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Similarity Search in Protein Structure Databases
Galgonek, Jakub
Proteins are one of the most important biopolymers having a wide range of functions in living organisms. Their huge functional diversity is achieved by their ability to fold into various 3D structures. Moreover, it has been shown that proteins sharing similar structure often share also other properties (e.g, a biological function, an evolutionary origin, etc.). Therefore, protein structures and methods to identify their similarities are so widely studied. In this thesis, we introduce a system allowing similarity search in pro- tein structure databases. The system retrieves, given a query structure, all database structures being similar to the query structure. It employs several key components. We have introduced a novel similarity measure assigning similarity scores to pairs of protein structures. We have designed specific access method based on LAESA metric indexing and using the proposed measure. The access method allows to search similar structures more effi- ciently than when a sequential scan of a database is employed. To achieve further speedup, the measure and the access method have been parallelized, resulting in almost linear speedup with the respect to the number of available cores. The last component is a web user interface that allows to accept a query structure and to present a list of...
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Hlasové ovládání pro efektivní editaci textu
Citorík, Juraj ; Lokoč, Jakub (advisor) ; Skopal, Tomáš (referee)
The aim of this thesis is to provide a comprehensive introduction to digital sound processing and speech recognition. Selected speech recognition features as well as algorithms are introduced and utilized in a voice controlled text editor and a .NET class library. The performance of the features is evaluated in both speaker-dependent and speaker-independent recognition of commands related to text editing. The library provides a straightforward way of implementing a speaker-dependent, domain-constrained voice recognition in an arbitrary application. It is used in a simple voice controlled text editor. The editor allows the user to assign voice commands to built-in actions. In this way, it is possible for inexperienced users to access and use advanced features of the program without having to learn complex workflows. Moreover, this approach is language-agnostic and can even be used by people with speech impairments as opposed to majority of presently used voice recognition systems. The results of the experiments indicate that, given a recording of sufficient quality, the presented features and algorithms provide an effective means to implement a speaker-dependent speech recognition system, which can be used in a voice controlled text editor. Powered by TCPDF (www.tcpdf.org)
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Similarity search in Mass Spectra Databases
Novák, Jiří ; Skopal, Tomáš (advisor) ; Svozil, Daniel (referee) ; Nahnsen, Sven (referee)
Shotgun proteomics is a widely known technique for identification of protein and peptide sequences from an "in vitro" sample. A tandem mass spectrometer generates tens of thousands of mass spectra which must be annotated with peptide sequences. For this purpose, the similarity search in a database of theoretical spectra generated from a database of known protein sequences can be utilized. Since the sizes of databases grow rapidly in recent years, there is a demand for utilization of various database indexing techniques. We investigate the capabilities of (non)metric access methods as the database indexing techniques for fast and approximate similarity retrieval in mass spectra databases. We show that the method for peptide sequences identification is more than 100x faster than a sequential scan over the entire database while more than 90% of spectra are correctly annotated with peptide sequences. Since the method is currently suitable for small mixtures of proteins, we also utilize a precursor mass filter as the database indexing technique for complex mixtures of proteins. The precursor mass filter followed by ranking of spectra by a modification of the parametrized Hausdorff distance outperforms state-of-the-art tools in the number of identified peptide sequences and the speed of search. The...
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Podobnostní vyhledávání obrázků na webu
Grošup, Tomáš ; Lokoč, Jakub (advisor) ; Hoksza, David (referee)
The subject of this bachelor thesis is to design and create a web portal, enabling efficient indexing and content-based searching of images obtained from various free image databases (e.g., results from a keyword-based search engine). The portal provides fast feature extraction technique and for the visual similarity, the signature quadratic form distance is utilized. The search supports various user settings and comparison of their results. Search results can also be presented using a layout based on particle physics, which supports exploration and multi-query.
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Nové dynamické metody konstrukce pro PM-strom
Čech, Přemysl ; Lokoč, Jakub (advisor) ; Pangrác, Ondřej (referee)
With the emerging applications dealing with complex multimedia retrieval, such as the multimedia exploration, appropriate indexing structures need to be designed. A formalism for compact metric region description can significantly simplify the design of algorithms for such indexes, thus more complex and efficient metric indexes can be developed. In this thesis, we introduce the cut-regions comprising compact metric region description and basic operations. To demonstrate their power, we redefine the PM-Tree using the cut-regions and, moreover, use the formalism to improve the PM-Tree construction techniques. We have experimentally evaluated that the improved construction techniques lead to query performance originally obtained just using expensive construction techniques. Also in comparison with other metric and spatial access methods, the revisited PM-Tree proved its benefits.
