VictorJuiz/thesis huggingface dataset:
Community structure of large networks [electronic resource]

One of the main organizing principles in real-world networks is that of network communities, which are sets of nodes that share common properties, functions, or roles. Communities in networks often overlap as nodes can belong to multiple communities at once. Identifying such overlapping network communities is crucial for an understanding of social, technological, and biological networks. In this thesis, we develop a family of accurate and scalable community detection methods and apply them to large networks. We begin by challenging the conventional view that defines network communities as densely connected clusters of nodes. We show that the conventional view leads to an unrealistic structure of community overlaps. We present a new conceptual model of network communities, which reliably captures the overall structure of a network as well as accurately models community overlaps. Based on our model, we develop accurate algorithms for detecting overlapping communities that scale to networks an order of magnitude larger than what was possible before. Our approach leads to novel insights that unify two fundamental organizing principles of networks: modular communities and the commonly observed core-periphery structure. In particular, our results show that dense network cores stem from the overlaps between many communities. As the final part of the thesis, we present several extensions of our models such that we can detect communities with a bipartite connectivity structure and we combine the node attributes and the network structure for community detection.

Keywords: Electrical Engineering.
Advisor: Garcia-Molina Hector primary advisor. Thesis advisor
Leskovec Jurij primary advisor. Thesis advisor
Guibas Leonidas J. advisor. Thesis advisor
Comparative analysis of stomatal development networks in Arabidopsis and Brachypodium [electronic resource]

Stomata, epidermal valves made up of paired guard cells flanking a central pore, are found in most aerial tissues of plants, where they function to regulate gas exchange. Production of mature stomata involves a series of asymmetric cell divisions (ACDs) and cell fate transitions, and the molecular genetic regulation of this process has been extensively studied in the dicot Arabidopsis thaliana (thale cress). Yet, it remains largely unknown whether the same genetic regulators are used across a range of taxa, and how genes and networks might differ between species to produce (or accommodate) distinct developmental patterns. Indeed, stomatal ontogeny is remarkably diverse among plant species, with particularly intriguing differences between dicots and grasses. Whereas Arabidopsis stomata are sprinkled across the leaf surface seemingly at random, grasses produce stomata oriented along the leaf axis in specific linear cell files. In my thesis work, I have examined the genetic networks controlling stomatal development in grasses, focusing particularly on how these networks resemble or differ from those of Arabidopsis. My studies are conducted using the forage grass Brachypodium distachyon, a recently developed, genetically tractable model species related to wheat and barley. First, I report the basic characterization of Brachypodium stomatal development, as well as the identification of stomatal mutants via a forward genetic screen. Subsequently, I describe mutations in two orthologues of known Arabidopsis stomatal regulators: the bHLH gene BdICE1, which is required for production of mature stomata, and the MAPKKK gene BdYDA1, which enforces correct stomatal patterning. Although both mutants resemble their Arabidopsis counterparts, their phenotypes suggest subtly but intriguingly different roles in Brachypodium. BdICE1, unlike Arabidopsis ICE1, is not functionally redundant with its paralogue BdSCRM2, and the two Brachypodium genes have roles in promoting GMC and guard cell identity, respectively. Further, preliminary data suggest that the ICEs of Brachypodium may differ from those of Arabidopsis in their interactions with SPCH family bHLHs. Similarly, although BdYDA1, like Arabidopsis YDA, enforces stomatal patterning, it also regulates a number of other asymmetrically dividing epidermal cell lineages (e.g., hair and silica cell lineages), suggesting a role as a general regulator of fate asymmetry. Finally, I discuss prospects for using timelapse imaging and computational modeling to gain insight into stomatal lineage polarity, division, and fate specification processes in both dicots and grasses.

Keywords: Biology.
Advisor: Bergmann Dominique primary advisor. Thesis advisor
Axelrod Jeffrey (Jeffrey David)
Long Sharon R. advisor. Thesis advisor
Walbot Virginia
The comparative grammaticality of the English comparative [electronic resource]

