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SANTOS, Gilmar Pereira. Earley’s syntactic analyzer for adaptive context-free grammars and its application in the characterization of RNA families with pseudoknot. 2018. 172 p. Dissertation (Master of Science) – School of Arts, Sciences and Humanities, University of São Paulo, São Paulo, 2018. The theory of formal languages is widely used to solve problems of different natures as it can deal with artificial and natural languages. The grammars, formalisms able to synthesize languages, can also be used in pattern recognition problems due to the ability to model the language components hierarchies, decomposing patterns in substructures. Based on this idea, the framework GrammarLab was designed to facilitate the work involved in implementing, generating and testing different grammar based sequence classifiers, providing regular and context free grammar in the prior version. However, some problems need a formalism that can be found only in higher classes of grammars in the Chomsky hierarchy. The problem of using a higher class of grammar is the high computational time complexity for parsing. While the problem of recognizing sequences using regular and context free grammars is solved at polynomial time, the same problem in general case is NP-Complete for context sensitive grammars and undecidable for unrestricted grammars. Nevertheless, the use of adaptive methods allows a grammar to alter the set of production rules during sentences generation, including context sensitivity even to grammars that were designed to be context free, without increasing the polynomial parsing complexity. This work was focused in improving the GrammarLab framework by including the ability to deal with adaptive methods and in the creation of an adaptive version of Earley’s algorithm. To test the solution in real world problems, it was conducted a preliminary study of the use of the framework in characterizing RNA functional families with conserved secondary structure, including pseudoknots. The pseudoknot pattern, represented by crossing dependences among RNA sequence nucleotides, is an example of context dependence, so it is a good test case for the use of a model that consider adaptability in the constitution. The obtained results with two families of RNAs with pseudoknots show that the approach is promising.

Analisador sintático de Earley para gramáticas livres de contexto adaptativas e sua aplicação na caracterização de famílias de RNAs com pseudonós