Publication Details

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

HAMMER, J.; KŘIVKA, Z. Practical Aspects of Membership Problem of Watson-Crick Context-free Grammars. In Proceedings 12th International Workshop on Non-Classical Models of Automata and Applications. Electronic Proceedings in Theoretical Computer Science, EPTCS. Debrecen: School of Computer Science and Engineering, University of New South Wales, 2022. p. 88-111. ISSN: 2075-2180.
Czech title
Praktické aspekty problému členství Watson-Crick bezkontextových gramatik
Type
conference paper
Language
English
Authors
Hammer Jan, Ing.
Křivka Zbyněk, Ing., Ph.D. (DIFS)
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, EPTCS, 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
DOI
10.4204/EPTCS.367.7
UT WoS
001047943700008
EID Scopus
2-s2.0-85137611300
BibTeX 
@inproceedings{BUT178926,
  author="Jan {Hammer} and Zbyněk {Křivka}",
  title="Practical Aspects of Membership Problem of Watson-Crick Context-free Grammars",
  booktitle="Proceedings 12th International Workshop on Non-Classical Models of Automata and Applications",
  year="2022",
  journal="Electronic Proceedings in Theoretical Computer Science, EPTCS",
  number="367",
  pages="88--111",
  publisher="School of Computer Science and Engineering, University of New South Wales",
  address="Debrecen",
  doi="10.4204/EPTCS.367.7",
  issn="2075-2180",
  url="http://eptcs.web.cse.unsw.edu.au/paper.cgi?NCMA2022.7"
}
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