The goal of this dissertation is to investigate systematic variation in English comparative adjective formation using the insights of lexical prosody and Optimality Theory. I provide a sustained argument in favor of lexically specified, representationally rich prosodic structure. Chapter 1 introduces comparative adjective variation (CAVE) in the context of morphological-periphrastic alternations in language and draws particular attention to comparative grammaticality as a theoretically appropriate solution to the systematic nature of CAVE. Chapter 2 provides an in-depth corpus analysis of spoken and written English from the Corpus of Contemporary American English. Alongside replicating several earlier results, the chapter provides evidence for the variable, systematic nature of suffixation to adjectives of different prosodic and morphological shapes. In Chapter 3, I make two major claims. First, I argue that morphemes can exhibit various degrees of prosodic strength, spelled out as differences in structure, an inherent property of morphemes as they are stored as Roots in an abstract lexicon. Second, I argue that token frequency influences prosodic strength through the direct modulation of prosodic structure; infrequent and phonotactically complex short adjectives are less likely to undergo reduction processes because of their more articulated prosodic structure. In contrast, frequently used adjectives have less articulated prosodic structure, which results in more reduction processes. These two claims set the basis for a representational difference between high- and low-frequency adjectives, which accounts for their divergent susceptibility to phonological reduction and phonetic shortening. Chapter 4 is concerned with spelling out the structure of the grammar of comparative suffixation. It divides the grammar into Stem and Word strata and argues that variable suffixation rates require both stratal and representational (morphological and prosodic) routes of explanation. In sum, variable suffixation results from the representational differences argued for in Chapter 3, as well as the dual-stratum membership of -er at the Stem and Word strata. A variety of adjective types are considered. Chapter 5 addresses comparative grammaticality at the level of syntax and sketches a preliminary analysis of how phrasal prosody may also affect suffixation rates, which has implications for the phonology-syntax interface and the degree to which lexical and syntactic information should be separated in linguistic theory. Chapter 6 concludes the dissertation, comparing present contributions to previous work on CAVE.

Keywords: Linguistics.
Advisor: Anttila Arto primary advisor. Thesis advisor
Gribanova Vera advisor. Thesis advisor
Kiparsky Paul advisor. Thesis advisor
Levin Beth advisor. Thesis advisor
Comparing Fiscal Strategies for the U.S. in a New Keynesian Framework

In this paper, I use Coenen, McAdam, and Straub’s (2008) (CMS) structural macroeconomic model to compare and contrast three fiscal strategies for the U.S.: (1) short-run stimulus followed by fiscal consolidation, with stimulus financed by future spending reductions, (2) short-run stimulus followed by fiscal consolidation, with stimulus financed by future tax rate increases, and (3) short-run stimulus followed by permanently higher spending in the form of transfers. My analysis follows the framework of analysis done by Cogan et al. (2013) on fiscal consolidation strategies in the same model. I find that the model produces a temporary positive output effect from the short-run stimulus, followed by negative effects on output due to the conclusion and subsequent payment of stimulus. Long-run fiscal consolidation after stimulus is more favorable than permanently higher spending because it decreases the medium- and long-run output cost of stimulus and creates favorable conditions for long-run growth. Stimulus financed by spending reductions is preferable to tax financed stimulus in terms of output growth generated. Lastly, permanently higher spending in terms of transfers is particularly harmful to growth.

Keywords:  Department of Economics
Stanford Department of Economics
fiscal consolidation
CMS model
stimulus
output growth
structural model
Thesis
Advisor: Boskin Michael J.
Composition and molecular architecture of the sonic hedgehog morphogen [electronic resource]

The Hedgehog signaling pathway performs essential and diverse roles in embryonic development and adult tissue homeostasis throughout the animal kingdom. Hedgehog proteins are secreted morphogens that emanate from localized pools of cells, generating a concentration gradient that communicates positional information to the cells within the tissue. A distinctive feature of Hedgehog proteins is covalent modification with a N-terminal palmitate and a C-terminal cholesterol, which strongly tether Hedgehog to cell membranes and modulate its distribution in tissues. Despite this hydrophobic character, Hedgehog proteins mobilize from expressing cells and travel far from their source to act directly upon distant responding cells. Although evidence exists for multiple mechanisms of Hedgehog mobilization, the actual physical form of the Hedgehog morphogen, as it is packaged and deployed in tissues, remains unknown. Studies in zebrafish have revealed a secreted factor, Scube2, that functions non-cell-autonomously to enable Hedgehog signaling. This led to the discovery that the mouse Scube2 protein can drive release of fully-lipidated Sonic Hedgehog from cell membranes in a soluble form that is potent in signaling assays. In this study, we have taken advantage of Scube2 activity to investigate the physical form of the active Shh morphogen. The signaling activity of this Scube2-released ShhNp is associated predominantly with a large, but discrete, protein complex approximately 250-300 kilodaltons in size. Further analysis suggests that this consists largely of a Scube2:Shh complex, although fully-lipidated Shh could also be present in other forms. Exracellular matrix glycans, such as heparan sulfate, contribute to the assembly and release of soluble, high molecular weight form of Shh by Scube2, and a heparin chain of 16 units suffices to potentiate Scube2-mediated release of ShhNp. This defined system has allowed us to produce large quantities of active morphogen for analysis, thus enabling us to begin addressing questions about the composition, stoichiomentry, and molecular architecture of the active morphogen.

