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Evolutionary computing
Popelka, Jan ; Smékal, Zdeněk (referee) ; Karásek, Jan (advisor)
The aim of this Bachelor's Thesis was to get acquainted with the Evolutionary Optimization Techniques, mainly with the Genetic Algorithm and Genetic Programming. It was subsequently described the role of optimization problem TSP solved using Genetic Algorithms and other Chapter solving Symbolic Regression using Genetic Programming. This optimalization problems were created in the programming JAVA and there are solved practical part of the thesis.
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Methods to detect selection in DNA sequences
Procházka, Ondřej ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
The topic of semestral thesis is methods to detect selection in DNA sequences. In the begining of the thesis we will describe molecular evolution. It will be written what made the evolution and how the evolution is shown. Moreover there are gen mutations and mechanisms of diffuse and fixation. It will be defined what pozitive, negative and neutral selection is. The thesis is focused on evolution distance of synonymous and nonsynonymous substitution. There will be described three methods – Nei-Gojobori, Li-Wu-Luo and Comeron. All these methods will be described with mathematic formulas. There will be statistic test to decide what kind of selection ti is – there will be used z-test. In the practical part, there will be information about developed software what counts selection pressure from sequences from databazes in format GenBank and it shows parts where selection is. The software will be used for two data sets with two different genetic codes. The result will be discussed. We will discuss results of all three methods of selection pressure and influence of input parametrs.
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Genetic programming - Java implementation
Tomaštík, Marek ; Kuba,, Martin (referee) ; Matoušek, Radomil (advisor)
This Master´s thesis implements computer program in Java, useful for automatic model generating, specially in symbolic regression problem. Thesis includes short description of genetic programming (GP) and own implementation with advanced GP operands (non-destructive operations, elitism, exptression reduction). Mathematical model is generating by symbolic regression, exacly for choosen data set. For functioning check are used test tasks. Optimal settings is found for choosen GP parameters.
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Advanced Editor of 3D Scene
Bišof, Martin ; Žák, Pavel (referee) ; Přibyl, Jaroslav (advisor)
This work describes important periods of making application on editing 3D scene. It concerns a program which makes possible visualization of objects and simulation graphic scene. The introduction of this document is dedicated to theorical analysis, which is oriented on objects presentation in computer graphic with detailed orientation on Boundary Representation. The following chapter is about transformations and manipulators. Design part introduces basic problems and apprises with exercise solutions on general level. In the part of the implementation, we find detailed description of actual solution for particular phase of proposal. It states description of advanced camera system and transformation of objects by the help of graphic manipulators. The next chapter discuss implement effects, modifications and solution for graphical user interface.
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The global optimalization methods
Dudová, Aneta ; Kozumplík, Jiří (referee) ; Mézl, Martin (advisor)
This bachelor work is dedicated to advanced methods of global optimization, and especially problem traveling salesman. It focuses on the description of the problem and its various options, including graph theory, heuristic algorithms, evolutionary algorithms, in which mainly genetic algorithms and optimization by ant colonies. In conclusion, the implementation of these methods and performed testing on different data sets of algorithms that approximately solve the traveling salesman problem.
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Paralinguistic signals recognition in spoken dialogs
Mašek, Jan ; Míča, Ivan (referee) ; Atassi, Hicham (advisor)
This document describes the three methods for the detection and classification of paralinguistic expressions such as laughing and crying from usual speech by analysis of the audio signal. The database of records was originally designed for this purpose. When analyzing everyday dialogs, music might be included, so the database was extended by four new classes as speech, music, singing with music and usual speech with background music. Feature extraction, feature reduction and classification are common steps in recognizing for all three methods. Difference of the methods is given by classification process in detail. One classification of all six classes at once is proposed in the first method called straight approach. In the second method called decision tree oriented approach we are using five intuitive sub classifiers in the tree structure and the final method uses for classification emotion coupling approach. The best features were reduced by feature evaluation using F-ratio and GMM classifiers were used for the each classification part.