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Similarity Search in Protein Structure Databases
Galgonek, Jakub ; Skopal, Tomáš (advisor) ; Porto, Markus (referee) ; Svozil, Daniel (referee)
Proteins are one of the most important biopolymers having a wide range of functions in living organisms. Their huge functional diversity is achieved by their ability to fold into various 3D structures. Moreover, it has been shown that proteins sharing similar structure often share also other properties (e.g, a biological function, an evolutionary origin, etc.). Therefore, protein structures and methods to identify their similarities are so widely studied. In this thesis, we introduce a system allowing similarity search in pro- tein structure databases. The system retrieves, given a query structure, all database structures being similar to the query structure. It employs several key components. We have introduced a novel similarity measure assigning similarity scores to pairs of protein structures. We have designed specific access method based on LAESA metric indexing and using the proposed measure. The access method allows to search similar structures more effi- ciently than when a sequential scan of a database is employed. To achieve further speedup, the measure and the access method have been parallelized, resulting in almost linear speedup with the respect to the number of available cores. The last component is a web user interface that allows to accept a query structure and to present a list of...
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Index Suitable for Similar Search in High-dimensional Spaces
Krejčová, Martina ; Kopecký, Michal (advisor) ; Skopal, Tomáš (referee)
In this paper, we focus on indexing and searching in high-dimensional data. To achieve the target we implemented the Metric Index, a model of the similarity search based on the metric spaces, that employs many of known principles of partitioning and filtering. The metric space is a general model of similarity, which enables the usage of implemented index for various data. With this index, stored data could be searched effectively. The internal structure of data is hidden, we just require an implementation of the function for feature extraction, which produces a vector representing data, and the metric function applicable to the given data. The Metric Index was implemented as a data cartridge, the mechanism for extending the capabilities of the Oracle server. This data cartridge enables indexing of large unstructured data in the Oracle server known as LOBs.
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Similarity search in image collections
Navrátil, Lukáš ; Bartoš, Tomáš (advisor) ; Skopal, Tomáš (referee)
Detection of keypoints from image and their characterization by using descriptors is common technique in some branches of computer vision. The goal of this thesis is to explore and confirm usability of this technique for similarity retrieval in image collections. For this purpose it will be created a web application used for collecting ratings of similarity from users which will be subsequently compared with results computed by the implementation of SURF algorithm, one of algorithms used for detection and description of image keypoints. It will also be discussed the impact of metrics and parameters influencing results of computation of similarity between images and it will be made an effort to find settings for which computed results will be closest to user's similarity perception.
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Modification of Pivot Tables method for persistent metric indexing
Moško, Juraj ; Skopal, Tomáš (advisor) ; Hoksza, David (referee)
The pivot tables is one of the most effective metric access method optimized for a number of distance computations in similarity search. In this work the new modification of the pivot tables method was proposed that is besides distance computations optimized also for a number of I/O operations. Proposed Clustered pivot tables method is indexing clusters of similar objects that were created by another metric access method - the M-tree. The indexing of clustered objects has a positive effect for searching within indexed database. Whereas the clusters are paged in second memory, page containing such cluster, which do not satisfy particular query, is not accessed in second memory at all. Non-relevant objects, that are out of the query range, are not loaded into memory, what has the effect of decreasing number of I/O operations and total volume of transferred data. The correctness of proposed approach was experimentally proved and experimental results of proposed method was compared to selected metric access methods.
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Automatically Updated Bibliography
Valo, Boris ; Škoda, Petr (referee) ; Smrž, Pavel (advisor)
This paper describes the development of application for automatically updated bibliography. Nowadays, many Internet users search informations they need, this is important especially in sets of scientific publications and articles. The aim of this thesis is convenient tool for users to create their own portal. This is achieved by storing documents and their subsequent search using ElasticSearch. Retrieval is made by Boolean queries and additional search using similarity search tool MoreLikeThis. At the end of this thesis is described the way of testing and evaluation of retrieval.
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