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http://hdl.handle.net/10061/3225
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| Title: | Stochastic multiple context-free grammar for RNA pseudoknot modeling |
| Authors: | Kato, Yuki
Seki, Hiroyuki
カトウ, ユウキ
セキ, ヒロユキ
加藤, 有己
関, 浩之 |
| 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. |
| URI: | http://hdl.handle.net/10061/3225 |
| URI: | http://library.naist.jp/mylimedio/dllimedio/show.cgi?bookid=90078 |
| Fulltext: | http://library.naist.jp/mylimedio/dllimedio/show.cgi?bookid=90078 |
| ISSN: | 0919-9527 |
| Text Version: | author |
| Appears in Collections: | テクニカルレポート / Technical Report
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