Browsing by Subject "Dynamic models"
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Item Open Access Bayesian Analysis and Computational Methods for Dynamic Modeling(2009) Niemi, JaradDynamic models, also termed state space models, comprise an extremely rich model class for time series analysis. This dissertation focuses on building state space models for a variety of contexts and computationally efficient methods for Bayesian inference for simultaneous estimation of latent states and unknown fixed parameters.
Chapter 1 introduces state space models and methods of inference in these models. Chapter 2 describes a novel method for jointly sampling the entire latent state vector in a nonlinear Gaussian state space model using a computationally efficient adaptive mixture modeling procedure. This method is embedded in an overall Markov chain Monte Carlo algorithm for estimating fixed parameters as well as states. In Chapter 3 the method of the previous chapter is implemented in a few illustrative
nonlinear models and compared to standard existing methods. This chapter also looks at the effect of the number of mixture components as well as length of the time series on the efficiency of the method. I then turn to an biological application in Chapter 4. I discuss modeling choices as well as derivation of the state space model to be used in this application. Parameter and state estimation are analyzed in these models for both simulated and real data. Chapter 5 extends the methodology introduced in Chapter 2 from nonlinear Gaussian models to general state space models. The method is then applied to a financial
stochastic volatility model on US $ - British £ exchange rates. Bayesian inference in the previous chapter is accomplished through Markov chain Monte Carlo which is suitable for batch analyses, but computationally limiting in sequential analysis. Chapter 6 introduces sequential Monte Carlo. It discusses two methods currently available for simultaneous sequential estimation of latent states and fixed parameters and then introduces a novel algorithm that reduces the key, limiting degeneracy issue while being usable in a wide model class. Chapter 7 implements the novel algorithm in a disease surveillance context modeling influenza epidemics. Finally, Chapter 8 suggests areas for future work in both modeling and Bayesian inference. Several appendices provide detailed technical support material as well as relevant related work.
Item Open Access Dynamic Compensation and Investment with Limited Commitment(2014) Feng, Felix ZhiyuIn this dissertation I study the role of limited commitment in dynamic models. In the first part, I consider firms that face uncertainty shocks in a principal-agent setting but have only limited ability to commit to long-term contracts. Limited commitment firms expedite payments to their managers when uncertainty is high, a finding that helps to explain the puzzling large bonuses observed during the recent financial crisis. In the second part, I examine a dynamic investment model where firms invest in a risky asset but cannot hedge the risk of their investment because they lack the ability to commit to future repayments of debt. Once firms have access to exogenous supply of risk free assets they may, on the aggregate level, invest more in the risky asset because risk free technology allows them to grow richer in equilibrium. This result helps to explain the asset price booms in emerging countries when those countries experience substantial capital outflow.
Item Open Access Dynamic Deep Learning Acceleration with Co-Designed Hardware Architecture(2023) Hanson, Edward ThorRecent advancements in Deep Learning (DL) hardware target the training and inference of static DL models, thus simultaneously achieving high runtime performance and efficiency.However, dynamic DL models are seen as the next step in further pushing the accuracy-performance tradeoff of DL inference and training in our favor; by reshaping the model's parameters or structure based on the input, dynamic DL models have the potential to boost accuracy while introducing marginal computation cost. As the field of DL progresses towards dynamic models, much of the advancements in DL accelerator design are eclipsed by data movement-related bottlenecks introduced by unpredictable memory access patterns and computation flow. Additionally, designing hardware for every niche task is inefficient due to the high cost of developing new hardware. Therefore, we must carefully design DL hardware and software stack to support future, dynamic DL models by emphasizing flexibility and generality without sacrificing end-to-end performance and efficiency.
This dissertation targets algorithmic-, hardware-, and software-level optimizations to optimize DL systems.Starting from the algorithm level, the robust nature of DNNs is exploited to reduce computational and data movement demand. At the hardware level, dynamic hardware mechanisms are investigated to better serve a broad range of impactful future DL workloads. At the software level, statistical patterns of dynamic models are leveraged to enhance the performance of offline and online scheduling strategies. Success of this research is measured by considering all key metrics associated with DL and DL acceleration: inference latency and accuracy, training throughput, peak memory occupancy, area efficiency, and energy efficiency.
Item Open Access Dynamic modeling and Bayesian predictive synthesis(2017) McAlinn, KenichiroThis dissertation discusses model and forecast comparison, calibration, and combination from a foundational perspective. For nearly five decades, the field of forecast combination has grown exponentially. Its practicality and effectiveness in important real world problems concerning forecasting, uncertainty, and decisions propels this. Ample research-- theoretical and empirical-- into new methods and justifications have been produced. However, its foundations-- the philosophical/theoretical underpinnings on which methods and strategies are built upon-- have been unexplored in recent literature. Bayesian predictive synthesis (BPS) defines a coherent theoretical basis for combining multiple forecast densities, whether from models, individuals, or other sources, and generalizes existing forecast pooling and Bayesian model mixing methods. By understanding the underlying foundation that defines the combination of forecasts, multiple extensions are revealed, resulting in significant advances in the understanding and efficacy of the methods for decision making in multiple fields.
The extensions discussed in this dissertation are into the temporal domain. Many important decision problems are time series, including policy decisions in macroeconomics and investment decisions in finance, where decisions are sequentially updated over time. Time series extensions of BPS are implicit dynamic latent factor models, allowing adaptation to time-varying biases, mis-calibration, and dependencies among models or forecasters. Multiple studies using different data and different decision problems are presented, demonstrating the effectiveness of dynamic BPS, in terms of forecast accuracy and improved decision making, and highlighting the unique insight it provides.
Item Open Access Modeling Biological Systems from Heterogeneous Data(2008-04-24) Bernard, Allister P.The past decades have seen rapid development of numerous high-throughput technologies to observe biomolecular phenomena. High-throughput biological data are inherently heterogeneous, providing information at the various levels at which organisms integrate inputs to arrive at an observable phenotype. Approaches are needed to not only analyze heterogeneous biological data, but also model the complex experimental observation procedures. We first present an algorithm for learning dynamic cell cycle transcriptional regulatory networks from gene expression and transcription factor binding data. We learn regulatory networks using dynamic Bayesian network inference algorithms that combine evidence from gene expression data through the likelihood and evidence from binding data through an informative structure prior. We next demonstrate how analysis of cell cycle measurements like gene expression data are obstructed by sychrony loss in synchronized cell populations. Due to synchrony loss, population-level cell cycle measurements are convolutions of the true measurements that would have been observed when monitoring individual cells. We introduce a fully parametric, probabilistic model, CLOCCS, capable of characterizing multiple sources of asynchrony in synchronized cell populations. Using CLOCCS, we formulate a constrained convex optimization deconvolution algorithm that recovers single cell estimates from observed population-level measurements. Our algorithm offers a solution for monitoring individual cells rather than a population of cells that lose synchrony over time. Using our deconvolution algorithm, we provide a global high resolution view of cell cycle gene expression in budding yeast, right from an initial cell progressing through its cell cycle, to across the newly created mother and daughter cell. Proteins, and not gene expression, are responsible for all cellular functions, and we need to understand how proteins and protein complexes operate. We introduce PROCTOR, a statistical approach capable of learning the hidden interaction topology of protein complexes from direct protein-protein interaction data and indirect co-complexed protein interaction data. We provide a global view of the budding yeast interactome depicting how proteins interact with each other via their interfaces to form macromolecular complexes. We conclude by demonstrating how our algorithms, utilizing information from heterogeneous biological data, can provide a dynamic view of regulatory control in the budding yeast cell cycle.