ToyArchitecture: Unsupervised Learning of Interpretable Models of the World

Research in Artificial Intelligence (AI) has focused mostly on two extremes: either on small improvements in narrow AI domains, or on universal theoretical frameworks which are usually uncomputable, incompatible with theories of biological intelligence, or lack practical implementations. The goal of this work is to combine the main advantages of the two: to follow a big picture view, while providing a particular theory and its implementation. In contrast with purely theoretical approaches, the resulting architecture should be usable in realistic settings, but also form the core of a framework containing all the basic mechanisms, into which it should be easier to integrate additional required functionality. In this paper, we present a novel, purposely simple, and interpretable hierarchical architecture which combines multiple different mechanisms into one system: unsupervised learning of a model of the world, learning the influence of one's own actions on the world, model-based reinforcement learning, hierarchical planning and plan execution, and symbolic/sub-symbolic integration in general. The learned model is stored in the form of hierarchical representations with the following properties: 1) they are increasingly more abstract, but can retain details when needed, and 2) they are easy to manipulate in their local and symbolic-like form, thus also allowing one to observe the learning process at each level of abstraction. On all levels of the system, the representation of the data can be interpreted in both a symbolic and a sub-symbolic manner. This enables the architecture to learn efficiently using sub-symbolic methods and to employ symbolic inference.Comment: Revision: changed the pdftitl

IRESite—a tool for the examination of viral and cellular internal ribosome entry sites

The IRESite (http://www.iresite.org) presents carefully curated experimental evidence of many eukaryotic viral and cellular internal ribosome entry site (IRES) regions. At the time of submission, IRESite stored >600 records. The IRESite gradually evolved into a robust tool providing (i) biologically meaningful information regarding the IRESs and their experimental background (including annotation of IRES secondary structures and IRES trans-acting factors) as well as (ii) thorough concluding remarks to stored database entries and regularly updated evaluation of the reported IRES function. A substantial portion of the IRESite data results purely from in-house bioinformatic analyses of currently available sequences, in silico attempts to repeat published cloning experiments, DNA sequencing and restriction endonuclease verification of received plasmid DNA. We also present a newly implemented tool for displaying RNA secondary structures and for searching through the structures currently stored in the database. The supplementary material contains an updated list of reported IRESs

NA2Dsearch: rychlý a snadný nástroj pro vyhledávání sekundárních struktur v databázích nukleových kyselin v paralelním režimu

Diplomová práce se zabývá prohledáváním sekundárních struktur nukleových kyselin. Byla vytvořena aplikace NA2Dsearch, která umožňuje vyhledávat strukturní motiv v databázích sekundárních struktur. Aplikace nabízí uživatelsky přívětivé grafické rozhraní pomocí kterého je možné pohodlné vytváření dotazu (hledaného motivu) za použití přetahování vizuálních komponent myší. Struktury nalezených výsledků i struktury z databází je možné procházet a vizualizovat. Pro aplikaci byly vytvořeny původní algoritmy na interaktivní vizualizování struktur a na prohledávání struktur. Vyhledávací algoritmus umí vyhledávat strukturní motiv v databázích struktur (na rozdíl od existujících programů, které vyhledávají strukturní motiv v databázích sekvencí). Vyhledávání motivu funguje tak, že uživatel vytvoří dotaz který popisuje strukturu motivu a definuje variability (např. délku smyčky vlásenky) které budou akceptovány. Výsledky hledání jsou seřazeny podle skóre jež vyjadřuje podobnost nalezené struktury a dotazu. NA2Dsearch také umožňuje prohledávání sekvencí, za použití externích programů pro predikci struktur. Vyhledávání bylo demonstrováno na několika experimentech se strukturami HCV IRES a tRNA. Byly provedeny tři vyhledávání struktury HCV IRES: vyhledávání struktury HCV IRES v databázi obsahující více než tisících...The diploma thesis is dealing with searching in secondary structures of nucleic acids. The NA2Dsearch application was developed that allows to search databases of secondary structures for a structural motif. The application offers user-friendly graphical user interface where a query motif can be constructed in comfortable visual way using drag&drop, database and result structures can be browsed and visualized. The application contains original interactive nucleic acid structure visualization algorithm and novel search algorithm. The search algorithm can perform a motif search on structural data (unlike existing programs that can perform a motif search on sequence data). The motif search means that a query is created that describes the structure of motif of our interest with variabilities (e.g. the length of hairpin loop) that can be tolerated. Search results are ordered by the score computed according to the resemblance of hit and the query. The NA2Dsearch also supports searching in sequence data which are folded by external folding program. Searching capabilities are demonstrated on several search experiments involving HCV IRES and tRNA. Three searches for HCV IRES were performed: a search for HCV IRES structure in database of more than thousand of HCV genomic sequences, a folding analysis of HCV IRES...Katedra genetiky a mikrobiologieDepartment of Genetics and MicrobiologyPřírodovědecká fakultaFaculty of Scienc

