Formal grammars for estimating partition functions of double-stranded chain molecules

Authors:
David Chiang;Aravind K. Joshi
Affiliations:
Philadelphia, PA;Philadelphia, PA
Venue:
HLT '02 Proceedings of the second international conference on Human Language Technology Research
Year:
2002

Citing 3
Cited 0

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Abstract

This paper looks at an algorithm due to Chen and Dill for estimating the partition functions of a restricted subclass of double-stranded polymers, and shows how it can be translated into a context-free grammar, so that their algorithm reduces to a variant of the CKY parsing algorithm. Our formulation clarifies the structure of Chen and Dill's algorithm, leading to revised complexity analyses and an optimization in one case, and lays a formal foundation for generalizing this method to more complex cases by the use of grammars beyond context-free power such as tree adjoining grammars.