VictorJuiz/thesis huggingface dataset:
Filtering and parameter estimation for partially observed generalized Hawkes processes [electronic resource]

We consider the nonlinear filtering problem for partially observed Generalized Hawkes Processes, which can be applied in the context of portfolio credit risk. The problem belongs to the larger class of hidden Markov models, where the counting process is observed at discrete points in time and the observations are sparse, while the intensity driving process in unobservable. We construct the conditional distribution of the process given the information filtration and we discuss the analytical and numerical properties of the corresponding filters. In particular, we study the sensitivity of the filters with respect to the parameters of the model, and we obtain a monotonicity result with respect to the jump and the volatility terms driving the intensity. Using the scaled process, we provide necessary and sufficient conditions for the frequency of time observations in terms of the parameters of the model, to ensure a good performance of the filter. We also address the problem of parameter estimation for the Generalized Hawkes Process in the framework of the EM algorithm, and we analyze the effect of the self-exciting feature of our process on the asymptotic and numerical properties of the estimators.

Keywords: Mathematics
Advisor: Papanicolaou George primary advisor. Thesis advisor
Dembo Amir advisor. Thesis advisor
Giesecke Kay advisor. Thesis advisor
Fine-scale spatial organization of face- and limb-selective regions in human high-level visual cortex [electronic resource]

Neurophysiology and optical imaging studies in monkeys and functional magnetic resonance imaging (fMRI) studies in both monkeys and humans have localized clustered neural responses in high-level visual cortex selective for images of biologically relevant categories such as faces and limbs. Implementing higher resolution (1.5mm voxels) fMRI scanning methods than prior studies (3-5mm voxels), the results reported in this dissertation illustrate a topographic organization of face- and limb-selective regions in adjacent and alternating clusters in both ventral temporal and lateral occipitotemporal cortices. Region of interest analyses in a series of experiments indicate distinct category and position sensitivities within these clusters and multivoxel pattern analyses indicate different amounts of information in highly-, weakly-, and non-selective voxels for these categories. These results mediate the debate between modular and distributed theories of high-level visual cortex, as well as support a novel, sparsely-distributed organization including both locally clustered and distributed elements for face and limb representations. These results also reveal two new basic organization principles of high-level visual cortex where there is both a consistency in the anatomical location of functional regions, as well as a preserved spatial relationship among functional regions. Employing these two principles enables the first framework for consistent parcellation of high-level visual regions outside of retinotopic cortex. Importantly, this framework can also be applied to other sensory and nonsensory cortical systems.

Keywords: Psychology
Advisor: Grill-Spector Kalanit primary advisor. Thesis advisor
Wagner Anthony David advisor. Thesis advisor
Wandell Brian A. advisor. Thesis advisor
First principles molecular dynamics and control of photochemical reactions [electronic resource]

In this thesis, we develop and use an ab initio molecular dynamics method to investigate the mechanisms of photochemical reactions, working towards the goal of controlling these reactions. We use and extend the ab initio multiple spawning (AIMS) method for this purpose. AIMS solves the Schrodinger equation for both the nuclear and electronic wavefunctions on multiple potential energy surfaces (PESs) and adaptively expands the nuclear basis set at critical regions on the PES to account for nonadiabatic events. In this thesis, we improve the accuracy of the electronic wavefunction by implementing a higher level quantum chemical method, multi-state second-order perturbation theory (MS-CASPT2). AIMS with MS-CASPT2 is then applied to the photochemistry of ethylene, the prototype of photoisomerization reactions. Good agreement in terms of the excited state lifetime is achieved between theory and time-resolved experiments. The agreement demonstrates the importance of faithful comparison between experiment and simulation, and provides us with mechanistic insights for photoisomerization reactions, which lies at the center of many important phenomena in nature. AIMS is then applied to two molecules where the excited state dynamics may be controlled in different ways. In the case of propanal cation, we show that careful initial state preparation can lead to distinct excited state dynamics and the effects of this distinct dynamics persist in the product distribution which is formed through dissociation on the ground electronic state. AIMS reveals the mechanism of the dramatic branching ratio difference between two product channels measured by experimentalists, and identifies the critical role of conical intersections and dark states in causing the observed conformational selectivity. We follow our study of the excited dynamics with modeling of the ground state kinetics, which allows us to make a quantitative comparison with experiment. We then investigate the potential for control of the ring-opening reaction of cyclohexadiene (CHD), using an external laser field to alter the dynamics after photoexcitation. We explicitly incorporate light-matter interactions within the framework of AIMS. The augmented method is first tested on one- and two-dimensional model problems before applying it to the CHD ring-opening reaction. The results of the extended AIMS method are compared to recent experiments on CHD and we are able to successfully predict the change in product branching ratio as a function of the time delay between the excitation and control pulses. In conclusion, our recent improvements in the accuracy of the underlying electronic structure and the incorporation of an explicit treatment of light-matter interactions have made AIMS more powerful as a means of understanding photochemical reactions and designing control strategies.

