VictorJuiz/thesis huggingface dataset:
Inferring nonlinear computation in multilayered neural circuits [electronic resource]

The brain performs of a remarkable variety of computations. These computations arise in circuits comprised of interconnected neurons and mediated by a rich diversity of biophysical mechanisms. Neuroscientists are tasked with characterizing and understanding this complexity using a combination of experimental and theoretical tools. In particular, we typically have to infer computations and mechanisms underlying neural processing given limited experimental recordings. In this thesis, I describe my work on developing and applying computational tools to study these issues in multilayered neural circuits in the retina. Speciﬁcally, I am interested in the following fundamental questions: What computations do early sensory neurons perform on their inputs? How do biophysical mechanisms mediate these computations? And finally, what can we infer about these computations and mechanisms given partial experimental observation of a multilayered circuit? Chapter 1 introduces these questions in more detail, and Chapter 2 covers relevant background material. Chapter 3 discusses quantitatively the relationship between these encoding models and commonly used descriptive statistics of the neural code. Chapter 4 explores a particular encoding model, a two layer linear-nonlinear cascade (LN-LN). Chapter 5 uses encoding models to better understand the retinal response to natural scenes. Finally, Chapter 6 discusses implications of this work and touches on future directions.

Keywords: Neurosciences.
Advisor: Baccus Stephen A. primary advisor. Thesis advisor
Ganguli Surya
Boahen Kwabena (Kwabena Adu) advisor. Thesis advisor
Newsome William T. advisor. Thesis advisor
Raymond Jennifer L. advisor. Thesis advisor
The influence of a robot's mere presence on human communication [electronic resource]

Does the mere presence of a robot change the way that a patient thinks about and behaves toward her medical provider? We investigated this question using a commercially-available robot that millions of people will soon encounter. Fifty-one participants interacted with a nutritionist in the presence of either a tablet (control), a robot with unmoving eyes that stared toward the participant (nonsocial implicit cue), or a robot with eyes that tracked the participant's face (social implicit cue). Participants in the social robot condition looked at the nutritionist more than those in the nonsocial condition, and perceived her less warmly than those in the control condition. Those in the presence of either robot also contributed less to their conversations with the nutritionist than those in the presence of a tablet. Discussion focuses on causal mechanisms; the validity of concepts like sociality; the ambiguous meaning of eye movements; and implications for design, doctor-patient rapport, and human culture.

Keywords: Communication.
Advisor: Bailenson Jeremy primary advisor. Thesis advisor
Ju Wendy
Reeves Byron
Schwartz Daniel L. advisor. Thesis advisor
Influences of Evaporite Minerals on the Vertical Distribution, Storage, and Mobility of Uranium in Response to Hydrological Conditions

Uranium-contaminated groundwater in Riverton, Wyoming persists despite anticipated natural attenuation outside of a former uranium ore processing facility. The inability of natural flushing to dilute the uranium below the regulatory threshold indicates that sediments act as secondary sources likely (re)supplying uranium to groundwater. Throughout the contaminated floodplain, uranium rich-evaporites are readily abundant in the upper 2 m of sediments and are spatially coincident with the location of the plume, which suggests a likely link between evaporites and increased uranium levels. Systematic sampling before and after a flooding event and sequential chemical extractions were used to decipher the concentration, hosted phase, and relative vertical mobility of uranium in the sediments/soil. The sum of these analyses provides a model for the effect of seasonal hydrologic changes on uranium incorporation within evaporite sediments. These findings hold implications for the fate of uranium throughout contaminated sites across the Colorado River Basin.

