Acknowledgements I am especially grateful to my supervisor dr. Daniel Zeman for providing me a wise supervision, helpful advices, instant replies and encouragement. I am happy to have a chance to acknowledge the work of my coordinators from Charles University in Prague, for being in touch with me since the first year of Masters program, for being patient, kind, very attentive and helpful with a...

Most modern lossless data compression techniques used today, are based in dictionaries. If some string of data being compressed matches a portion previously seen, then such string is included in the dictionary and its reference is included every time it occurs. A possible generalization of this scheme is to consider not only strings made of consecutive symbols, but more general patterns with ga...

Automatically building domain-specific ontologies is a highly challenging task as it requires extracting domain-specific terms from a corpus and assigning them relevant domain concept labels. In this paper, we focus on the second task: i.e., assigning domain concepts to domain-specific terms. Motivated by previous approaches in related research (such as word sense disambiguation (WSD) and named...

This paper surveys and extends models and algorithms for identifying binding sites in non-coding regions of DNA. These sites control the transcription of genes into messenger RNA in preparation for translation into proteins. We summarize the underlying biology, review three different models for binding site identification, and present a unified model that borrows from the previous models and in...

In this article we describe the workflow implemented to convert a dictionary saved as a PDF file into an XML document and posterior importation into an XML aware database, and the process to edit, add and delete new entries. The conversion process was challenging given the format of the PDF file, and the fine grained detail of the XML schema that was used. For that, an iterative filtering appro...