Effects of chronic growth hormone and melatonin administration on EEG delta power in old rats

Charles University in Prague Faculty of Pharmacy in Hradec Králové Department of Pharmacology & Toxicology Student: Petr Hlubuček Supervisor: Doc. PharmDr. Petr Pávek, Ph.D. Title of diploma thesis: Effects of chronic growth hormone and melatonin administration on EEG delta power in old rats. Slow wave sleep (SWS), characterized by an increase in delta power (typically 0.1-4 Hz) of EEG spectral analysis is considered to be a core component of deep sleep and is associated with sleep's anabolic restorative properties necessary for good mental and physical health. The reduction of delta power represents one of the hallmarks of sleep alterations with age. In order to study effects of chronic growth hormone (GH) and melatonin administration on sleep EEG power spectra, young (3-4 months) and old (22-23 months) male Wistar rats were implanted with EEG and EMG electrodes. During one month a group of old animals was treated with GH administered intraperitonealy (i.p.), second group of old animals was treated with melatonin diluted in drinking water. Additional two groups of young and old rats with no treatment served as controls. After the treatment, EEG and EMG were recorded and analyzed. Then Fast Fourier transform was used to compute spectral power of REM and NREM sleep. Our results show rapid..

Effects of chronic growth hormone and melatonin administration on EEG delta power in old rats

Charles University in Prague Faculty of Pharmacy in Hradec Králové Department of Pharmacology & Toxicology Student: Petr Hlubuček Supervisor: Doc. PharmDr. Petr Pávek, Ph.D. Title of diploma thesis: Effects of chronic growth hormone and melatonin administration on EEG delta power in old rats. Slow wave sleep (SWS), characterized by an increase in delta power (typically 0.1-4 Hz) of EEG spectral analysis is considered to be a core component of deep sleep and is associated with sleep's anabolic restorative properties necessary for good mental and physical health. The reduction of delta power represents one of the hallmarks of sleep alterations with age. In order to study effects of chronic growth hormone (GH) and melatonin administration on sleep EEG power spectra, young (3-4 months) and old (22-23 months) male Wistar rats were implanted with EEG and EMG electrodes. During one month a group of old animals was treated with GH administered intraperitonealy (i.p.), second group of old animals was treated with melatonin diluted in drinking water. Additional two groups of young and old rats with no treatment served as controls. After the treatment, EEG and EMG were recorded and analyzed. Then Fast Fourier transform was used to compute spectral power of REM and NREM sleep. Our results show rapid..

NA2Dsearch: a fast and easy tool for secondary structure searches through databases of nucleic acids in parallel

The diploma thesis is dealing with searching in secondary structures of nucleic acids. The NA2Dsearch application was developed that allows to search databases of secondary structures for a structural motif. The application offers user-friendly graphical user interface where a query motif can be constructed in comfortable visual way using drag&drop, database and result structures can be browsed and visualized. The application contains original interactive nucleic acid structure visualization algorithm and novel search algorithm. The search algorithm can perform a motif search on structural data (unlike existing programs that can perform a motif search on sequence data). The motif search means that a query is created that describes the structure of motif of our interest with variabilities (e.g. the length of hairpin loop) that can be tolerated. Search results are ordered by the score computed according to the resemblance of hit and the query. The NA2Dsearch also supports searching in sequence data which are folded by external folding program. Searching capabilities are demonstrated on several search experiments involving HCV IRES and tRNA. Three searches for HCV IRES were performed: a search for HCV IRES structure in database of more than thousand of HCV genomic sequences, a folding analysis of HCV IRES..

NA2Dsearch: a fast and easy tool for secondary structure searches through databases of nucleic acids in parallel

The diploma thesis is dealing with searching in secondary structures of nucleic acids. The NA2Dsearch application was developed that allows to search databases of secondary structures for a structural motif. The application offers user-friendly graphical user interface where a query motif can be constructed in comfortable visual way using drag&drop, database and result structures can be browsed and visualized. The application contains original interactive nucleic acid structure visualization algorithm and novel search algorithm. The search algorithm can perform a motif search on structural data (unlike existing programs that can perform a motif search on sequence data). The motif search means that a query is created that describes the structure of motif of our interest with variabilities (e.g. the length of hairpin loop) that can be tolerated. Search results are ordered by the score computed according to the resemblance of hit and the query. The NA2Dsearch also supports searching in sequence data which are folded by external folding program. Searching capabilities are demonstrated on several search experiments involving HCV IRES and tRNA. Three searches for HCV IRES were performed: a search for HCV IRES structure in database of more than thousand of HCV genomic sequences, a folding analysis of HCV IRES..