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The use of numerical representations in processing of nucleotide sequences
Košíček, Adam ; Maděránková, Denisa (referee) ; Kubicová, Vladimíra (advisor)
Conversion of DNA sequences for appropriate representation is important task before initiation of analyzes and further processing. The main goal of this work was to get familiar with types of numerical and graphical representations and their application for DNA analyzes. In consideration of great volume of methods and procedures, only a few were chosen for this work. Some methods can not be classified only as numerical or graphical representations, because of option allowing them to be converted into both of these representations. These methods were classified as graphical representations. Phylogenetic trees were programmed for chosen methods to compare its precision. Outcome of this work is summing up the results.
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Generic Reverse Compilation to Recognize Specific Behavior
Ďurfina, Lukáš ; Šaloun, Petr (referee) ; Zahradnický,, Tomáš (referee) ; Kolář, Dušan (advisor)
Práce je zaměřena na rozpoznávání specifického chování pomocí generického zpětného překladu. Generický zpětný překlad je proces, který transformuje spustitelné soubory z různých architektur a formátů objektových souborů na stejný jazyk na vysoké úrovni. Tento proces se vztahuje k nástroji Lissom Decompiler. Pro účely rozpoznání chování práce zavádí Language for Decompilation -- LfD. LfD představuje jednoduchý imperativní jazyk, který je vhodný pro srovnávaní. Konkrétní chování je dáno známým spustitelným souborem (např. malware) a rozpoznání se provádí jako najítí poměru podobnosti s jiným neznámým spustitelným souborem. Tento poměr podobnosti je vypočítán nástrojem LfDComparator, který zpracovává dva vstupy v LfD a rozhoduje o jejich podobnosti.
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Clustering of Biological Sequences
Kubiš, Radim ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
One of the main reasons for protein clustering is prediction of structure, function and evolution. Many of current tools have disadvantage of high computational complexity due to all-to-all sequence alignment. If any tool works faster, it does not reach accuracy as other tools. Further disadvantage is processing on higher rate of similarity but homologous proteins can be similar with less identity. The process of clustering often ends when reach the condition which does not reflect sufficient quality of clusters. Master's thesis describes the design and implementation of new tool for clustering of protein sequences. New tool should not be computationally demanding but it should preserve required accuracy and produce better clusters. The thesis also describes testing of designed tool, evaluation of results and possibilities of its further development.
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Automatic image annotation
Hegmon, Jiří ; Karásek, Jan (referee) ; Burget, Radim (advisor)
Recognition and comparison of image is one of the main problems and area of the field of computer vision. This thesis adds to these two issues the third, the recognition image semantics, so called annotations or labels. This work uses the knowledge of methods of recognizing the similarity of images to create a tool that is able based on training dataset of images and annotations, create a group most likely annotation for the test set of images. This work presents several types of test datasets suitable for the detection of annotation information for images. Subsequently, best set with the necessary training dataset size and enough information about annotations is selected. Based on this training dataset algorithm is designed for easy loading test set without large demands on computer performance. Evaluation of annotation information is done based on different similarity algorithms. At the beginning of this work was to use a simple, but not very effective method of MSE and comparison of color histograms, but gradually it was necessary to move to using more advanced methods (such as Tamura, Gabor, CEDD nebo různé druhy hostistogramů). The results of this comparison are then taken to evaluate the likelihood of the annotation for the image specified test set. The last part is an evaluation of the accuracy of annotation based on information from the test set.
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Comparison of 3D objects in JAVA language
Zapletal, Tomáš ; Smékal, Zdeněk (referee) ; Šmirg, Ondřej (advisor)
The main aim of the thesis is loading of 3D models in different file formats and its displaying, creating of slices from 3D models and vice versa making 3D models from slices, quantify inaccuracy of anti-aliasing and other formatting and investigate similarity of original and edited models. Everything in Java programming language and its extensions for 3D object tasks. Thesis builds on earlier project „3D shape from MRI“.
