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The remarkable ability of the human brain to draw an accurate percept from imprecise sensory information is not well understood. Bayesian inference provides an optimal means for drawing perceptual conclusions from sensorineural activity. This approach has frequently been applied to visual and auditory studies but only rarely to studies of tactile perception. We explored whether a Bayesian observer model could replicate fundamental aspects of human tactile spatial perception. The model consisted of an encoder that simulated sensorineural responses with Poisson statistics followed by a decoder that interpreted the observed firing rates. We compared the performance of our Bayesian observer on a battery of tactile tasks to human participant data collected previously by our laboratory and others. The Bayesian observer replicated human performance trends on three spatial acuity tasks: classic two-point discrimination (C2PD), sequential two-point discrimination (S2PD), and two-point orientation discrimination (2POD). We confirmed the widely reported observation that C2PD is the least reliable method of assessing tactile acuity due presumably to the presence of non-spatial cues. Additionally, the Bayesian observer performed similarly to humans on raised letter and Braille character-recognition tasks. The Bayesian observer further replicated two illusions previously reported in humans: an adaptation-induced repulsion illusion and an orientation anisotropy illusion. Taken together, these results suggest that human tactile spatial perception may arise from a Bayesian-like decoder that is unaware of the precise characteristics of its inputs. / Thesis / Master of Science (MSc)

There still is a practical need for improved closure models for the Reynolds-averaged Navier-Stokes (RANS) equations. This dissertation explores two different approaches for using experimental data to provide improved closure for the Reynolds stress tensor field. The first approach uses machine learning to learn a general closure model from data. A novel framework is developed to train deep neural networks using experimental velocity and pressure measurements. The sensitivity of the RANS equations to the Reynolds stress, required for gradient-based training, is obtained by means of both variational and ensemble methods. The second approach is to infer the Reynolds stress field for a flow of interest from limited velocity or pressure measurements of the same flow. Here, this field inversion is done using a Monte Carlo Bayesian procedure and the focus is on improving the inference by enforcing known physical constraints on the inferred Reynolds stress field. To this end, a method for enforcing boundary conditions on the inferred field is presented. The two data-driven approaches explored and improved upon here demonstrate the potential for improved practical RANS predictions. / Doctor of Philosophy / The Reynolds-averaged Navier-Stokes (RANS) equations are widely used to simulate fluid flows in engineering applications despite their known inaccuracy in many flows of practical interest. The uncertainty in the RANS equations is known to stem from the Reynolds stress tensor for which no universally applicable turbulence model exists. The computational cost of more accurate methods for fluid flow simulation, however, means RANS simulations will likely continue to be a major tool in engineering applications and there is still a need for improved RANS turbulence modeling. This dissertation explores two different approaches to use available experimental data to improve RANS predictions by improving the uncertain Reynolds stress tensor field. The first approach is using machine learning to learn a data-driven turbulence model from a set of training data. This model can then be applied to predict new flows in place of traditional turbulence models. To this end, this dissertation presents a novel framework for training deep neural networks using experimental measurements of velocity and pressure. When using velocity and pressure data, gradient-based training of the neural network requires the sensitivity of the RANS equations to the learned Reynolds stress. Two different methods, the continuous adjoint and ensemble approximation, are used to obtain the required sensitivity. The second approach explored in this dissertation is field inversion, whereby available data for a flow of interest is used to infer a Reynolds stress field that leads to improved RANS solutions for that same flow. Here, the field inversion is done via the ensemble Kalman inversion (EKI), a Monte Carlo Bayesian procedure, and the focus is on improving the inference by enforcing known physical constraints on the inferred Reynolds stress field. To this end, a method for enforcing boundary conditions on the inferred field is presented. While further development is needed, the two data-driven approaches explored and improved upon here demonstrate the potential for improved practical RANS predictions.

