Reducing the worst case running times of a family of RNA and CFG problems, using Valiant's approach

Authors:
Shay Zakov;Dekel Tsur;Michal Ziv-Ukelson
Affiliations:
Department of Computer Science, Ben-Gurion University of the Negev, Israel;Department of Computer Science, Ben-Gurion University of the Negev, Israel;Department of Computer Science, Ben-Gurion University of the Negev, Israel
Venue:
WABI'10 Proceedings of the 10th international conference on Algorithms in bioinformatics
Year:
2010

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Abstract

We study Valiant's classical algorithm for Context Free Grammar recognition in sub-cubic time, and extract features that are common to problems on which Valiant's approach can be applied. Based on this, we describe several problem templates, and formulate generic algorithms that use Valiant's technique and can be applied to all problems which abide by these templates. These algorithms obtain new worst case running time bounds for a large family of important problems within the world of RNA Secondary Structures and Context Free Grammars.