Keywords:  Earth Systems Program
School of Earth Energy &amp; Environmental Sciences
uranium
evaporite
Thesis
Advisor: Fendorf Scott
Bargar John
Information-theoretic limits of distributed randomness generation [electronic resource]

Randomness generation has numerous important applications, for example, in statistical sampling, randomized algorithms and cryptography. In this dissertation, we study randomness generation from an information-theoretic point of view. Extending the seminal work of Knuth and Yao on generating random variables from coin flips, we investigate several multi-terminal randomness generation settings. First we consider the distributed generation setting in which Alice and Bob share a common random source, and each of them would like to generate a random variable such that the two random variables follow a prescribed joint distribution. The goal is to minimize the amount of common randomness needed. We show that for log-concave distributions, the amount of common randomness is within a constant gap of the mutual information. The proof uses a novel construction called dyadic decomposition. We then consider the remote generation setting in which Alice, who knows the chosen distribution, wishes to send a message to Bob to enable him to generate a random variable distributed according to this distribution. We design a scheme that applies to any continuous distribution and establish an upper bound on its expected codeword length using dyadic decomposition. Finally, we consider the one-shot channel simulation setting with unlimited common randomness. We strengthen the result by Harsha et al. using a new strong functional representation lemma, and show that it can be applied in designing schemes for one-shot lossy source coding, and providing a simple proof of the Gelfand-Pinsker theorem for channels with state.

Keywords: Electrical Engineering.
Advisor: El Gamal Abbas A. primary advisor. Thesis advisor
Özgür Ayfer advisor. Thesis advisor
Weissman Tsachy advisor. Thesis advisor
Inhomogeneity in complex oxides [electronic resource] : probing superconductivity and magnetism with scanning SQUID

Complex oxides, materials consisting of two or more metals and oxygen, are studied widely in condensed matter physics. Heterostructures made of complex oxides are highly tunable platforms for realizing novel electronic and magnetic states. I used a local mangetic imaging technique, scanning superconducting quantum interference device (SQUID) microscopy, to investigate the role of inhomogeneity in two complex oxide heterostructures. By mapping the diamagnetic susceptibility of superconducting delta-doped SrTiO3 and LaAlO3/SrTiO3 as a function of temperature, I showed that an intrinsic source of inhomogeneity—domains of different orientations of the crystallographic unit cell formed at a structural phase transition—causes the superconducting transition temperature to spatially vary in both materials. Previous scanning SQUID measurements as well as other techniques found magnetism in LaAlO3/SrTiO3. Oxygen vacancies were proposed as a possible source. I measured a series of samples with different levels of oxygen vacancies and, finding no magnetism, set limits that are comparable to or are more stringent than signal sizes previously reported in the literature, placing strong constraints on the role of oxygen vacancies in producing magnetism in LaAlO3/SrTiO3 heterostructures. Both heterostructures that I studied exhibit two-dimensional superconductivity. Pointlike defects have the simplest possible geometry for a defect in two dimensions. I compared susceptibility images of several two-dimensional, complex-oxide-based superconductors to a model for the way in which our scanning SQUID susceptometers image defects in two-dimensional superconductors that are much smaller than the length scales of our sensor and found good agreement.

Keywords: Applied Physics.
Advisor: Moler Kathryn A. primary advisor. Thesis advisor
Fisher Ian R. (Ian Randal) advisor. Thesis advisor
Kivelson Steven advisor. Thesis advisor
An inquiry into "a history of the rise and fall of Japanese literature" by Takahashi Genichiro [electronic resource]

This dissertation comprises a study and a partial annotated translation of "Nihon bungaku seisuishi" (A History of the Rise and Fall of Japanese Literature) by Takahashi Gen'ichirō. The study focuses on the confrontation between literary history and the contemporary frame dramatized in the narrative of "Seisuishi, " a novel that combines the staid discourse of literary historiography with the semiotic chaos of postmodern fiction. As bungaku literature, a self-reflexive genre attuned to the cultural specificities of its own mode of textuality, "Seisuishi" radically recontextualizes classic works of modern Japanese literature to generate the possibility of authentic encounters with the literary past that are nonetheless thoroughly of the present moment. Through opening and interrogating spaces of literary secularity, "Seisuishi" serves as fruitful grounds for exploring the applicability of religious metaphors in figuring authorial stances vis-à-vis the concept and practice of literature. The final portion of the study examines how the novel incorporates marginalized female voices to highlight and critique its status as a work of male literature.

