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

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216305%3A26230%2F22%3APU145365" target="_blank" >RIV/00216305:26230/22:PU145365 - isvavai.cz</a>

Výsledek na webu

<a href="http://eptcs.web.cse.unsw.edu.au/paper.cgi?NCMA2022.7" target="_blank" >http://eptcs.web.cse.unsw.edu.au/paper.cgi?NCMA2022.7</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.4204/EPTCS.367.7" target="_blank" >10.4204/EPTCS.367.7</a>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

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

Popis výsledku anglicky

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.

Druh

D - Stať ve sborníku

CEP obor

—

OECD FORD obor

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Projekt

<a href="/cs/project/LL1908" target="_blank" >LL1908: Efektivní konečné automaty pro automatické usuzování</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>S - Specificky vyzkum na vysokych skolach

Rok uplatnění

2022

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název statě ve sborníku

Proceedings 12th International Workshop on Non-Classical Models of Automata and Applications

ISBN

—

ISSN

2075-2180

e-ISSN

—

Počet stran výsledku

24

Strana od-do

88-111

Název nakladatele

School of Computer Science and Engineering, University of New South Wales

Místo vydání

Debrecen

Místo konání akce

Debrecen

Datum konání akce

26. 8. 2022

Typ akce podle státní příslušnosti

WRD - Celosvětová akce

Kód UT WoS článku

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