VictorJuiz/thesis huggingface dataset:
Accelerating Successive Approximation Algorithm Via Action Elimination

This research is an effort to improve the performance of successive approximation algorithm with a prime aim of solving finite states and actions, infinite horizon, stationary, discrete and discounted Markov Decision Processes (MDPs). Successive approximation is a simple and commonly used method to solve MDPs. Successive approximation often appears to be intractable for solving large scale MDPs due to its computational complexity. Action elimination, one of the techniques used to accelerate solving MDPs, reduces the problem size through identifying and eliminating sub-optimal actions. In some cases successive approximation is terminated when all actions but one per state are eliminated. The bounds on value functions are the key element in action elimination. New terms (action gain, action relative gain and action cumulative relative gain) were introduced to construct tighter bounds on the value functions and to propose an improved action elimination algorithm. When span semi-norm is used, we show numerically that the actual convergence of successive approximation is faster than the known theoretical rate. The absence of easy-to-compute bounds on the actual convergence rate motivated the current research to try a heuristic action elimination algorithm. The heuristic utilizes an estimated convergence rate in the span semi-norm to speed up action elimination. The algorithm demonstrated exceptional performance in terms of solution optimality and savings in computational time. Certain types of structured Markov processes are known to have monotone optimal policy. Two special action elimination algorithms are proposed in this research to accelerate successive approximation for these types of MDPs. The first algorithm uses the state space partitioning and prioritize iterate values updating in a way that maximizes temporary elimination of sub-optimal actions based on the policy monotonicity. The second algorithm is an improved version that includes permanent action elimination to improve the performance of the algorithm. The performance of the proposed algorithms are assessed and compared to that of other algorithms. The proposed algorithms demonstrated outstanding performance in terms of number of iterations and omputational time to converge.

Keywords: successive approximation, action elimination, heuristic action elimination, action elimination for monotone policy MDPs
Advisor: Lee, Chi-Guhn
Design and Analysis of Micro-electromechanical Resonant Structures

Dynamics of a beam-based micro-electromechanical resonator is investigated theoretically and experimentally. The resonant structure comprises a micro-beam and two electrostatic comb-drives, one for exciting the vibration, and the other for detecting the response. Two identical resonators of this type can form a double-ended tuning fork. An analytical linear model of these resonators is developed by assuming the beam to obey the thin beam theory subjected to an axial force. The comb-drives are initially treated as a point mass. The point mass is free to be placed anywhere along the beam span. The exact natural frequencies and mode shapes of vibration are obtained. Further, the mass is considered to have rotary inertia. The influence of the rotary inertia on the natural frequencies and mode shapes of vibration are investigated. Subsequently, the model of a beam with a guided mass is studied to determine the upper limit of the natural frequencies of the resonator. The advantage of this model over the previous ones is in providing detailed insight into the dynamics of the resonator, particularly when the comb-drives are placed at locations other than the mid-point of the beam. It has been shown that the mode shapes of vibration of these resonators are not orthogonal to each other under its classic definition. The orthogonality condition of the mode shapes of the beam-lumped mass system is introduced, and used for studying the forced vibration response. The nonlinear vibration of the system due to stretching is considered for the case of free vibration and the primary resonance. The nonlinear model is used to investigate the effect of damping on the resonator response. The interaction of the electrostatic governing equations and the mechanical model is studied. This model is employed for designing the experiment circuits for testing fabricated resonators. The fabrication processes used are explained, and the design parameters of each resonator are provided. The experimental results are reported, and used to find the axial force and stress of the resonant beams. The model and results of this dissertation can be used in the design of beam-based micromachined resonators for different applications.

Keywords: Mechanical Engineering
Micro-electromechanical System
Vibration
Nonlinear Oscillation
Axial Force
Orthogonality
Advisor: Cleghorn, William L.
Esmailzadeh, Ebrahim
Mills, James
3D-tracking of A Priori Unknown Objects in Cluttered Dynamic Environments

