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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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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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