Keywords: East Asian Languages and Cultures.
Advisor: Carter Steven D. primary advisor. Thesis advisor
Reichert Jim (James Robert) primary advisor. Thesis advisor
Levy Indra A. advisor. Thesis advisor
Insights into Interactions Between Staphylococcus aureus, Keratinocyte RabGEF1, and other Host Factors in the Development of Atopic Dermatitis-like Skin Pathology

The causes of atopic dermatitis (AD), or eczema, are currently unknown. However, it is thought that there are immunomodulatory pathways that affect skin barrier function that can lead to the development of AD, and that the disease can be exacerbated by colonization of the skin with the bacterium, Staphylococcus aureus (S. aureus). Here, we exploit a model involving genetically-modified mice (“Rabgef1KERT2-KO” mice) in which treatment of the skin with tamoxifen can result in depletion of keratinocyte levels of RAB guanine nucleotide exchange factor (RabGEF1, also known as RABEX-5). Upon repetitive tamoxifen treatment, these mice develop skin pathology with many of the features of AD. Using this model, we investigated whether a depletion of keratinocyte RabGEF1 influenced colonization of the skin with S. aureus and whether such skin tissue exhibited changes in levels of antimicrobial activity. We found that the skin of tamoxifen-treated RabGEF1-depleted mice exhibited increased growth of S. aureus as well as stronger antimicrobial properties and increased epidermal thickness compared to identically-treated control (RabGEF1-sufficient) mice. In a preliminary experiment, we also found that there were higher numbers of S. aureus in the skin of RabGEF1-depleted mice which also were deficient in RIP3, a protein kinase that is required for programmed necroptosis. These results suggest that RabGEF1 and RIP3 are host factors which can importantly influence both the skin pathology associated with this AD model and also the extent of S. aureus colonization of the animals’ AD-like skin lesions.

Keywords:  Department of Biology
Biology
atopic dermatitis
bacteria
Staphylococcus aureus
keratinocytes
skin barrier function
pathology
Thesis
Advisor: Galli Stephen J.
Long Sharon
Institutional effects in the worldwide expansion of the innovation economy [electronic resource]

In this work, I conceptualize innovation as a core institution of the world economy and society, and study the factors involved in its expansion across the globe. Specifically, I examine local conditions and global institutional pressures affecting a country's willingness to take part in the innovation economy, its level of expenditure on innovation, and the actual product of those expenditures. I use event-history models and panel regressions to test the aforementioned relationships on a sample of 132 countries from 1996 to 2012. There are four main findings. First, developing nations that are close to the advanced countries (in the core of the global political economy) are likely to follow the norms of the core and initiate actions to be considered as participants of the innovation economy. Second, countries are likely to mimic neighbors in their innovation spending patterns. Third, most developing regions of the world show signs of decoupling (producing significantly less innovation patents at the same level of R& D spending than the core). And, fourth, local competition is associated to mimetic isomorphism regarding innovation but also to lower levels of decoupling in the production of patents (by increasing the efficiency of R& D investments). These results suggest that there is imitation of the global core and of neighbors (oftentimes) despite sub-standard levels of efficiency, and that participating in innovation is as important as producing actual innovation.