Keywords: Chemistry
Advisor: Martinez Todd J. (Todd Joseph)
Andersen Hans
Bucksbaum Philip H. advisor. Thesis advisor
Flow reactor study of oxidation of dimethyl ether and methane binary mixtures at intermediate temperatures [electronic resource]

Oxygenated fuels, such as dimethyl ether (DME), are hydrocarbon fuels with oxygen incorporated in the fuel molecule. These fuels can be made from a variety of feedstocks, and a major advantage is their ability to reduce the formation of soot. This makes them particularly well suited for use in Diesel engines, in addition to power generation and utility fuel applications. The combustion chemistry of oxygenated fuels is not well understood, motivating the present study. As the simplest ether, DME oxidation chemistry is present in the oxidation of all larger oxygenates. In this work, the pre-ignition oxidation chemistry of DME was investigated under vitiated conditions in a variable pressure flow reactor (VPFR) facility at a temperature of 1200 K and pressures of 1-2 atm for six different DME and DME-methane mixtures. The study of DME-methane mixtures was motivated by the role of methane as a major reaction intermediate in DME oxidation. An existing reaction mechanism for DME oxidation was updated based on recent literature developments, and a one-dimensional mixing-reacting modeling approach was used to describe the reacting flow. Measured species time histories are in good agreement with the proposed model. Validation of the reaction mechanism against experimental data reported elsewhere in the literature shows reasonable agreement. The effects of equivalence ratio, pressure and methane addition, as well as weak points in the present description of DME oxidation kinetics are discussed.

Keywords: Mechanical Engineering
Advisor: Bowman Craig T. (Craig Thomas)
Golden David
Hanson Ronald advisor. Thesis advisor
Food vs Fuel: Can Biofuels Improve the Incomes of Rural Farmers in Nigeria?

In 2007, the Nigerian government made plans to develop a biofuel sector to reduce dependence on imported gasoline and improve the welfare of farmers. This paper investigates the effect of biofuel on rural farmers’ incomes. In Nigeria, 70% of the 150 million inhabitants are employed in the Agricultural sector; the majority are farmers, many of which are low skilled, low income and reside in underdeveloped areas. When biofuels are introduced in any society, farmers experience a trade off between increased revenue from biofuel sales and increased food expenditures as food prices rise, thus an increase in their income is not inevitable. The Nigerian government appears to be neglecting the consequences of this trade off; officials consistently highlight that the increased demand for biofuel will increase farmers incomes, while ignoring potential negative consequences. I run simulations to determine whether farmers can realize positive net income without jeopardizing ethanol production and my results indicate that this is possible. However, the result depends on how consumption demand and biofuel production interact with the price of biofuel.

Keywords:  Department of Economics
Stanford Department of Economics
biofuels
Nigeria
rural poverty
ethanol
rural economy
Thesis
Advisor: Rothwell Geoffrey
Foodways and sociopolitics in the Wari Empire of Peru, A.D. 600 - 900 [electronic resource]

Food is at the intersection of nature and culture, being a requirement of human life but always being socially transformed and loaded with cultural meaning. This dissertation shows that it is possible to study ancient sociopolitical roles of animal food through the analysis of meal refuse in the archaeological record. Specifically, the project expands beyond the traditional focus in zooarchaeology on human subsistence by seeing food as a critical element in the creation, negotiation, and manipulation of human relationships. In particular, it shows how during the ancient Wari Empire of Peru (A.D. 600 -- 900) meat feasts and animal offerings played different roles in consolidating the empire both in the province and in the heartland. This study compares faunal remains from the Middle Horizon sites of Conchopata (Ayacucho), Cotocotuyoc (Cuzco), and Chokepukio (Cuzco). Expectations are developed to evaluate, analyze, and contrast quotidian trash, feasting remains, and animal offerings deposits. Feasts and offerings can be instruments of political action to pursue economic and political goals. They served a variety of roles in articulating the politics of the Wari Empire. During the early times of the Wari influence in provincial Cotocotuyoc, offerings of camelids served to acquire and maintain symbolic capital by the local leaders. At Conchopata, a site in the Wari heartland, feasts in public open patios served to legitimize institutionalized relations of power, while feasts related to mortuary activity in private rooms functioned to naturalize status differences across this socially stratified town. Although certainly not the only practice used to retain power differences, offerings and feasts involving camelid meat, chicha beverages, and special Wari ceramics were key to build and maintain a vast and complex polity such as the Wari Empire.

