Algebraic Dynamic Programming on Trees

Where string grammars describe how to generate and parse strings, tree grammars describe how to generate and parse trees. We show how to extend generalized algebraic dynamic programming to tree grammars. The resulting dynamic programming algorithms are efficient and provide the complete feature set...

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Vydáno v:Algorithms Ročník 10; číslo 4; s. 135
Hlavní autoři: Berkemer, Sarah, Höner zu Siederdissen, Christian, Stadler, Peter
Médium: Journal Article
Jazyk:angličtina
Vydáno: Basel MDPI AG 01.12.2017
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ISSN:1999-4893, 1999-4893
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Abstract Where string grammars describe how to generate and parse strings, tree grammars describe how to generate and parse trees. We show how to extend generalized algebraic dynamic programming to tree grammars. The resulting dynamic programming algorithms are efficient and provide the complete feature set available to string grammars, including automatic generation of outside parsers and algebra products for efficient backtracking. The complete parsing infrastructure is available as an embedded domain-specific language in Haskell. In addition to the formal framework, we provide implementations for both tree alignment and tree editing. Both algorithms are in active use in, among others, the area of bioinformatics, where optimization problems on trees are of considerable practical importance. This framework and the accompanying algorithms provide a beneficial starting point for developing complex grammars with tree- and forest-based inputs.
AbstractList Where string grammars describe how to generate and parse strings, tree grammars describe how to generate and parse trees. We show how to extend generalized algebraic dynamic programming to tree grammars. The resulting dynamic programming algorithms are efficient and provide the complete feature set available to string grammars, including automatic generation of outside parsers and algebra products for efficient backtracking. The complete parsing infrastructure is available as an embedded domain-specific language in Haskell. In addition to the formal framework, we provide implementations for both tree alignment and tree editing. Both algorithms are in active use in, among others, the area of bioinformatics, where optimization problems on trees are of considerable practical importance. This framework and the accompanying algorithms provide a beneficial starting point for developing complex grammars with tree- and forest-based inputs.
Author Höner zu Siederdissen, Christian
Stadler, Peter
Berkemer, Sarah
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  surname: Stadler
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CitedBy_id crossref_primary_10_1186_s13015_023_00229_z
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  article-title: Minimum mutation fits to a given tree
  publication-title: Biometrics
  doi: 10.2307/2529676
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Snippet Where string grammars describe how to generate and parse strings, tree grammars describe how to generate and parse trees. We show how to extend generalized...
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StartPage 135
SubjectTerms Algebra
Algorithms
Bioinformatics
Domain specific languages
Dynamic programming
Forest management
formal language
Grammars
Parsers
Strings
tree alignment
tree editing
Trees
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Title Algebraic Dynamic Programming on Trees
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https://doaj.org/article/716dec7cc2394d7986e8c73cab57f317
Volume 10
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