Publication Details

Practical Aspects of Membership Problem of Watson-Crick Context-free Grammars

HAMMER Jan and KŘIVKA Zbyněk. Practical Aspects of Membership Problem of Watson-Crick Context-free Grammars. In: Proceedings 12th International Workshop on Non-Classical Models of Automata and Applications . Debrecen: School of Computer Science and Engineering, University of New South Wales, 2022, pp. 88-111. ISSN 2075-2180. Available from: http://eptcs.web.cse.unsw.edu.au/paper.cgi?NCMA2022.7
Czech title
Praktické aspekty problému členství Watson-Crick bezkontextových gramatik
Type
conference paper
Language
english
Authors
Hammer Jan, Ing. (FIT BUT)
Křivka Zbyněk, Ing., Ph.D. (DIFS FIT BUT)
URL
Keywords

Watson-Crick languages, DNA computing, formal grammars, membership problem, state space search

Abstract

This paper focuses on Watson-Crick languages inspired by DNA computing, their models, and algorithms for deciding the language membership. It analyzes a recently introduced algorithm called WK-CYK and introduces a state space search algorithm that is based on regular Breadth-first search but uses a number of optimizations and heuristics to be efficient in practical use and able to analyze longer inputs. The key parts are the heuristics for pruning the state space (detecting dead ends) and heuristics for choosing the most promising branches to continue the search.

These two algorithms have been tested with 20 different Watson-Crick grammars (40 including their Chomsky normal form versions). While WK-CYK is able to decide the language membership in a reasonable time for inputs of the length of roughly 30-50 symbols and its performance is very consistent for all kinds of grammars and inputs, the state space search is usually (89-98 % of cases) more efficient and able to do the computation for inputs with lengths of hundreds or even thousands of symbols. Thus, the state space search has the potential to be a good tool for practical Watson-Crick membership testing and is a good basis for improvement the efficiency of the algorithm in the future.

Published
2022
Pages
88-111
Journal
Electronic Proceedings in Theoretical Computer Science, no. 367, ISSN 2075-2180
Proceedings
Proceedings 12th International Workshop on Non-Classical Models of Automata and Applications
Conference
12th International Workshop on Non-Classical Models of Automata and Applications, Debrecen, HU
Publisher
School of Computer Science and Engineering, University of New South Wales
Place
Debrecen, HU
DOI
10.4204/EPTCS.367.7
EID Scopus
2-s2.0-85137611300
BibTeX 
@INPROCEEDINGS{FITPUB12770,
   author = "Jan Hammer and Zbyn\v{e}k K\v{r}ivka",
   title = "Practical Aspects of Membership Problem of Watson-Crick Context-free Grammars",
   pages = "88--111",
   booktitle = "Proceedings 12th International Workshop on Non-Classical Models of Automata and Applications ",
   journal = "Electronic Proceedings in Theoretical Computer Science",
   number = 367,
   year = 2022,
   location = "Debrecen, HU",
   publisher = "School of Computer Science and Engineering, University of New South Wales",
   ISSN = "2075-2180",
   doi = "10.4204/EPTCS.367.7",
   language = "english",
   url = "https://www.fit.vut.cz/research/publication/12770"
}
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