Keywords: Management Science and Engineering.
Advisor: Barley Stephen R. primary advisor. Thesis advisor
Hinds Pamela primary advisor. Thesis advisor
Meyer John
Integrated, locally-synthesized, and genetically-targeted polymer systems in neural tissue [electronic resource]

Recent advancements in the development of implantable brain-machine interfaces have bridged the communication gap between the brain and modern electronics. While much work has been done to optimize the electrode-tissue interface of these devices, a bioelectronic system that can reliably interact with and identify genetically-specific neural circuits within whole, intact 3D volumes of tissue is yet to be realized. Therefore, novel approaches for building seamlessly integrated tools that are more intimately connected to biological elements in tissue are highly desirable. An alternative to pre-fabrication and subsequent implantation of small-scale, mechanically compliant electronic devices is locally-performed synthesis that directly integrates material with cells and soft tissue, for which there has been little precedence. In this work, the mechanical and chemical properties of polymer-brain hybrid materials synthesized directly inside of rodent brains using CLARITY were obtained to more deeply understand the interactions amongst polymer precursor reagents and tissue, which can significantly alter optical properties of tissue while preserving molecular structure. Next, a novel strategy was developed to generate functional organic materials directly on specific neurons and their subcomponents using a genetically-encoded enzyme to trigger polymerization. Quantitative analysis of the resulting material verified the genetically-specific and enzyme-mediated synthesis of a conductive polymer layer proximal to the surface of neurons. Furthermore, whole-cell patch clamp and extracellular electrical recording measurements indicated that this polymerization strategy did not have short-term cytotoxic effects in cultured unfixed neurons and acute mouse brain slices. These studies demonstrate the feasibility of new methodologies for in situ polymer synthesis to maintain intimate connections with biological targets in the brain, and inspire next-generation bioelectronic tissue-device interfaces that can enhance our study of intact, whole-tissue dynamics with exceptional control and spatial resolution.

Keywords: Bioengineering.
Advisor: Bao Zhenan primary advisor. Thesis advisor
Deisseroth Karl primary advisor. Thesis advisor
Heilshorn Sarah advisor. Thesis advisor
Integrating Gender Equality into an Improved Model of Technology-Based National Development: A Critical Exploration of Internet Diffusion in Pakistan

Widespread belief in the Internet's potential to increase access to information and contribute to development has given rise to movements aimed at providing Internet to distant parts of the world that do not yet have it. Spearheaded by Western corporations, these efforts at connecting the unconnected draw support from a conventional understanding of Internet diffusion that stresses the Internet's positive contribution to development in third world countries. Development, however, cannot only be measured by economic growth. Gender equality, too, is a fundamental piece of the puzzle. Furthermore, the conventional understanding of Internet diffusion ignores the sociocultural factors that are preventing the Internet from reaching those who need it most. Using Facebook's Free Basics initiative in Pakistan as a case study, this paper will draw on findings from original ethnographic research to examine the consequences of current corporate Internet diffusion strategies, specifically with regards to gender inequality. A close analysis of Internet diffusion will show that without measures to ensure fair and equal distribution of information, the spread of the Internet not only is ineffective in catalyzing development, but can also aggravate the social injustice that already exists in target societies. This paper will propose a modified Internet diffusion strategy, one that prioritizes making the Internet wholly accessible and beneficial for all members of society, regardless of gender. The modified strategy will seek to address the shortcomings of current attempts at Internet diffusion by focusing on human-centered development, community engagement, and collaboration with local governments and NGOs. Ultimately, this paper’s recommendations can improve current and future diffusion strategies so that the Internet can reach and benefit all members of society, especially women, as quickly and effectively as possible.

Keywords:  Department of Science
internet
development
gender
diffusion
Science Technology and Society
Thesis
Advisor: McGinn Robert
Intelligent systems for personalized genomic medicine [electronic resource]