Keywords: Anthropology.
Advisor: Rick John W. primary advisor. Thesis advisor
Gifford-Gonzalez Diane (Diane Patrice) advisor. Thesis advisor
McEwan Gordon Francis advisor. Thesis advisor
Robertson Ian advisor. Thesis advisor
The Frankencamera [electronic resource] : building a programmable camera for computational photography

Digital cameras, both in traditional form factors and as parts of cell phones, have become ubiquitous over the last decade. But for the most part, they remain black boxes to the end-user, and cannot be reprogrammed or modified. This has become an obstacle to researchers in the new field of computational photography, who want to use the growing computing power of digital cameras to create images no traditional camera could produce. This dissertation presents the Frankencamera platform, a digital camera system designed for computational photography. The Frankencamera is a fully open, fully programmable digital camera, which can be easily modified to test out new research ideas. The Frankencamera architecture allows for per-frame control of the capture process, and accurate synchronization of all the components that make up the camera. Based on this architecture, this dissertation details two hardware platforms: the F2, a flexible custom-built camera; and the Nokia N900, a commercial smartphone. Both platforms can be easily programmed at a high level using the FCam API, written to embody the Frankencamera architecture. Finally, this dissertation presents several sample applications for the Frankencamera platform. Several of these applications could not have been developed for any existing camera platform, and the ease and speed at which they were written show that the Frankencamera platform is a compelling tool for computational photography.

Keywords: Electrical Engineering
Advisor: Horowitz Mark (Mark Alan) primary advisor. Thesis advisor
Hanrahan P. M. (Patrick Matthew) advisor. Thesis advisor
Levoy Marc advisor. Thesis advisor
Frequency stability of MEMS timing references with nonlinearities [electronic resource]

The increasing demand for miniaturized electronic devices has heightened the need for tiny oscillators suitable to provide an accurate reference signal to electronics. In this sense, MEMS (microelectromechanical systems) resonator and oscillator have drawn a great deal of attention because they can be integrated onto silicon chips in a small form factor. This work describes the design, theory, and demonstration of MEMS resonator and oscillator with improved mid-term and short-term stability, especially when a resonator has nonlinearities. In the temperature stability study, electrostatic tuning was applied to Si−SiO2 composite resonators, which were made of single- crystal silicon with a silicon dioxide coating. The hybrid of these two temperature compensation methods achieved less than ± 2.5 parts per million frequency variation over a 90°C-wide temperature range, which is comparable with commercial quartz oscillators. In addition, the effect of nonlinearities of resonators on temperature sta- bility was analyzed: the temperature-dependent nonlinear effect model was theorized and verified with single-crystal silicon and Si−SiO2 composite resonator-based oscil- lators; a new feedback circuit architecture that improves temperature stability was then developed based on the model. In the phase-noise performance study, oscillator stability far above the critical vibration amplitude in the nonlinear regime was first demonstrated by using a novel variable-phase closed-loop setup. After that, more than twentyfold improvement in the power-handling and far-from-carrier phase-noise performances were achieved by operating an oscillator in the nonlinear regime. In addition, the nonlinear phase-noise model was verified by using the same closed-loop setup. In conjunction with the recently developed nonlinear motional impedance model, this phase-noise model enables further improvement in the phase-noise per- formance of MEMS resonator-based oscillators.

Keywords: Mechanical Engineering
Advisor: Howe Roger Thomas primary advisor. Thesis advisor
Kenny Thomas William primary advisor. Thesis advisor
Solgaard Olav advisor. Thesis advisor
From single molecules to single cells [electronic resource] : mechanistic studies of myosin VI and cardiac myosin

Myosins are a superfamily of molecular motors that couple the chemical energy derived form adenosine triphosphate (ATP) hydrolysis to precise mechanical movements along the filamentous cytoskeletal protein actin. There exist more than 20 distinct classes of myosins within this superfamily, and their specific biophysical and biochemical properties likely allow them to function accordingly in vivo. My research has focused on understanding the how the structural and kinetic characteristics of a particular myosin, myosin VI, relate to its proposed trafficking and tethering functions. In the first section of this dissertation, I perform single molecule studies on the contribution of an unexpected structural domain in the myosin VI tail to the efficiency of processive stepping, especially against external forces. I additionally use optical trapping to examine the load-dependent kinetics of the motor in the second section, and propose that external load in vivo likely regulates myosin VI's dual functions as cellular transporter and cytoskeletal anchor. The specific cellular cargoes as well as oligomerization states of different myosins are defined by their tail domain, which is the most divergent structural region among myosin classes. Myosin VI, shown to be monomeric when purified in its native form, likely dimerizes upon cargo binding. As most in vitro work on myosin VI so far have been performed on a truncated, artificially forced myosin VI dimer, I discuss in the third section steps taken toward achieving a more native, biochemically reconstituted full-length myosin VI molecule bound to its bona fide cargo. Having gained a better understanding of the biophysics, kinetics and biochemistry of myosin at the single molecule level, I moved on to studying myosin function at the cellular level. In the forth section of this dissertation, I examine the effects of a familial hypertrophic cardiomyopathy (FHC) mutation, R403Q in cardiac myosin, on the contractile function of single mouse cardiomyocytes. I find that the functional effects of the R403Q mutation in the diseased FHC heart are manifest at the level of cardiomyocytes as well, suggesting that these effects are cell autonomous. From these studies, we can better appreciate the structural and kinetic properties of myosin VI that make it uniquely suited for its functions. This knowledge is also beneficial in aiding the understanding of other molecular motors that may employ similar mechanisms. We are now also aware of the cell-autonomy of particular dysfunctions exhibited by diseased R403Q FHC hearts, and are better poised to understand the complex disorder as a whole.

