The Application of Grammar Space Entropy in RNA Secondary Structure Modeling
A. Manzourolajdad National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
Abstract
Stochastic context-free grammars (SCFGs) have been used in RNA secondary structure modeling. An SCFG consists of a set of grammar rules with a probability for each rule. Given a grammar design, finding the best set of probabilities that yield optimum performance can be challenging. Although current expectation maximization (EM) maximum likelihood (ML)-based model training approaches have been effective, there is no guarantee that they provide parameter sets for the grammar to have optimum performance. ...
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