Society today faces a variety of front-end and back-end sanitation challenges. In low- and middle-income countries, a large fraction of the population lacks access to proper front-end sanitation, toilet facilities that are clean and reliably isolate waste from people. An even larger fraction lacks back-end waste management systems that will minimize the potential for excreta to cause illness or environmental damage. In wealthier countries, we have largely delivered front-end and back-end sanitation, but the infrastructure that supports these services is old and needs replacement under new financial, regulatory, and environmental constraints. This dissertation examines the potential for container-based sanitation (CBS) and resource recovery from waste to reduce the costs of sanitation service delivery in various contexts. Case studies in Cap Haitien, Haiti; Bocas del Toro, Panama; and San Francisco, USA are used to quantify material and resource fluxes in human waste; evaluate the cost of capturing those fluxes; and determine the potential value of the resources. The dissertation also provides a discussion of conditions under which these approaches can provide viable and effective alternatives to conventional sanitation approaches.

Keywords: Civil and Environmental Engineering.
Advisor: Criddle Craig primary advisor. Thesis advisor
Davis J. A. (Jennifer Ann)
Luthy Richard G. advisor. Thesis advisor
The return of tragedy [electronic resource] : an ecology of form from Ancient Greece to 1904

This dissertation examines the ways in which tragedy produces, and challenges, human subjectivity in three distinct periods of western theatrical production. It also tells a story of their ahistorical continuity based on tragic repetition. Readings of Aeschylus' Oresteia, Sophocles' Oedipus Tyrannos, and Euripides' Bacchae ground this argument in the Greek original. Specific constructions of fate, agency and justice provide sites for understanding the evolution of a tragic consciousness. Charting a meta-narrative of tragic inheritance through Greek tragedy, Renaissance tragic drama, and the modern drama, I establish an alternative view of western theatre's past—one that embodies its own consciously adopted tragic form. Renaissance artists repressed the knowledge structures contained in the artifacts of a past consciousness in service of Christian morality and bourgeois rationality. By creating a hybrid moral tragedy rooted in contemporary ways of knowing, they valorized the human perspective in contradiction to the world-centered one that Greek tragedy staged. As a result, the dramatic tradition increasingly excluded that which could not self-disclose from its catalogue of the real. It secured the illusion of autonomous human agency, creating the conditions for its own literary and historical tragic reversal. Marlowe's Doctor Faustus, Shakespeare's Macbeth, Hamlet and Winter's Tale model this contradiction. Finally, I retheorize Szondi's "crisis of the drama" reading Strindberg's Miss Julie, Ibsen's Hedda Gabler and Chekhov's The Cherry Orchard as a final cycle of tragedy that stages historical transformation as the suicide of dramatic realism.

Keywords: Theater and Performance Studies.
Advisor: Rehm Rush primary advisor. Thesis advisor
Brooks Helen
Hill Leslie advisor. Thesis advisor
Rayner Alice advisor. Thesis advisor