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Extending Stochastic Context-Free Grammars for an Application in Bioinformatics

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Language and Automata Theory and Applications (LATA 2010)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 6031))

Abstract

We extend stochastic context-free grammars such that the probability of applying a production can depend on the length of the subword that is generated from the application and show that existing algorithms for training and determining the most probable parse tree can easily be adapted to the extended model without losses in performance. Furthermore we show that the extended model is suited to improve the quality of predictions of RNA secondary structures.

The extended model may also be applied to other fields where SCFGs are used like natural language processing. Additionally some interesting questions in the field of formal languages arise from it.

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Authors and Affiliations

  1. Department of Computer Sciences, University of Kaiserslautern, Gottlieb-Daimler-Straße, D-67663, Kaiserslautern, Germany

    Frank Weinberg & Markus E. Nebel

Authors
  1. Frank Weinberg
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  2. Markus E. Nebel
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Editor information

Editors and Affiliations

  1. Research Group on Mathematical Linguistics, Universitat Rovira i Virgili, Avinguda Catalunya, 35, 43002, Tarragona, Spain

    Adrian-Horia Dediu  & Carlos Martín-Vide  & 

  2. Fachbereich IV - Informatik, Universität Trier, Campus II, Behringstraße, 54286, Trier, Germany

    Henning Fernau

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Weinberg, F., Nebel, M.E. (2010). Extending Stochastic Context-Free Grammars for an Application in Bioinformatics. In: Dediu, AH., Fernau, H., Martín-Vide, C. (eds) Language and Automata Theory and Applications. LATA 2010. Lecture Notes in Computer Science, vol 6031. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-13089-2_49

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  • DOI: https://doi.org/10.1007/978-3-642-13089-2_49

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-13088-5

  • Online ISBN: 978-3-642-13089-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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