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Prediction of Transposons in DNA
Černohub, Jan ; Vogel, Ivan (referee) ; Martínek, Tomáš (advisor)
Cílem práce je seznámení se s problematikou uchovávání informace v DNA, provést rešerši na téma transpozony, bioinformatické nástroje a algoritmy, které jsou používány k jejich detekci v nasekvenovaných genomech a vytvořit tak stručný úvod do obsáhle problematiky, včetně jejího zasazení do kontextu současně probíhajícího výzkumu v dané oblasti. Na základě přehledu stávajících algoritmů a nástrojů pro detekci transpozonů je navržen a implementován nástroj pro hledání tzv. LTR transpozonů.
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Genetic Improvement of Cartesian Genetic Programming Software
Husa, Jakub ; Jaroš, Jiří (referee) ; Sekanina, Lukáš (advisor)
Genetic programming is a nature-inspired method of programming that allows an automated creation and adaptation of programs. For nearly two decades, this method has been able to provide human-comparable results across many fields. This work gives an introduction to the problems of evolutionary algorithms, genetic programming and the way they can be used to improve already existing software. This work then proposes a program able to use these methods to improve an implementation of cartesian genetic programming (CGP). This program is then tested on a CGP implementation created specifically for this project, and its functionality is then verified on other already existing implementations of CGP.
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Evolutionary Solving of the Rubik's Cube
Mališ, Radim ; Sekanina, Lukáš (referee) ; Jaroš, Jiří (advisor)
This thesis deals with an evolutionary solving of the Rubik's cube. The worldwide known puzzle has been for several decades not only a toy for children and adults, but also almost a lifestyle for crowds of fans and definitely a big challenge in the world of computation, where scientists seek to find an effective automated solution. The potential for its solution could also be borne by evolutionary algorithms. The author of this thesis has developed an application employing, apart from genetic algorithms, also many advanced technics, such as linear genetic programming or local search. The goal of this special technics is to make the evolutionary process more effective. There have also been made tests of the crossover, the population size and the mutation probability influence. All the tests have been statistically evaluated.
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Evolutionary models for evaluation of organisms relationship
Gregorová, Kateřina ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
The work is focused on the study and description of evolutionary models for the evaluation of the evolutionary distances of DNA sequences and protein sequences in the amino acids and the codon representation. In the framework of this work was created a program that evaluates the genetic distance between DNA sequences and protein sequences for the use of some evolutionary models. The program calculates the genetic distance of the compared sequences and on the basis thereof renders the phylogenetic tree. This can be relatively easily and quickly evaluate the affinity of the organisms. For easy operation is part of the evaluation program also graphical user interface (GUI).
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Historical Overwiev of F1 Chassis and Engines Evolution
Hrudík, Jan ; Svída, David (referee) ; Dundálek, Radim (advisor)
This thesis is focused on the overwiev of main periods in the area of race car construction development. In the first chapter, main attention is dedicated to Formula One cars, attending races since 1950. In spite of this, there is briefly noted the technological development before FIA Formula One Championship. Next chapter is dealing with technical restrictions and regulations restraining construction of Formula One car. Data are situated in the table, ascending sequenced according to the year. Next part refers to the actual Fia Formula One Championship season 2008. There is abstract of technical regulations and the list of actual Formula One teams, their cars and drivers. There is some pages acting with one of the Formula One team. In the last chapter some of technological experiments are presented.
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Application of SAT Solvers in Circuit Optimization Problem
Minařík, Vojtěch ; Mrázek, Vojtěch (referee) ; Vašíček, Zdeněk (advisor)
This thesis is focused on the task of application of SAT problem and it's modifications in area of evolution logic circuit development. This task is supposed to increase speed of evaluating candidate circuits by fitness function in cases where simulation usage fails. Usage of SAT and #SAT problems make evolution of complex circuits with high input number significantly faster. Implemented solution is based on #SAT problem. Two applications were implemented. They differ by the approach to checking outputs of circuit for wrong values. Time complexity of implemented algorithm depends on logical complexity of circuit, because it uses logical formulas and it's satisfiability to evaluate logic circuits.
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Evolutionary Resynthesis of Combinational Circuits
Kocnová, Jitka ; Sekanina, Lukáš (referee) ; Vašíček, Zdeněk (advisor)
This master thesis is concerned about the resynthesis of combinational circuits with the help of evolutional principles. The first part of this text describes logic synthesis and its weak spots, evolutional synthesis and its advantages, and also some of the existing synthesis programs. The second part shows usage of graph algorithms in logic synthesis and their possible usage in an extension for the chosen synthesis program. Suggested design and practical implementation of the extension is also described in this part. In the third part extension testing is mentioned. The fourth part is the last one and concludes gained knowledge and results.
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Self-Modifying Programs in Cartesian Genetic Programming
Minařík, Miloš ; Slaný, Karel (referee) ; Sekanina, Lukáš (advisor)
During the last years cartesian genetic programming proved to be a very perspective area of the evolutionary computing. However it has its limitations, which make its use in area of large and generic problems impossible. These limitations can be eliminated using the recent method allowing self-modification of programs in cartesian genetic programming. The purpose of this thesis is to review the development in this area done so far. Next objective is to design own solutions for solving various problems that are hardly solvable using the ordinary cartesian genetic programming. One of the problems to be considered is generating the terms of various Taylor series. Due to the fact that the solution to this problem requires generalisation, the goal is to prove that the self-modifying cartesian genetic programming scores better than classic one for this problem. Another discussed problem is using the self-modifying genetic programming for developing arbitrarily large sorting networks. In this case, the objective is to prove that self-modification brings new features to the cartesian genetic programming allowing the development of arbitrarily sized designs.
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Warehouse Simulation and Product Distribution Optimization for Increased Throughput
Kočica, Filip ; Kolář, Martin (referee) ; Kodym, Oldřich (advisor)
This thesis focuses on the storage location assignment problem using modern meta-heuristic techniques combined with realistic simulation. A graphical tool implemented as part of this work is capable of warehouse model creation, generation of synthetic customer orders, optimization of product allocation using state of the art techniques, extensive warehouse simulation, and a pathfinder capable of finding the shortest path for orders going through the system. The work presents the comparison between different approaches based on many parameters to reach the most efficient allocation of products to warehouse slots. The author conducted tests on an experimental warehouse featuring almost twice the throughput -- 57%. The benefit of this work is a possibility to create model of an already built warehouse and its simulation and optimization, driving impact on the throughput of the warehouse, saving the user's resources, or helping him in planning and bottle-neck identification. Furthermore, this thesis introduces a new approach to warehouse optimization and new optimization criteria.
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