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Detection of positive selection in reproductive genes of songbirds
Cakl, Lukáš ; Reifová, Radka (advisor) ; Těšický, Martin (referee)
Reproductive genes are assumed to play an important role in adaptive evolution and speciation, yet little is known about the patterns of molecular evolution in these genes within avian species. This thesis is focused on identifying reproductive genes under positive selection and analyzing their function in songbirds, the largest and most diverse suborder of modern birds. Using existing bioinformatic approaches and published genomic data of 14 songbird species, we have first constructed 12000 groups of orthologous genes and detected significant traces of recurrent positive selection within 385 of them. Using proteomic data, this genome wide set of genes was then filtered to obtain genes expressed within songbird spermatozoa and fluids from the female reproductive tract. Within spermatozoa 22 out of 940 expressed genes were positively selected, while female fluids were found to be more conserved, as only 6 out of 529 expressed genes have shown traces of positive selection. We have then computed the enrichment of gene ontology terms within the positively selected genes. The enriched terms suggest evolutionary pres- sures acting on spermatozoa cytoskeleton, molecular motors and energetic metabolism, highlighting the importance of sperm morphology and swimming speed. Furthermore, the enrichment results...
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Advanced Evolutionary Optimisation of TSP-Based Problems
Hladyuk, Vadym ; Vašíček, Zdeněk (referee) ; Bidlo, Michal (advisor)
This paper solves the traveling salesman problem using an evolutionary algorithm, specifically a genetic algorithm. It is a hybrid of the genetic algorithm, using a local search algorithm and other enhancements that further improve the results obtained. The traveling salesman problem will be solved from 20 cities to 25,000 cities. In the experiments chapter, I have determined the best settings for all the parameters in the program and properly tested their appropriateness. In the next part of the experiments chapter, I found out the performance of the full version of the genetic algorithm and its variants. In the last section, I compared the evolution of fitness values of different variants of genetic algorithms and different variants of crossover operators, I also compared the time consumption. I suggested further possible improvements either to the local search algorithm or to another approach to solve the TSP.
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Genomická selekce v chovu skotu
BARTŮŇKOVÁ, Lenka
This thesis analyses genomic selection with an emphasis on cattle breeding. Genomic selection is starting to become a common element of breeding programmes of livestock animals rearing and this is a new approach to marker-assisted selection (MAS), where instead of identifying individual interconnected loci all information for predictions is obtained from markers, thus making them more accurate. This thesis aims to approach genomic selection, individual methods of selection and their uses, as much as their implementation in cattle rearing. The work devotes a section to applications of genomic selection in Czech Republic. The possible future development of genomic selection is being hinted in the conclusion.
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The struggle for human dignity in the era of modern eugenics. Molecular genome editing tool CRISPR/CAS9 and its use in human genome therapy from the perspective of theological ethics
Auxt, Miroslav ; Štica, Petr (advisor) ; Fošum, Jan (referee)
The recent breakthrough discovery of the molecular genome editing tool CRISPR/CAS9 represents a complete revolution in the field of molecular biology, biomedicine and other related fields. It is a highly effective biomolecular tool, derived from the bacterial immune system, with which it is possible to introduce precise changes in the genomes of all organisms. The thesis is limited to the ethical evaluation of the use of CRISPR/CAS9 exclusively in human gene therapy. Thanks to its efficiency, simplicity, accuracy and low financial costs, the CRISPR/CAS9 editing tool, in compliance with ethical parameters, already has a broad spectrum of use in therapeutic procedures on somatic or body cells in the treatment of human genetically determined diseases without introducing a change into the future offspring of the given individual. In addition to great therapeutic potential, the application of CRISPR/CAS9 raises many ethical questions related to the possibilities of its further use, possibly misuse. Ethically problematic genetic procedures include: human hereditary genome editing, i.e. the targeted alteration of the genome of sex cells, progenitor cells and cells of early embryonic development stages with the therapeutic goal of eliminating a genetically determined disease associated with the...
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