Tracking of an object's full six degree-of-freedom (6-dof) position and orientation (pose) would allow a robotic system to autonomously perform a variety of complex tasks, such as docking from any preferred angle, surveillance of moving subjects, etc. Computer vision has been commonly advocated as an effective tool for 3D (i.e., 6-dof) tracking Objects of Interest (OIs). However, the vast majority of vision-based 6-dof pose trackers reported in the literature require a model of the OI to be provided a priori. Finding/selecting the OI to track is also essential to autonomous operation. A problem that has often been neglected. This Thesis proposes a novel, real-time object-tracking system that solves all of the aforementioned problems. The tracking procedure begins with OI selection. Since what constitutes an OI is application dependent, selection is achieved via a customizable framework of Interest Filters (IFs) that highlight regions of interest within an image. The region of greatest interest becomes the selected OI. Next, an approximate visual 3D model of the selected OI is built on-line by a real-time modeller. Unlike previously proposed techniques, this modeller can build the model of the OI even in the presence of background clutter; an essential task for tracking one object amongst many. Once a model is built, a real-time 6-dof tracker (i.e., the third sub-component) performs the actual 6-dof object tracking via 3D model projection and optical flow. Performing simultaneous modelling and tracking presents several challenges requiring novel solutions. For example, a novel data-reduction scheme based on colour-gradient redundancy is proposed herein that facilitates using colour input images whilst still maintaining real-time performance on current computer hardware. Likewise, a per-pixel occlusion-rejection scheme is proposed which enables tracking in the presence of partial occlusions. Various other techniques have also been developed within the framework of this Thesis in order to achieve real-time efficiency, robustness to lighting variations, ability to cope with high OI speeds, etc. Extensive experiments with both synthetic and real-world motion sequences have demonstrated the ability of the proposed object-tracking system to track a priori unknown objects. The proposed algorithm has also been tested within two target applications: autonomous convoying, and dynamic camera reconfiguration.

Keywords: computer vision
object tracking
real-time
3D
Advisor: Benhabib, Beno
Power and Influence: The Effects of Embeddedness on Cooperative Strategic Decision Making

This dissertation investigates whether and why social structure influences cooperative organizational strategic decision making in an international relations context, and in particular, similar voting in the United Nations General Assembly (UNGA). The economic and institutional embeddedness of organizations which are operationalized using network concepts are posited as and found to be influences. Additionally, nested institutional embeddedness is investigated in an inter-organizational setting. Based on a sensitivity analysis, nested organizational embeddedness can potentially have both negative and positive effects. Multiple issues and network methodology combined with an enormous and varied data set offer a wide-range of future research opportunities. More specifically, trade, military alliances, diplomatic visits, and two-mode International Government Organizational (IGO) networks affect voting behaviour in the UNGA due to power and influence relationships that demand or encourage organizational level reciprocity, either as vote buying in backroom bargaining situations or for compliance reasons; maintaining the nation’s good reputation is of importance in international relations. Each type of inter-organizational network involves an interesting theoretical twist that makes it worth researching and while theory testing is the primary objective, outcomes include practical implications for negotiators. Finally, an advantageous data set offers an excellent context for unique and successful testing of embeddedness view concepts in tighter causal relationships compared to other studies that observe performance rather than decision outcomes. Moreover, the methodological approach is a demonstration of how to deal with a multi-faceted econometric challenge.

Keywords: Management
Strategy
Organizational Theory
International Relations
Embeddedness View
United Nations
Advisor: Amburgey, Terry
The Role of Default Correlation in Valuing Credit Dependant Securities

In this thesis, I imply a forward-looking systematic factor from CDO market spreads; I show that this factor is a measure of CDO market's expectation of future default correlation, and I empirically show that it is positively related to bond credit spreads. From this, I infer that corporate bond credit spreads are positively related to expected default correlation. The forward-looking factor stems from a CDO valuation model that I propose. The model assumes default can be characterized as a random event that occurs with an uncertain hazard rate that is mixture-Weibull distributed. Calibrating the model to CDO market spreads implies the model parameters. Using two and three mixing densities and data spanning January 2004 to February 2008, I show that the model calibrates to both the North American and European investment grade CDOs with negligible error. The factor I imply from the CDO market quotes is the standard deviation of the implied hazard rate density. I then show that the standard deviation of the implied hazard rate density increases as default correlation increases. This is done by characterizing firms' defaults with stochastic hazard rates that are defined by jump-diffusion processes that are correlated only through the Weiner processes, only through systematic jumps, or both. I use the models to generate CDO model spreads that are used to imply mixture-Weibull hazard rate densities. In addition, I provide evidence that the implied hazard rate density standard deviation has time variation that is independent to that of other common systematic factors. Lastly, I show that bond credit spreads are positively correlated with the standard deviation of the implied hazard rate density, and I conclude that credit spreads are positively related to expected default correlation. I provide evidence that firms' credit spreads are decreasing in firm diversity; that credit spread sensitivity to default correlation is decreasing in firm equity option implied volatility and decreasing in firm diversity; and that the variation in high credit quality bond spreads is predominantly explained by systematic factors whereas the variation in low credit quality bond spreads is explained by systematic and idiosyncratic factors.

