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ModuleInducer: Automating the Extraction of Knowledge from Biological SequencesKorol, Oksana 14 October 2011 (has links)
In the past decade, fast advancements have been made in the sequencing, digitalization and collection of the biological data. However the bottleneck remains at the point of analysis and extraction of patterns from the data. We have developed a method that is aimed at widening this bottleneck by automating the knowledge extraction from the biological data. Our approach is aimed at discovering patterns in a set of DNA sequences based on the location of transcription factor binding sites or any other biological markers with the emphasis of discovering relationships. A variety of statistical and computational methods exists to analyze such data. However, they either require an initial hypothesis, which is later tested, or classify the data based on its attributes. Our approach does not require an initial hypothesis and the classification it produces is based on the relationships between attributes. The value of such approach is that is is able to uncover new knowledge about the data by inducing a general theory based on basic known rules.
The core of our approach lies in an inductive logic programming engine, which, based on positive and negative examples as well as background knowledge, is able to induce a descriptive, human-readable theory, describing the data. An application provides an end-to-end analysis of DNA sequences. A simple to use Web interface accepts a set of related sequences to be analyzed, set of negative example sequences to contrast the main set (optional), and a set of possible genetic markers as position-specific scoring matrices. A Java-based backend formats the sequences, determines the location of the genetic markers inside them and passes the information to the ILP engine, which induces the theory.
The model, assumed in our background knowledge, is a set of basic interactions between biological markers in any DNA sequence. This makes our approach applicable to analyze a wide variety of biological problems, including detection of cis-regulatory modules and analysis of ChIP-Sequencing experiments. We have evaluated our method in the context of such applications on two real world datasets as well as a number of specially designed synthetic datasets. The approach has shown to have merit even in situations when no significant classification could be determined.
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An inductive logic programming approach to statistical relational learningKersting, Kristian. January 1900 (has links)
Thesis (Ph. D.)--Albert-Ludwigs-Universität Freiburg im Breisgau, 2006. / Description based on print version record. Includes bibliographical references (p. 201-221) and index.
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Hazard detection with VHDL in combinational logic circuits with fixed delays /Chu, Ming-Cheung, January 1992 (has links)
Thesis (M.S.)--Virginia Polytechnic Institute and State University, 1992. / Vita. Abstract. Includes bibliographical references (leaves 181-182). Also available via the Internet.
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The role of type equality in meta-programming /Pasalic, Emir. January 2004 (has links)
Thesis (Ph. D.)--OGI School of Science & Engineering at OHSU, 2004. / Includes bibliographical references (leaves 229-239).
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An inductive logic programming approach to statistical relational learningKersting, Kristian. January 1900 (has links)
Thesis (Ph.D.)--Albert-Ludwigs-Universität Freiburg im Breisgau, 2006. / Includes bibliographical references (p. 201-221) and index.
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Integrating top-down and bottom-up approaches in inductive logic programming applications in natural language processing and relational data mining /Tang, Lap Poon Rupert, Mooney, Raymond J. January 2003 (has links) (PDF)
Thesis (Ph. D.)--University of Texas at Austin, 2003. / Supervisor: Raymond Mooney. Vita. Includes bibliographical references. Available also from UMI Company.
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Automated reasoning about actionsLee, Joohyung, Lifschitz, Vladimir, January 2005 (has links) (PDF)
Thesis (Ph. D.)--University of Texas at Austin, 2005. / Supervisor: Vladimir Lifschitz. Vita. Includes bibliographical references.
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Επαγωγικός λογικός προγραμματισμός και Progol : προβλήματα εκμάθησης γραμματικήςΠετρόπουλος, Κωνσταντίνος 31 August 2012 (has links)
Σε αυτήν την εργασία μελετάται ο Επαγωγικός Λογικός Προγραμματισμός μέσα απο το πρίσμα της μάθησης της Γραμματικής της αγγλικής γλώσσας. Ο λόγος που
επιλέχθηκε αυτό το πρόβλημα είναι ότι εξομοιώνει, μέχρι ενός σγημείου, τον τρόπο
που τα παιδιά μαθαίνουν να μιλούν κάποια γλώσσα, υπό την έννοια ότι μαθαίνουν
να μιλάνε χωρίς να έρθουν σε επαφή με τους κανόνες – τη γραμματική – της γλώσσας, αλλά από την επαφή τους με τα με τα ερεθίσματα – τα παραδείγματα – που
έχουν από τον περίγυρό τους. / This paper is about Inductive Logic Programming through the prism of a problem. In our case Grammar Learning.