Increases in demand have driven the development of complex processing technology for separating mineral resources from exceedingly low grade multi- component resources. Low mineral concentrations and variable feedstocks can make separating signal from noise difficult, while high process complexity and the multi-component nature of a feedstock can make testwork, optimization, and process simulation difficult or infeasible. A prime example of such a scenario is the recovery and separation of rare earth elements (REEs) and other critical minerals from acid mine drainage (AMD) using a solvent extraction (SX) process. In this process the REE concentration found in an AMD source can vary site to site, and season to season. SX processes take a non-trivial amount of time to reach steady state. The separation of numerous individual elements from gangue metals is a high-dimensional problem, and SX simulators can have a prohibitive computation time. Bayesian statistical methods intrinsically quantify uncertainty of model parameters and predictions given a set of data and a prior distribution and model parameter prior distributions. The uncertainty quantification possible with Bayesian methods lend well to statistical simulation, model selection, and sensitivity analysis. Moreover, Bayesian models utilizing Gaussian Process priors can be used for active learning tasks which allow for prediction, optimization, and simulator calibration while reducing data requirements. However, literature on Bayesian methods applied to separations engineering is sparse. The goal of this dissertation is to investigate, illustrate, and test the use of a handful of Bayesian methods applied to process engineering problems. First further details for the background and motivation are provided in the introduction. The literature review provides further information regarding critical minerals, solvent extraction, Bayeisan inference, data reconciliation for separations, and Gaussian process modeling. The body of work contains four chapters containing a mixture of novel applications for Bayesian methods and a novel statistical method derived for the use with the motivating problem. Chapter topics include Bayesian data reconciliation for processes, Bayesian inference for a model intended to aid engineers in deciding if a process has reached steady state, Bayesian optimization of a process with unknown dynamics, and a novel active learning criteria for reducing the computation time required for the Bayesian calibration of simulations to real data. In closing, the utility of a handfull of Bayesian methods are displayed. However, the work presented is not intended to be complete and suggestions for further improvements to the application of Bayesian methods to separations are provided. / Doctor of Philosophy / Rare earth elements (REEs) are a set of elements used in the manufacture of supplies used in green technologies and defense. Demand for REEs has prompted the development of technology for recovering REEs from unconventional resources. One unconventional resource for REEs under investigation is acid mine drainage (AMD) produced from the exposure of certain geologic strata as part of coal mining. REE concentrations found in AMD are significant, although low compared to REE ore, and can vary from site to site and season to season. Solvent extraction (SX) processes are commonly utilized to concentrate and separate REEs from contaminants using the differing solubilities of specific elements in water and oil based liquid solutions. The complexity and variability in the processes used to concentrate REEs from AMD with SX motivates the use of modern statistical and machine learning based approaches for filtering noise, uncertainty quantification, and design of experiments for testwork, in order to find the truth and make accurate process performance comparisons. Bayesian statistical methods intrinsically quantify uncertainty. Bayesian methods can be used to quantify uncertainty for predictions as well as select which model better explains a data set. The uncertainty quantification available with Bayesian models can be used for decision making. As a particular example, the uncertainty quantification provided by Gaussian process regression lends well to finding what experiments to conduct, given an already obtained data set, to improve prediction accuracy or to find an optimum. However, literature is sparse for Bayesian statistical methods applied to separation processes. The goal of this dissertation is to investigate, illustrate, and test the use of a handful of Bayesian methods applied to process engineering problems. First further details for the background and motivation are provided in the introduction. The literature review provides further information regarding critical minerals, solvent extraction, Bayeisan inference, data reconciliation for separations, and Gaussian process modeling. The body of work contains four chapters containing a mixture of novel applications for Bayesian methods and a novel statistical method derived for the use with the motivating problem. Chapter topics include Bayesian data reconciliation for processes, Bayesian inference for a model intended to aid engineers in deciding if a process has reached steady state, Bayesian optimization of a process with unknown dynamics, and a novel active learning criteria for reducing the computation time required for the Bayesian calibration of simulations to real data. In closing, the utility of a handfull of Bayesian methods are displayed. However, the work presented is not intended to be complete and suggestions for further improvements to the application of Bayesian methods to separations are provided.

This thesis demonstrates a parameter estimation technique for bioprocesses that utilizes measurement noise in experimental data to determine credible intervals on parameter estimates, with this information of potential use in prediction, robust control, and optimization. To determine these estimates, the work implements Bayesian inference using nested sampling, presenting an approach to develop neural network (NN) based surrogate models. To address challenges associated with non-uniform sampling of experimental measurements, an NN structure is proposed. The resultant surrogate model is utilized within a Nested Sampling Algorithm that samples possible parameter values from the parameter space and uses the NN to calculate model output for use in the likelihood function based on the joint probability distribution of the noise of output variables. This method is illustrated against simulated data, then with experimental data from a Sartorius fed-batch bioprocess. Results demonstrate the feasibility of the proposed technique to enable rapid parameter estimation for bioprocesses. / Thesis / Master of Applied Science (MASc) / Bioprocesses require models that can be developed quickly for rapid production of desired pharmaceuticals. Parameter estimation is necessary for these models, especially first principles models. Generating parameter estimates with confidence intervals is important for model based control. Challenges with parameter estimation that must be addressed are the presence of non-uniform sampling and measurement noise in experimental data. This thesis demonstrates a method of parameter estimation that generates parameter estimates with credible intervals by incorporating measurement noise in experimental data, while also employing a dynamic neural network surrogate model that can process non-uniformly sampled data. The proposed technique implements Bayesian inference using nested sampling and was tested against both simulated and real experimental fed-batch data.

During the last decade, a new trend in medicine is transforming the nature of healthcare from reactive to proactive. This new paradigm is changing into a personalized medicine where the prevention, diagnosis, and treatment of disease is focused on individual patients. This paradigm is known as P4 medicine. Among other key benefits, P4 medicine aspires to detect diseases at an early stage and introduce diagnosis to stratify patients and diseases to select the optimal therapy based on individual observations and taking into account the patient outcomes to empower the physician, the patient, and their communication. This paradigm transformation relies on the availability of complex multi-level biomedical data that are increasingly accurate, since it is possible to find exactly the needed information, but also exponentially noisy, since the access to that information is more and more challenging. In order to take advantage of this information, an important effort is being made in the last decades to digitalize medical records and to develop new mathematical and computational methods for extracting maximum knowledge from patient records, building dynamic and disease-predictive models from massive amounts of integrated clinical and biomedical data. This requirement enables the use of computer-assisted Clinical Decision Support Systems for the management of individual patients. The Clinical Decision Support System (CDSS) are computational systems that provide precise and specific knowledge for the medical decisions to be adopted for diagnosis, prognosis, treatment and management of patients. The CDSS are highly related to the concept of evidence-based medicine since they infer medical knowledge from the biomedical databases and the acquisition protocols that are used for the development of the systems, give computational support based on evidence for the clinical practice, and evaluate the performance and the added value of the solution for each specific medical problem. / Tortajada Velert, S. (2012). Incremental Learning approaches to Biomedical decision problems [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/17195