This thesis explores applications of artificial intelligence in personalized genomic medicine, focusing on three central challenges: decoding raw genomic sequence, interpreting genetic mutations, and making predictions based on this data. The first part of the thesis focuses on the sequencing problem. We argue that the cost of genome resequencing can be significantly reduced by leveraging vast existing amounts of genetic data to train statistical models of the human genome. Specifically, we introduce a new sequencing technology which reduces the cost of genome haplotyping by up to ten fold by augmenting an existing wetlab protocol with statistical models. We also extend this technology to the analysis of the human gut microbiome, enabling scientists to study for the first time the fine variation among individual microbial strains. The second part of the thesis focuses on the problem of interpretation. We introduce GWASdb, a machine reading system that enables researchers and clinicians to access tens of thousands of genotype-phenotype associations in the form of a structured database automatically constructed from the biomedical literature. We find that our system discovers thousands of genetic associations that are missing in even the largest human-curated repositories. These associations can be used to predict disease risks and shed light on genome biology. More generally, our system represents the largest fully automated information extraction effort in the GWAS domain, and demonstrates the feasibility and the value of human-machine literature curation. Finally, the last part of the thesis focuses on prediction. We study two core machine learning problems that arise in biomedical applications: uncertainty estimation and semi-supervised prediction. We present techniques for estimating disease risk that do not assume that data originates from an underlying probability distribution, allowing it instead to be generated by a malicious adversary. We also introduce a new semi-supervised framework that helps researchers leverage large amounts of unlabeled data and that bridges two fundamental types of machine learning methods: discriminative and generative. Our approach extends to modern deep learning algorithms and establishes a new state-of-the-art semi-supervised accuracy on standard benchmarks. In summary, our work will help scientists better understand the human genome and turn this knowledge into personalized medical technologies.

Advisor: Batzoglou Serafim primary advisor. Thesis advisor
Snyder Michael
Kundaje Anshul
Interactive Circuit Debugging and Simulation with Just In Time Compilation

Hardware development is traditionally viewed as significantly more challenging and costly than software development, partly due to the relative difficulty of debugging and validating hardware when compared to software. This work aims to reduce these barriers by employing new hardware circuit simulation techniques to achieve user friendly and interactive debugging of hardware circuits similar to current software debugging solutions.

Keywords:  Department of Computer Science
Computer Science
Simulation
Debugging
Thesis
Advisor: Hanrahan Pat
International Monetary Policy Spillover in Colombia: An SVAR Analysis

United States monetary policy plays an oversized role in determining worldwide financial conditions. Recent research has demonstrated that emerging markets economies are vulnerable to pressure from the policy stance of the Federal Reserve. Furthermore, monetary authorities in these countries have been shown to systematically respond to the Federal Funds rate, indicating that international monetary policy spillovers have eroded these nations’ monetary policy independence. This paper examines the transmission dynamics underlying these spillovers by estimating various structural vector autoregressions (SVARs) in an emerging market economy, Colombia. The analysis finds that U.S. monetary policy shocks are a significant determinant of Colombia’s central bank policy rate. In addition, it is shown that the transmission process of these spillovers changed after the global financial crisis of 2008.

Keywords:  Department of Economics
International monetary policy spillover
Monetary policy independence
Colombian central bank
Structural vector autoregression
Stanford Department of Economics
Thesis
Advisor: Taylor John B.
Interplay between thermal and electrical effects in phase-change memory [electronic resource]

Phase-change memory~(PCM) has undergone significant academic and industrial research improvements in the last 15 years. After much development, it is now poised to enter the market as a storage-class memory~(SCM), with performance and cost between NAND flash and DRAM. This thesis presents research works that center around improved thermal understanding with a view toward improving the PCM characteristics. The chapters focus on the following areas: thermal characterization of phase-change layers (PCL) using a micro-thermal stage (MTS), thermal conductivity measurements of amorphous dielectric multilayers, implementation of a low-thermal conductivity insulating multilayer for low-energy PCM, and thermal simulations to explore design choices in a 3D vertical chain cell-type (VCC) PCM. This work will highlight the performance gains attained and the future prospects which will help drive PCM to be as ubiquitous as NAND flash in the upcoming decade.

Keywords: Electrical Engineering.
Advisor: Wong Hon-Sum Philip
Asheghi Mehdi
Pop Eric advisor. Thesis advisor