Extending stochastic context-free grammars for an application in bioinformatics

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. © 2010 Springer-Verlag Berlin Heidelberg.