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|Title: ||Stochastic multiple context-free grammar for RNA pseudoknot modeling|
|Authors: ||Kato, Yuki|
|Issue Date: ||Mar-2006|
|Publisher: ||Nara Institute of Science and Technology|
|Series/Report no.: ||Information Science Technical Report ~ TR2006002|
|Abstract: ||Several formal grammars have been proposed for modeling RNA secondary structure including substructure called pseudoknot. In this paper, we focus on multiple context-free grammars (MCFGs), which are natural extension of context-free grammars and can represent pseudoknots, and extend a specific subclass of MCFGs to a probabilistic model called a stochastic MCFG (SMCFG). We design a polynomial time parsing algorithm for finding the most probable derivation tree and a probability parameter estimation method based on the EM (expectation maximization) algorithm. Also, we show some experimental results of RNA secondary structure prediction with pseudoknots using SMCFG algorithm.|
|Text Version: ||author|
|Appears in Collections:||テクニカルレポート / Technical Report|
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