Keywords: Developmental Biology.
Advisor: Beachy Philip Arden primary advisor. Thesis advisor
Nusse Roel
Shapiro Lucy advisor. Thesis advisor
Villeneuve Anne
Comprehensive modeling of complex silicon microelectromechanical (MEMS) resonators [electronic resource]

There is intense interest in micro and nanomechanical resonators for a variety of scientific and commercial applications. Microelectromechanical (MEMS) resonators are employed as frequency reference in various applications to generate an oscillatory signal from mechanical resonance. Dissipation of oscillation energy attenuates resonator's output signal. This attenuation is measured by the quality factor of the resonator. Therefore, high quality factor is a key factor for accurate measurement of frequency. Fundamental physical processes related to energy dissipation in MEMS resonators are not fully understood in general. For various resonators, different processes contribute to a different degree to the total energy dissipation. Due to interaction of mechanical vibration and energy dissipating processes, a strong coupling can take place leading to dissipation and a low quality factor. For simple geometries like a thin beam, quality factor can be reasonably predicted when resonating in the fundamental flexure mode but predictions deteriorate drastically as the designs get more complex to fulfill higher frequency and quality factor requirements. Dissipation in these resonators is generally complex and rarely well understood, and can be limited by quantum mechanical mechanisms. This thesis demonstrates exceptional modeling capability for a set of fundamentally different resonators. First, we provide a clear description of the relevant dissipation mechanisms and discuss models for accurate prediction of the quality factor. The essential difference of frequency reference technologies is set by resonator characteristics including frequency, quality factor and temperature sensitivity. We show by comparison to measurements of various devices built in our lab that we are able to predict performance for a wide range of resonators. As this level of agreement between modeling and measurement is generally unprecedented for arbitrarily complex devices, we hope it clarifies the relationship between the dissipation mechanisms and the probability of their appearance in different categories of resonators.

Keywords: Mechanical Engineering.
Advisor: Kenny Thomas William primary advisor. Thesis advisor
Howe Roger Thomas advisor. Thesis advisor
Sheppard S. (Sheri) advisor. Thesis advisor
Comprehensive non-invasive prenatal diagnostics for genetic diseases [electronic resource]

We are entering an era where invasive procedures such as amniocentesis for genetic testing are being replaced with non-invasive, safe, earlier-to-detect, and more cost-effective technologies that take advantage of circulating (cell-free) fetal DNA in maternal blood. Currently, the new non-invasive technologies are clinically indicated mainly for aneuploidies, which is only a fraction of genetic diseases indicated for detection by invasive procedures. This thesis focuses on using digital PCR and high throughput sequencing tools, both of which are exponentially decreasing in cost, to achieve new diagnostic capabilities using cell-free DNA. The first portion of the thesis covers using targeted amplicons to diagnose Mendelian diseases and to obtain the fetal fraction—an important measurement for quality control of many genetic tests. The second portion covers sequencing approaches to detect microdeletions greater than 1 Mbp. This was demonstrated by detecting Digeorge syndrome, a relatively common ~3 Mbp deletion that can result in several life threatening health conditions. The final portion covers the whole genome determination of the fetus using either linked targets for inherited diseases or direct sequencing at high coverage for the exome component. Here, de novo mutations are covered with direct sequencing while many other mutations, such as deletions and trinucleotide repeats, can be covered by linked targets. This new toolbelt of techniques, in combination with comprehensive carrier screening, will help to dramatically widen the impact of non-invasive prenatal diagnostics to nearly all genetic diseases.

Keywords: Bioengineering.
Advisor: Quake Stephen Ronald primary advisor. Thesis advisor
Kim Stuart
Utz Paul advisor. Thesis advisor
Computational electromagnetics for nanophotonic design and discovery [electronic resource]

Computational electromagnetics has become an essential tool for designing nanophotonic devices. While there exist many general purpose computational methods, we show that tailored approaches can be dramatically faster for solving design problems requiring millions to billions of iterations. In the first half of this dissertation, we describe a particular method designed for photonic crystal structures, and apply it to the design of extremely compact aperiodic devices such as wavelength division multiplexers, waveguide mode converters, and multimode waveguide bends. Next, we describe the Fourier Modal Method (FMM), a computational technique designed for layered periodic structures. We extend the method by deriving new formulations for the mode expansions, and demonstrate its improved accuracy and discuss its applicability for modeling structures with metals. Finally, the FMM is applied to investigate optical forces in coupled photonic crystal slabs. We demonstrate the role that optically bright and dark resonances play in the enhancement of optical forces.

