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Methods of processing Oxford Nanopore sequencing data for metagenomics
Barilíková, Lujza ; Provazník, Ivo (referee) ; Kupková, Kristýna (advisor)
The revolutionary sequencing technology introduced by Oxford Nanopore Technologies – MinION holds a great promise in the field of metagenomics. Low cost, produced long reads and portability, due to its small dimensions, represents only one of the many advantages of this technology. Despite the benefits, there is a lack of available computational tools for handling the produced data. The theoretical part of the thesis first introduces current sequencing technologies with main focus on the third-generation sequencing and especially on nanopore sequencing. The recent possibilities of metagenomic data visualization are introduced. The main purpose of the bachelor thesis is to make an algorithm for binning of metagenomic samples based on use of dimensionality reduction techniques straight on raw data produced by nanopore sequencing.
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Air Quality Analysis in Office and Residential Areas
Tisovčík, Peter ; Korček, Pavol (referee) ; Kořenek, Jan (advisor)
The goal of the thesis was to study the indoor air quality measurement focusing on the concentration of carbon dioxide. Within the theoretical part, data mining including basic classification methods and approaches to dimensionality reduction was introduced. In addition, the principles of the developed system within IoTCloud project and available possibilities for measurement of necessary quantities were studied. In the practical part, the suitable sensors for given rooms were selected and long-term measurement was performed. Measured data was used to create the system for window opening detection and for the design of appropriate way of air change regulation in a room. The aim of regulation was to improve air quality using natural ventilation.
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Machine Learning in Image Classification
Král, Jiří ; Španěl, Michal (referee) ; Hradiš, Michal (advisor)
This project deals vith analysis and testing of algorithms and statistical models, that could potentionaly improve resuts of FIT BUT in ImageNet Large Scale Visual Recognition Challenge and TRECVID. Multinomial model was tested. Phonotactic Intersession Variation Compensation (PIVCO) model was used for reducing random e ffects in image representation and for dimensionality reduction. PIVCO - dimensionality reduction achieved the best mean average precision while reducing to one-twenyth of original dimension. KPCA model was tested to approximate Kernel SVM. All statistical models were tested on Pascal VOC 2007 dataset.
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Data mining
Mrázek, Michal ; Sehnalová, Pavla (referee) ; Bednář, Josef (advisor)
The aim of this master’s thesis is analysis of the multidimensional data. Three dimensionality reduction algorithms are introduced. It is shown how to manipulate with text documents using basic methods of natural language processing. The goal of the practical part of the thesis is to process real-world data from the internet forum. Posted messages are transformed to the numerical representation, then to two-dimensional space and visualized. Later on, topics of the messages are discovered. In the last part, a few selected algorithms are compared.
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Use of Knowledge Discovery for Data from PDF Files
Dvořáček, Libor ; Burgetová, Ivana (referee) ; Bartík, Vladimír (advisor)
This bachelor thesis deals with the extraction of tables from digitally created pdfs and the subsequent use of the obtained data for data analysis. Methods of dimension reduction and cluster analysis are used. The main content is an analysis of available tools for data extraction in the python language, a description and comparison of the used machine learning methods and implementation of an application that combines all these topics into one functional unit at: http://extraktor.herokuapp.com
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Dimensionality reduction of statistical dataset
Sabo, Adam ; Kosová, Petra (referee) ; Hrabec, Pavel (advisor)
This thesis introduces methods which are used to reduce dimensionality and their subsequent application to selected sets of sports statistical data. The first part of the thesis deals with the theoretical apparatus of mathematical statistics, in particular with the Principal Component Analysis and its alternative - the Factor Analysis. The second part provides a brief explanation of the terms related to the selected sets of football statistics where these methods are applied. The third part introduces the results of the application of both methods to statistical files. Data obtained through calculations performed in Python programming language are organized and interpreted by means of graphs and tables.
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Some Robust Approaches to Reducing the Complexity of Economic Data
Kalina, Jan
The recent advent of complex (and potentially big) data in economics requires modern and effective tools for their analysis including tools for reducing the dimensionality (complexity) of the given data. This paper starts with recalling the importance of Big Data in economics and with characterizing the main categories of dimension reduction techniques. While there have already been numerous techniques for dimensionality reduction available, this work is interested in methods that are robust to the presence of outlying measurements (outliers) in the economic data. Particularly, methods based on implicit weighting assigned to individual observations are developed in this paper. As the main contribution, this paper proposes three novel robust methods of dimension reduction. One method is a dimension reduction within a robust regularized linear regression, namely a sparse version of the least weighted squares estimator. The other two methods are robust versions of feature extraction methods popular in econometrics: robust principal component analysis and robust factor analysis.
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High-performance exploration and querying of selected multi-dimensional spaces in life sciences
Kratochvíl, Miroslav ; Bednárek, David (advisor) ; Glaab, Enrico (referee) ; Svozil, Daniel (referee)
This thesis studies, implements and experiments with specific application-oriented approaches for exploring and querying multi-dimensional datasets. The first part of the thesis scrutinizes indexing of the complex space of chemical compounds, and details a design of high-performance retrieval system for small molecules. The resulting system is then utilized within a wider context of federated search in heterogeneous data and metadata related to the chemical datasets. In the second part, the thesis focuses on fast visualization and exploration of many-dimensional data that originate from single- cell cytometry. Self-organizing maps are used to derive fast methods for analysis of the datasets, and used as a base for a novel data visualization algorithm. Finally, a similar approach is utilized for highly interactive exploration of multimedia datasets. The main contributions of the thesis comprise the advancement in optimization and methods for querying the chemical data implemented in the Sachem database cartridge, the federated, SPARQL-based interface to Sachem that provides the heterogeneous search support, dimensionality reduction algorithm EmbedSOM, design and implementation of the specific EmbedSOM-backed analysis tool for flow and mass cytometry, and design and implementation of the multimedia...
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Some Robust Approaches to Reducing the Complexity of Economic Data
Kalina, Jan
The recent advent of complex (and potentially big) data in economics requires modern and effective tools for their analysis including tools for reducing the dimensionality (complexity) of the given data. This paper starts with recalling the importance of Big Data in economics and with characterizing the main categories of dimension reduction techniques. While there have already been numerous techniques for dimensionality reduction available, this work is interested in methods that are robust to the presence of outlying measurements (outliers) in the economic data. Particularly, methods based on implicit weighting assigned to individual observations are developed in this paper. As the main contribution, this paper proposes three novel robust methods of dimension reduction. One method is a dimension reduction within a robust regularized linear regression, namely a sparse version of the least weighted squares estimator. The other two methods are robust versions of feature extraction methods popular in econometrics: robust principal component analysis and robust factor analysis.
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Dimensionality reduction of statistical dataset
Sabo, Adam ; Kosová, Petra (referee) ; Hrabec, Pavel (advisor)
This thesis introduces methods which are used to reduce dimensionality and their subsequent application to selected sets of sports statistical data. The first part of the thesis deals with the theoretical apparatus of mathematical statistics, in particular with the Principal Component Analysis and its alternative - the Factor Analysis. The second part provides a brief explanation of the terms related to the selected sets of football statistics where these methods are applied. The third part introduces the results of the application of both methods to statistical files. Data obtained through calculations performed in Python programming language are organized and interpreted by means of graphs and tables.
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