Thesis Details

Watson-Crick Models for Formal Language Processing

Master's Thesis Student: Hammer Jan Academic Year: 2021/2022 Supervisor: Křivka Zbyněk, Ing., Ph.D.
Czech title
Watson-Crick modely pro zpracování formálních jazyků

This work focuses on Watson-Crick languages inspired by DNA computing, their models and algorithms of deciding the language membership. It analyzes a recently introduced algorithm called WK-CYK and introduces a state space search algorithm which is based on regular Breath-first search but uses a number of optimizations and heuristics to be efficient in practical use and able to analyze inputs of greater lengths. 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 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 a potential to be a good tool for practical Watson-Crick membership testing and is a good basis to further build on and further improve the efficiency of the algorithm.


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

Degree Programme
defended, grade A
22 June 2022
Burget Radek, doc. Ing., Ph.D. (DIFS FIT BUT), předseda
Bartík Vladimír, Ing., Ph.D. (DIFS FIT BUT), člen
Grégr Matěj, Ing., Ph.D. (DIFS FIT BUT), člen
Matoušek Petr, doc. Ing., Ph.D., M.A. (DIFS FIT BUT), člen
Meduna Alexander, prof. RNDr., CSc. (DIFS FIT BUT), člen
Polčák Libor, Ing., Ph.D. (DIFS FIT BUT), člen
HAMMER, Jan. Watson-Crick Models for Formal Language Processing. Brno, 2022. Master's Thesis. Brno University of Technology, Faculty of Information Technology. 2022-06-22. Supervised by Křivka Zbyněk. Available from:
    author = "Jan Hammer",
    type = "Master's thesis",
    title = "Watson-Crick Models for Formal Language Processing",
    school = "Brno University of Technology, Faculty of Information Technology",
    year = 2022,
    location = "Brno, CZ",
    language = "english",
    url = ""
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