This thesis explores the theory and practice of sovereignty. I begin with a conceptual analysis of sovereignty, examining its theological roots in contrast with its later influence in contestations over political authority. Theological debates surrounding God’s sovereignty dealt not with the question of legitimacy, which would become important for political sovereignty, but instead with the limits of his ability. Read as an ontological capacity, sovereignty is coterminous with an existent’s activity in the world. As lived, this capacity is regularly limited by the ways in which space is produced via its representations, its symbols, and its practices. All collective appropriations of space have a nomos that characterizes their practice. Foucault’s account of “biopolitics” provides an account of how contemporary materiality is distributed, an account that can be supplemented by sociological typologies of how city space is typically produced. The collective biopolitical distribution of space expands the range of practices that representationally legibilize activity in the world, thereby expanding the conceptual limits of existents and what it means for them to act up to the borders of their capacity, i.e., to practice sovereignty. The desire for total authorial capacity expresses itself in relations of domination and subordination that never erase the fundamental precarity of subjects, even as these expressions seek to disguise it. I conclude with a close reading of narratives recounting the lives of residents in Chicago’s Englewood, reading their activity as practices of sovereignty which manifest variously as they master and produce space. / Ph. D. / For an empirical analysis the statistical model implied in the theoretical model is crucial. The statistical model is simply the set of probabilistic assumptions imposed on the data, and invalid probabilistic assumptions undermines the reliability of statistical inference, rendering the empirical analysis untrustworthy. Hence, for securing trustworthy evidence one should always validate the implicit statistical model before drawing any empirical result from a theoretical model. This perspective is used to shed light on a widely used category of macroeconometric models known as Dynamic Stochastic General Equilibrium (DSGE) Models. Using U.S. time-series data, the paper demonstrates that a widely used econometric model for the U.S. economy is severely statistically misspecified; almost all of its probabilistic assumptions are invalid for the data. The paper proceeds to respecify the implicit statistical model behind the theoretical model with a view to secure its statistical adequacy (validity of its probabilistic assumptions). Using the respecified statistical model, the paper calls into question the literature evaluating the theoretical adequacy of current DSGE models, ignoring the fact that such evaluations are untrustworthy because they are based on statistically unreliable procedures.

京都大学 / 新制・課程博士 / 博士(情報学) / 甲第25438号 / 情博第876号 / 新制||情||147(附属図書館) / 京都大学大学院情報学研究科数理工学専攻 / (主査)教授 梅野 健, 教授 辻本 諭, 教授 田口 智清 / 学位規則第4条第1項該当 / Doctor of Informatics / Kyoto University / DFAM

Neste trabalho é introduzido um novo modelo estatístico para modelar dados limitados no intervalo continuo (0;1). O modelo proposto é construído sob uma transformação de variáveis, onde a variável transformada é resultado da combinação de uma variável com distribuição normal padrão e a função de distribuição acumulada da distribuição valor extremo generalizado. Para o novo modelo são estudadas suas propriedades estruturais. A nova família é estendida para modelos de regressão, onde o modelo é reparametrizado na mediana da variável resposta e este conjuntamente com o parâmetro de dispersão são relacionados com covariáveis através de uma função de ligação. Procedimentos inferênciais são desenvolvidos desde uma perspectiva clássica e bayesiana. A inferência clássica baseia-se na teoria de máxima verossimilhança e a inferência bayesiana no método de Monte Carlo via cadeias de Markov. Além disso estudos de simulação foram realizados para avaliar o desempenho das estimativas clássicas e bayesianas dos parâmetros do modelo. Finalmente um conjunto de dados de câncer colorretal é considerado para mostrar a aplicabilidade do modelo. / In this research a new statistical model is introduced to model data restricted in the continuous interval (0;1). The proposed model is constructed under a transformation of variables, in which the transformed variable is the result of the combination of a variable with standard normal distribution and the cumulative distribution function of the generalized extreme value distribution. For the new model its structural properties are studied. The new family is extended to regression models, in which the model is reparametrized in the median of the response variable and together with the dispersion parameter are related to covariables through a link function. Inferential procedures are developed from a classical and Bayesian perspective. The classical inference is based on the theory of maximum likelihood, and the Bayesian inference is based on the Markov chain Monte Carlo method. In addition, simulation studies were performed to evaluate the performance of the classical and Bayesian estimates of the model parameters. Finally a set of colorectal cancer data is considered to show the applicability of the model