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Music information retrieval techniques for determining the place of origin of the Czech chamber and orchestral music interpretations
Miklánek, Štěpán ; Mekyska, Jiří (referee) ; Kiska, Tomáš (advisor)
This diploma thesis is focused on the statistical analysis of chamber and orchestral classical music recordings composed by Czech authors. One of the chapters is dedicated to the description of a feature extraction process that precedes the statistical analysis. Techniques of Music Information Retrieval are used during several stages of this thesis. Databases used for analysis are described and pre-processing steps are proposed. A tool for synchronization of the recordings was implemented in MATLAB. Finally the system used for classification of recordings based on their geographical origin is proposed. The recordings are sorted by a binary classifier into two categories of Czech and world recordings. The first part of the statistical analysis is focused on individual analysis of features. The features are evaluated based on their discrimination strength. The second part of the statistical analysis is focused on feature selection, which can improve the overall accuracy of the binary classifier compared to the individual analysis of the features.
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Content-Based Searching for Similar CT Scans
Hošek, Pavel ; Klíma, Ondřej (referee) ; Španěl, Michal (advisor)
The work deals with the design and implementation of tool for Content-Based Searching for similar CT scans. This work also deals with comparision of individual methods for searching for similar CT scans. Third-party libraries are used to extract individual descriptors. Furthermore, this work presents results of the implemented searching tool and also presents results of the comparision of individual methods for Content-Based Searching for similar CT scans and suggests possible improvements.
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Objects outline and image matching
Kvasnička, Petr ; Richter, Miloslav (referee) ; Janáková, Ilona (advisor)
The aim of the diploma thesis is to get acquainted with problem of detecting the object with sketch, diagram or contour, which should represent the object to be compared. The thesis deals with how to solve this problem. Part of the thesis contains theoretical methods that manage to evaluate the degree of similarity between the unknown object and less accurate sketch. Each of these methods includes customized edits from the viewpoint of image pre-processing. The thesis deals with some methods in more detail. Selected methods are implemented and tested on the created database. In the last step of the thesis these realized methods are compared to each other.
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Semantic Similarity Methods in Folksonomies
Kadlec, Jan ; Otrusina, Lubomír (referee) ; Schmidt, Marek (advisor)
Bakalářská práce byla vypracována na studijním pobytu na "Aalborg University" v Dánsku, a byla zpracována v angličtině. Folksonomie jsou nový, uživateli řízený přístup ke klasifikaci a důležitá čast Web 2.0. Jsou také jediným přístupem, který je schopen udržet krok s dnešní rychlostí expanze webu, tím že předá uživatelům odpovědnost za klasifikaci. Pokud folksonomie obsahují dostatečné množství dat, dají se k mnohému využít. Tato práce se zaměřuje na metody sémantické podobnosti ve folksonomiích. Cílem této práce bylo odzkoušet mnohé metody na vzorku tří datových sad - delicious.com, Last.fm a medworm.com. Toto bylo vykonáno za pomocí kotvících dat z WordNetu, Open Directory Project a zdravotně orientované ontologie. Výsledky přinesené touto prací indikují, že metody sémantické podobnosti mohou být použity k úspěšnému měření podobností v mnohých doménách.
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Estimation and analysis of speech signal periodicity
Malucha, Jan ; Poměnková, Jitka (referee) ; Sigmund, Milan (advisor)
Theoretical part starts with a short introduction to speech signals and short time analysis method. Concept of periodicity is clarified. This is followed by analysis of the speech signal parameters - voiced/unvoiced classification, intonation and short time period similarity. Next the overview of methods used to analyze the mentioned parameters together with concepts of their algorithms is provided. These methods include ZCR, STE, HNR, ACF, NCC, AMDF and DTW. Algorithms using the methods with supporting preprocessing algorithms were programmed in MATLAB for practical part. All were tested on real speech signals and the results are discussed at the end of the thesis.
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