Keywords: Default Correllation
Credit Spreads
Credit Derivatives
Collaterlalized Debt Oligations
Advisor: White, Alan
Hull, John
The Technological Landscape: Competition and Opportunity

Technological position is a dimension along which organizations can either differentiate from or mimic the behavior of other organizations in the technological landscape. This paper is aimed at providing empirical evidence of the specific ways in which an organization’s technological position choice is impacted by the tension that arises from technological co-location; the information available to the focal firm; and the focal firm’s usage of such information. In this dissertation I examine the factors influencing technological agglomerations in technological positions in the technological landscape. I further examine how the organization’s experience impacts its strategic positioning choice while facing the tradeoff between the expected derivatives of co-location - opportunities and competition. I argue and find that an organization strategically positions itself in the technological landscape based not only on the information it has gathered on its technological environment but also using its own experience and information. Further, my findings show that the organization’s technological positioning choice reflects the tension between opportunity and competition, which questions the notion of isomorphism.

Keywords: Technology
Competition
Agglomeration
Startegy
Knowledge
Innovation
Advisor: Silverman, Brian S.
Effects of Sam68 on HIV-1 RNA Processing and Gene Expression

The unspliced 9kb HIV-1 RNA (encoding Gag and GagPol) can undergo multiple splicing events to produce members of the 4kb (encoding Env, Vif, Vpr, and Vpu) or 2kb (encoding Tat, Rev and Nef), respectively. The incompletely spliced 9 and 4kb viral RNAs are exported by HIV-1 Rev which interacts with the RRE (Rev responsive element) in these RNAs as well as the nuclear export receptor Crm1. Several proteins can modulate Rev function and/or HIV-1 gene expression, including the nuclear phosphorprotein Sam68. We have found that overexpression of Sam68 stimulates HIV-1 structural gene expression and increases the proportion of unspliced, 3’ end processed viral RNA. This activity requires the RNA binding activity of Sam68. Surprisingly, Sam68 overexpression does not increase the proportion of unspliced, cleaved RNA found in the cytoplasm, suggesting that Sam68 alters the viral RNP to increase its translation. The Sam68 related proteins Slm1 and Slm2 also stimulate 3’ end cleavage and expression of unspliced HIV-1 RNAs. Sam68 and Slm2 were expressed in Hela cells, whereas Slm1 was not. Therefore, we reduced Sam68 expression alone or in combination with Slm2 to determine if these proteins were required for HIV-1 RNA processing or expression. Knockdown of Sam68 and/or Slm2 had little to no effect on viral RNA cleavage or structural gene expression from transiently transfected reporters. Furthermore, depletion of Sam68 only slightly reduced Gag expression from a stably expressed proviral reporter. These results suggest that additional redundant proteins may be present that functionally replace Sam68 and Slm2. We defined a region encompassing the N-terminal GSG (GRP33, Sam68, Gld1) and KH RNA binding motif as the minimal region of Sam68 required to stimulate HIV-1 gene expression in 293 and 293T cells. The minimal mutant enhanced unspliced RNA cleavage in 293T, but not in 293 cells suggesting that Sam68 may act at other stage of the viral lifecycle to increase gene expression.

Keywords: Sam68
HIV-1 gene expression
Advisor: Cochrane, Alan
Examination of Unspliced HIV-1 mRNA Translation

Replication of HIV-1 requires nuclear export and translation of the incompletely spliced 4 and 9 kb classes of HIV-1 mRNA, which encode the structural and enzymatic proteins of the virus. HIV-1 Rev binds to the Rev-responsive element (RRE) contained in the introns of incompletely spliced HIV-1 mRNAs and mediates their nuclear export via the Crm1 pathway. Sam68C, is a C-terminal deletion mutant of the endogenous human protein Sam68, and has been shown to be a potent inhibitor of Rev-dependent reporters. In this study we have performed deletion analysis of Sam68C, and determined the minimal mutant required for inhibition of Rev-dependent expression is Sam6814(45-54)-300. Sam68C inhibition is specific to RRE/Rev/Crm1 transported mRNAs: the Rev/Crm1 exported reporter construct GagRRE is inhibited while the Tap/p15 transported GagCTE reporter construct is not. Previous work from our lab showed that Sam68C co-localized with the Rev-exported mRNAs in perinuclear bundles. Further investigation has shown that Sam68C inhibition of incompletely spliced HIV-1 mRNAs is independent of the perinuclear bundling of the viral mRNA. We go on to show that Sam68C specifically inhibits the translation of the incompletely spliced HIV-1 mRNAs. Translational inhibition by Sam68C is correlated with a loss of PABP1 binding with no attendant change in abundance, polyadenylation or polyadenosine tail length of the affected mRNAs. The selective inhibition of Crm1 exported HIV-1 mRNAs by Sam68C suggests that it is able to recognize unique characteristics of these viral mRNPs. We show that Rev and the RRE are required, but individually neither is sufficient for complete Sam68C inhibition. Study of the incompletely spliced HIV-1 mRNP revealed that the nuclear cap binding complex, CBP20/80, is not exchanged for eIF4E. Additionally, in cells expressing the HIV-1 provirus, CBP80 relocalizes to the cytoplasm and co-sediments with polysomes. This supports the hypothesis that incompletely spliced HIV-1 mRNAs are translated in an eIF4E-independent, CBP20/80-dependent fashion. This property of the 9kb and 4kb HIV-1 mRNAs could be utilized to develop new therapeutic approaches to controlling HIV-1 infection.