Keywords: Biochemistry
Advisor: Spudich James A.
Dunn Alexander Robert advisor. Thesis advisor
Harbury Pehr advisor. Thesis advisor
Herschlag Daniel advisor. Thesis advisor
From stem cells to cancer [electronic resource] : the role of the RB family in cell cycle control and differentiation

Embryonic stem cells (ESCs) hold great therapeutic potential, but the regulation of their self-renewal and pluripotency is still not fully understood. Furthermore, ESCs display many similarities to cancer cells, including rapid proliferation and tumorigenic potential, making it critical to understand the basic properties of these cells. The RB family, consisting of RB, p107, and p130, are critical regulators of functions such as cell cycle progression, apoptosis, and differentiation that must be tightly regulated throughout development. Here, we used loss and gain of function experiments to understand the role of the RB family in regulating key properties of ESCs. In hESCs, the RB family is critical for self-renewal and survival. hESCs overexpressing RB arrest in the cell cycle and undergo spontaneous differentiation and apoptosis. Loss of RB family function in hESCs results in decreased self-renewal ability and a loss of pluripotency, as these cells display a defect in their differentiation capacity. hESCs undergo a G2/M arrest and apoptosis through activation of the p53 pathway and the cell cycle inhibitor p21 upon loss of RB family function. In contrast to hESCs, mESCS triple knockout (TKO) for the RB family are largely normal. However, both mouse and human ESCs display genomic instability upon loss of RB family function, highlighting a key function that is conserved between both species. The RB family also regulates many functions that are critical for tumor suppression. We investigated whether RB retains its tumor suppressive ability in cancer cells by re-introducing RB into Rb-/-; p53-/- small cell lung cancer (SCLC) tumors cells. Re-introduction of RB resulted in decreased growth and an increase in differentiation, similar to that seen in hESCs. Thus, the RB pathway is an important regulator of self-renewal and differentiation in both hESCs and SCLC.

Keywords: Genetics
Advisor: Sage Julien primary advisor. Thesis advisor
Baker Julie (Professor of genetics) advisor. Thesis advisor
Reijo Pera Renee advisor. Thesis advisor
Stearns Tim advisor. Thesis advisor
Functional heterogeneity in parietal cortex during episodic memory retrieval [electronic resource]

The memory for specific events and instances in time—episodic memory—is a central aspect of human cognition. It has long been thought that episodic memory is supported by a distributed network of regions in the brain, including frontal cortex and the medial temporal lobes. A growing body of neuroimaging evidence in the last several years has additionally suggested posterior parietal cortex (PPC) involvement during episodic retrieval. Several accounts have argued that the region's involvement reflects the engagement of two specific attentional processes, goal-driven and reflexive attention, distinctly residing in dorsal and ventral regions of PPC, respectively. Strict interpretations of such accounts, however, have recently been called into question, as attention- and memory-related processes might not occupy overlapping subregions of PPC. The research described here systematically assesses the anatomical and functional relationship between attention- and memory-related operations in PPC in a series of three experiments. The first experiment revealed four distinct patterns of activity across left lateral PPC—two thought to relate to mnemonic processes and two thought to relate to attention engaged during retrieval. The second experiment directly tested whether a region thought to index attention during retrieval from the first experiment was recruited in an independent attention task, with results suggesting that attention-sensitive regions are indeed engaged in a systematic manner during retrieval. The final experiment further probed the interaction between memory, attention, and decision-making processes engaged during retrieval, and replicated and extended the findings from the first experiment. Collectively, the findings from the research provide a more detailed depiction of how anatomically and functionally separable regions of PPC support distinct mechanisms of memory and attention.

Keywords: Psychology
Advisor: Wagner Anthony David primary advisor. Thesis advisor
McClelland James L. advisor. Thesis advisor
McClure Samuel M. advisor. Thesis advisor