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An Earley-style Parser for Solving the RNA-RNA Interaction Problem

Jun 2010 (Written: Jun 2010)

Sebastian Wild:

Bachelor’s Thesis
Department of Computer Science, Technische Universität Kaiserslautern

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In my bachelor’s thesis I extended an RNA secondary-structure prediction method based on stochastic context-free grammars to predicting the joint structure of pairs of interacting RNA molecules.

Technically, I wrote an efficient stochastic parser jackRIP in C++ that takes an arbitrary (stochastic) context-free grammar and determines the most likely derivation tree for a word, or the inside and outside probabilities. (The latter are a generalization of forward and backward probabilities know from hidden Markov models.)

I also worked through parsing and formal-language literature, in particular mildly context-sensitive formalisms. My alternative definition of multiple context-free grammars (see Section 2.8) makes this formalism more convenient to use to describe combinatorial classes.