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Bacteria Classification into Taxonomic Categories Based on Properties of 16s rRNA
Grešová, Katarína ; Hon, Jiří (referee) ; Smatana, Stanislav (advisor)
The main goal of this thesis was to design and implement a tool that would be able to classify the sequences of the 16S rRNA gene into taxonomic categories using the properties of the 16S rRNA gene. The created tool analyzes all input sequences simultaneously, which differs from common classification approaches, which classify input sequences individually. This tool relies on the fact that bacteria contain several copies of the 16S rRNA gene, which may differ in sequence. The main contribution of this work is design, implementation and evaluation of the capabilities of this tool. Experiments have shown that the proposed tool is able to identify the corresponding bacteria for smaller datasets and determine the correct ratios of their abundances. However, with larger datasets, the state space becomes very large and fragmented, which requires further improvements in order for it to search the state space in an efficient way.
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Sequential Monte Carlo Methods
Sobková, Eva ; Zikmundová, Markéta (advisor) ; Prokešová, Michaela (referee)
Monte Carlo methods are used for stochastic systems simulations. Sequential Monte Carlo methods take advantage of the fact that observations are coming sequentially. This allows us to refine our estimate sequentially in time We introduce a State Space Model as a Hidden Markov Model. We describe Perfect Monte Carlo Sampling, Importance Sampling, Sequential Importance Sampling and discuss advantages and disadvantages of these methods. This discussion brings us to add a resampling step in Sequential Importance Sampling and introduce Particle Filter and Particle Marginal Metropolis-Hastings algorithm. We choose a Hidden Markov Model used for stochastic volatility modeling and make a simulation study in Wolfram Mathematica, version 8.
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Bacteria Classification into Taxonomic Categories Based on Properties of 16s rRNA
Grešová, Katarína ; Hon, Jiří (referee) ; Smatana, Stanislav (advisor)
The main goal of this thesis was to design and implement a tool that would be able to classify the sequences of the 16S rRNA gene into taxonomic categories using the properties of the 16S rRNA gene. The created tool analyzes all input sequences simultaneously, which differs from common classification approaches, which classify input sequences individually. This tool relies on the fact that bacteria contain several copies of the 16S rRNA gene, which may differ in sequence. The main contribution of this work is design, implementation and evaluation of the capabilities of this tool. Experiments have shown that the proposed tool is able to identify the corresponding bacteria for smaller datasets and determine the correct ratios of their abundances. However, with larger datasets, the state space becomes very large and fragmented, which requires further improvements in order for it to search the state space in an efficient way.
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Sequential Monte Carlo Methods
Sobková, Eva ; Zikmundová, Markéta (advisor) ; Prokešová, Michaela (referee)
Monte Carlo methods are used for stochastic systems simulations. Sequential Monte Carlo methods take advantage of the fact that observations are coming sequentially. This allows us to refine our estimate sequentially in time We introduce a State Space Model as a Hidden Markov Model. We describe Perfect Monte Carlo Sampling, Importance Sampling, Sequential Importance Sampling and discuss advantages and disadvantages of these methods. This discussion brings us to add a resampling step in Sequential Importance Sampling and introduce Particle Filter and Particle Marginal Metropolis-Hastings algorithm. We choose a Hidden Markov Model used for stochastic volatility modeling and make a simulation study in Wolfram Mathematica, version 8.
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