Keywords: HIV
RNA
Sam68
Translation
Advisor: Cochrane, Alan
The Putative Transcription Factor Prdm8 is Required for the Differentiation and Maintenance of Rod and Cone Bipolar Cells in the Mammalian Retina

Highly conserved genes that are abundantly and specifically expressed in the retina are likely to be important for retinal physiology or development. Prdm8 is expressed abundantly in retina and belongs to the PRDM (PR domain containing) protein family, conserved transcription factors important in the regulation of development and cancer. To begin to understand the role of Prdm8 in the retina, I cloned the cDNA and characterized Prdm8 expression in the mouse. Prdm8 encodes a PR domain and three zinc finger domains and is expressed predominantly in the developing and mature nervous system, including the retina, hippocampus and cerebellum. In the developing retina, Prdm8 mRNA is enriched in differentiating neurons. Together, these findings suggested that Prdm8 might be important for both neural development and maintenance. To determine whether Prdm8 is necessary for neural development, I generated Prdm8 null mice. Prdm8eGFP/eGFP mice are born at expected Mendelian ratios and viable, but have a hypocellular retina, develop prominent ventral skin lesions and display defects in hindlimb coordination, impaired spatial learning and memory, and changes in the volume of brain substructures. To better understand the role of Prdm8 in development, I focused on the Prdm8eGFP/eGFP retinal phenotype. I determined that Prdm8 is expressed in subsets of bipolar, amacrine and ganglion cells, and at a low level in photoreceptors. In the Prdm8eGFP/eGFP retina, cell loss was restricted to the inner nuclear layer, due to a lack of rod bipolar and cone bipolar subtypes. I found that bipolar cells were specified, but lost due to a failure in maturation, including a decrease in Vsx1 and Bhlhb4 expression, two transcription factors necessary for bipolar cell development. Consistent with this defect, Prdm8eGFP/eGFP mice exhibited impaired electroretinogram b-wave responses. Given the abundant expression of Prdm8 in the developing and mature nervous system and the array of neurobehavioural phenotypes identified, Prdm8 is likely to be necessary for development in other regions of the brain. My work provides novel insight into the genetic control of visual disorders and a useful framework for understanding the role of Prdm8 and this class of transcription factors in the development of other parts of the nervous system.

Keywords: Genetics
Molecular
Neuroscience
Advisor: McInnes, Roderick
Embryonic Stem Cell Technologies for Understanding the Complexity of VEGF Function

Newly established F1 hybrid Embryonic Stem cells allow the production of ES cell-derived animals at a high enough efficiency to directly make ES cell based genetics feasible. An F1 hybrid ES cell line, G4 was used to generate transgenic over-expressing cell lines. The consequence of the expression of a panel of transgenes was assessed directly from ES cell-derived embryos produced by the tetraploid complementation assay. The generation of ES cell-derived embryos/animals was very efficient. A sufficient number of mutants for initial phenotypic analyses was derived only a few weeks after the establishment of the cell lines. The genes used in the study had either angiogenic/vasculogenic, anti-angiogenic or unknown properties. Of these transgenic mouse lines VEGF-A and Flt-Fc were used to further elucidate the effects of altered VEGF signaling on cell fate decisions in embryonic development and ES differentiation in two experimental systems. A. Early but transient Flk-1 activation led to enhanced generation of blood progenitors, whereas continuous activation of Flk-1 abolished this effect and enhanced endothelial cell generation. Ex vivo analysis of cells derived from E7.5 embryos demonstrated that sFlt-1-mediated control of Flk-1 activity also impacted the fate of hematopoietic and endothelial cells. The Flt-1-Fc transgenic mouse model was used to alter Flk-1 activation in vivo and show the relevance of the in vitro observations. These results demonstrate that sFlt-1 regulates Flk-1 activation in an oxygen responsive manner. Inhibition of Flk-1 activation by sFlt-1 increases the specification of hemangioblasts to blood cells consistent with a VEGF-independent default mechanism. B. Ubiquitous over-expression of VEGF164 isoform led to E8.75 embryonic lethality. The primary cause of lethality was the failure to form an organized cardiovascular system, which was manifested in three ways: the absence of yolk sac blood vessels, the lack of embryonic-maternal circulation due to the failure of allantochorionic fusion and improper cardiac function. The described phenotypes suggest that VEGF does not inhibit embryonic or extra-embryonic mesoderm formation at gastrulation but perturbs the balance amongst the mesodermal components.

Keywords: VEGF
embryonic development
embryonic stem cells
gastrulation
hematopoiesis
vasculogenesis
transgenes
Advisor: Nagy, Andras