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Numerical realization of the Bayesian inversion accelerated using surrogate models
Bérešová, Simona
The Bayesian inversion is a natural approach to the solution of inverse problems based on uncertain observed data. The result of such an inverse problem is the posterior distribution of unknown parameters. This paper deals with the numerical realization of the Bayesian inversion focusing on problems governed by computationally expensive forward models such as numerical solutions of partial differential equations. Samples from the posterior distribution are generated using the Markov chain Monte Carlo (MCMC) methods accelerated with surrogate models. A surrogate model is understood as an approximation of the forward model which should be computationally much cheaper. The target distribution is not fully replaced by its approximation. Therefore, samples from the exact posterior distribution are provided. In addition, non-intrusive surrogate models can be updated during the sampling process resulting in an adaptive MCMC method. The use of the surrogate models significantly reduces the number of evaluations of the forward model needed for a reliable description of the posterior distribution. Described sampling procedures are implemented in the form of a Python package.
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Spatial point process with interactions
Vícenová, Barbora ; Beneš, Viktor (advisor) ; Zikmundová, Markéta (referee)
This thesis deals with the estimation of model parameters of the interacting segments process in plane. The motivation is application on the system of stress fibers in human mesenchymal stem cells, which are detected by fluorescent microscopy. The model of segments is defined as a spatial Gibbs point process with marks. We use two methods for parameter estimation: moment method and Takacs-Fiksel method. Further, we implement algorithm for these estimation methods in software Mathematica. Also we are able to simulate the model structure by Markov Chain Monte Carlo, using birth-death process. Numerical results are presented for real and simulated data. Match of model and data is considered by descriptive statistics. Powered by TCPDF (www.tcpdf.org)
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Global exploration in Markov chain Monte Carlo methods for light transport simulation
Šik, Martin ; Křivánek, Jaroslav (advisor) ; Jakob, Wenzel (referee) ; Christensen, Per (referee)
Monte Carlo light transport simulation has become a de-facto standard tool for photorealistic rendering. However, the algorithms used by the current rendering systems are often ineffective, especially in scenes featuring light transport due to multiple highly glossy or specular interactions and complex visibility between the camera and light sources. It is therefore desirable to adopt more robust algorithms in practice. Light transport algorithms based on Markov chain Monte Carlo (MCMC) are known to be effective at sampling many different kinds of light transport paths even in the presence of complex visibility. However, the current MCMC algorithms often over-sample some of the paths while under-sampling or completely missing other paths. We attribute this behavior to insufficient global exploration of path space which leads to their unpredictable convergence and causes the occurrence of image artifacts. This in turn prohibits adoption of MCMC algorithms in practice. In this thesis we therefore focus on improving global exploration in MCMC algorithms for light transport simulation. First, we present a new MCMC algorithm that utilizes replica exchange to improve global exploration. To maximize efficiency of replica exchange we introduce tempering of the path space, which allows easier discovery of important...
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Spatial point process with interactions
Vícenová, Barbora ; Beneš, Viktor (advisor) ; Zikmundová, Markéta (referee)
This thesis deals with the estimation of model parameters of the interacting segments process in plane. The motivation is application on the system of stress fibers in human mesenchymal stem cells, which are detected by fluorescent microscopy. The model of segments is defined as a spatial Gibbs point process with marks. We use two methods for parameter estimation: moment method and Takacs-Fiksel method. Further, we implement algorithm for these estimation methods in software Mathematica. Also we are able to simulate the model structure by Markov Chain Monte Carlo, using birth-death process. Numerical results are presented for real and simulated data. Match of model and data is considered by descriptive statistics. Powered by TCPDF (www.tcpdf.org)
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Perfect simulation in stochastic geometry
Sadil, Antonín ; Prokešová, Michaela (advisor) ; Beneš, Viktor (referee)
Perfect simulations are methods, which convert suitable Markov chain Monte Carlo (MCMC) algorithms into algorithms which return exact draws from the target distribution, instead of approximations based on long-time convergence to equilibrium. In recent years a lot of various perfect simulation algorithms were developed. This work provides a unified exposition of some perfect simulation algorithms with applications to spatial point processes, especially to the Strauss process and area-interaction process. Described algorithms and their properties are compared theoretically and also by a simulation study.
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Evolution of brain size in bats (Chiroptera)
Králová, Zuzana ; Němec, Pavel (advisor) ; Kratochvíl, Lukáš (referee)
According to the prevailing doctrine, brain size has mainly increased throughout the evolution of mammals and reductions in brain size were rare. On the other hand, energetic costs of developing and maintaining big brain are high, so brain size reduction should occur every time when the respective selective pressure is present. Modern phylogenetic methods make it possible to test the presence of evolutionary trend and to infer the ancestral values of the trait in question based on knowledge of phylogeny and trait values for recent species. However, this approach has been rarely applied to study brain evolution so far. In this thesis, I focus on bats (Chiroptera). Bats are a suitable group for demonstrating the importance of brain size reductions. Considering their energetically demanding mode of locomotion, they are likely to have been under selection pressure for brain reduction. Furthermore, there is a large amount of data on body and brain mass of recent species available. Finally, phylogenetic relationships among bats are relatively well resolved. My present study is based on body masses and brain masses of 334 recent bat species (Baron et al., 1996) and on a phylogeny obtained by adjusting existing bat supertree (Jones et al., 2002) according to recent molecular studies. Analysing the data for...
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