Keywords: Electrical Engineering.
Advisor: Fan Shanhui
Brongersma Mark L. advisor. Thesis advisor
Miller D. A. B. advisor. Thesis advisor
Computational methods for default timing [electronic resource]

In risk management and derivatives pricing applications, one frequently works with a reduced-form model of correlated name-by-name default timing. In these models, a name defaults with some conditional default rate, an intensity. We develop, analyze and test transform, Monte Carlo and importance sampling methods for computing a variety of default timing problems. Transform methods are shown to yield (semi-)analytical formulae for various quantities of interest. Existing Monte Carlo simulation methods for default timing problems are surveyed. We introduce a novel concept of a simulation measure to provide a systematic approach to the efficiency and error analysis of these methods. A new Monte Carlo simulation algorithm is then devised to remove a significant source of bias inherent in existing techniques. The setting of rare-event simulation, which falls outside the scope of transform and plain Monte Carlo methods, is also addressed. A new importance sampling estimator which is applicable to any default timing model is proposed. Technical conditions guaranteeing the asymptotic optimality of the resulting estimator are studied in depth. Numerical results illustrate the performance of the estimator in a setting of a complex, portfolio credit risk application.

Advisor: Giesecke Kay primary advisor. Thesis advisor
Owen Art B. advisor. Thesis advisor
Papanicolaou George advisor. Thesis advisor
Computationally guided drug repurposing as a drug development strategy [electronic resource]

The pharmaceutical industry is experiencing unprecedented financial pressures and unsustainable research expenditures, threatening to compromise the robust development of new therapies. In response many pharmaceutical companies and translational research organizations have invested heavily in new technologies promising more efficient and productive research, including high-throughput screening, combinatorial chemistry for compound library generation, genetics and pharmacokinetics, and many others. Unfortunately these technologies have largely failed to significantly increase the efficiency of pharmaceutical research, as evidenced by the steady increase in research dollars required per new approved drug (currently estimated at nearly

Keywords: Chemistry.
Advisor: Pande Vijay primary advisor. Thesis advisor
Du Bois Justin advisor. Thesis advisor
Mochly-Rosen Daria advisor. Thesis advisor
Conjugated polymer sorting of semiconducting nanotubes and their electronic applications [electronic resource]

Single-walled carbon nanotubes (SWNTs) have excellent electrical properties for a wide range of applications such as transistors, solar cells, photodetectors and chemical/biologic sensors. However, for all these applications, it is necessary to separate semiconducting SWNTs from metallic ones. Sorting SWNTs using conjugated polymers has been demonstrated to be a simple and low-cost method to effectively sort large quantities of semiconducting SWNTs. In this thesis, I first describe how semiconducting SWNT sorting can be improved by judiciously considering polymer design and solvent effects. A mechanism for the selective dispersion of semiconducting SWNTs is also proposed. As a result of improved semiconducting SWNT sorting, the application of SWNTs in printed transistors, solar cells and logic circuits is made possible. In particular, high-mobility, high on/off ratio transistors from the sorted semiconducting SWNTs are achieved. Then, I explain the development of n-type molecular doping and fluorinated dielectrics to control the threshold voltage of SWNT transistors as well as to improve the bias stability of the devices under ambient conditions. These advancements allow the fabrication of the first flexible SWNT complementary logic circuits with high reliability (high noise margin) and low power-consumptions. Finally, I discuss a novel technique to conform the shape of flexible SWNT electronics into 3-dimensional objects by utilizing shape memory polymers. The technique also allows conformal coating of the SWNT transistors and sensors to any irregular shaped-objects without degradation of device performance.

Keywords: Materials Science and Engineering.
Advisor: Bao Zhenan primary advisor. Thesis advisor
Cui Yi
Wong Hon-Sum Philip
Connecting chemical features of drugs to molecular, cellular, and organismal phenotypes [electronic resource]

Recent progress in science and medicine has led to extensive advances in genetics, molecular medicine, and drug discovery. Despite these advances, the development of safe and effective drugs is still one of the most complex and expensive endeavors in modern medicine. Fortunately, advances in cheminformatics and and bioinformatics have enabled the development of new methods to identify drugs and quantify the effects of known drugs. Large databases of chemical compounds and their molecular and cellular effects are publicly available and can be combined with computational methods to aid drug discovery and development. Advances in genome sequencing and genomic medicine have led to increased research into pharmacogenetic markers that are predictive of individual patient responses to drugs. These developments provide opportunities to establish connections between features of drugs and the phenotypes induced by those drugs. In this thesis I present methods to quantify the connections between chemical features of drugs at the molecular, cellular, and organismal level. Specifically, I present a method for predicting activities among structurally diverse sets of drugs, a method for predicting up-regulation of genes based on chemical features of drugs, and a quantified analysis of the clinical impacts of genotype guided therapies. The work presented in this thesis provides methods to support drug discovery, drug development, and the establishment of safe and effective therapies.

Advisor: Altman Russ primary advisor. Thesis advisor
Ashley Euan A. advisor. Thesis advisor
Bustamante Carlos (Carlos D.) advisor. Thesis advisor
Pande Vijay advisor. Thesis advisor