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Component assembly and theorem proving in constraint handling rulesMário Oliveira Rodrigues, Cleyton 31 January 2009 (has links)
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Previous issue date: 2009 / Devido á grande demanda por softwares cada vez mais robustos, complexos e flexíveis,
e, sobretudo, pelo curtíssimo tempo de entrega exigido, a engenharia de software tem
procurado novos meios de desenvolvimento que supram satisfatoriamente essas demandas.
Uma forma de galgar esses novos patamares de produtividade provém do uso de
uma metodologia baseada em agentes que se comunicam e com isso, ao invés dos programas
serem estritamente programados, o comportamento destes sistemas de software
emerge da interação de agentes, robôs, ou subsistemas aut onomos, independentes, além
de declarativamente especificados. Isto provê a habilidade para automaticamente configurá
-los, otimizá-los, monitorá-los, adaptá-los, diagnosticá-los, repará-los e protegê-los
dentro do ambiente.
Contudo, um grande problema das linguagens declarativas é a falta de mecanismos
que permitem a melhor estruturação de dados, facilitando portanto, o reuso. Portanto,
esta dissertação explica o desenvolvimento de nova linguagem lógica declarativa para
programar sistemas de raciocínio automático de uma forma modularizada: C2HR∨. A
linguagem base escolhida para a extensão com componentes lógicos foi CHR. Os motivos
para essa escolha são definidos ao longo da dissertação. Duas abordagens, portanto,
são apresentadas: a primeira, conhecida como CHRat, foi desenvolvida numa parceria
juntamente com o grupo de pesquisas CONTRAINTES do INRIA/Rocquencourt-Paris,
onde o programador ´e o responsável direto por definir os componentes CHR, permitindo
o seu reuso por outros componentes; a segunda aplicação, CHRtp, visa atender prioritariamente
requisitos de completude e, por isso, se baseia em procedimentos lógicos de
inferência como: o raciocínio para frente, o raciocínio para trás, e a resolução/factoring.
A dissertação mostra também alguns exemplos práticos, onde uso de componentes
facilita radicalmente sua implementação. As contribuições almejadas com essa dissertação
são: a definição de uma família bem formalizada de provadores de teoremas automáticos,
que podem trabalhar com sentenças especificadas em lógica horn ou em lógica de primeira
ordem, a extensão de CHR como uma linguagem modular de propósito geral, a melhor
estruturação de bases conhecimentos e até o uso em conjunto de bases heterogêneas,
a definição de uma linguagem para a fácil e direta estruturação de dados por meio de
componentes, dentre outras
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[en] A LOGIC PROGRAMMING ENVIRONMENT SUPPORTED BY THE SEMANTIC GAMES TESTER / [pt] UM AMBIENTE DE PROGRAMAÇÃO LÓGICA SUPORTADO POR UM PROVADOR SEMÂNTICOALBERTO JOSE FONSECA ADEODATO 11 December 2006 (has links)
[pt] Haeusler e Pequeno desenvolveram um método de prova de
teoremas baseado em jogos semânticos introduzidos por
Hintikka. Posteriormente Rios desenvolveu o programa
PROGRAME que implementa este método. Este trabalho
descreve um ambiente de programação lógica desenvolvido
com a finalidade de oferecer ao usuário facilidades de
programação lógica suportada pelo provador PROGRAME. O
ambiente foi idealizado o mais próximo possível nos
ambientes PROLOG, com a facilidade adicional de permitir
que no código do programa a ele submetido sejam utilizados
indiferentemente goals a serem provados neste ambiente ou
PROGRAME. / [en] Haeusler and Pequeno developed a theorem proving method
based on semântica games introduced by Hintikka. Later,
Rios developed the program PROGRAME witch implements this
method. Our work describes a logic programming environment
developed with the aim of offering the user logic
programming facilities supported by the PROGRAME prover.
The programming environment was chosen to be PROLOG-like
with additional facility of permiting that a given goal
can b proved both by or environment and by the PROGRAME
prover
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