Automata in Text Pattern Matching

Lecturer:

Tutor:

Supervisor:

Department of Theoretical Computer Science

Synopsis:

Students learn algorithms for searching in texts using finite automata. They become acquainted with the searching problems taxonomy and learn the principles of automata constructions for solving these problems. They will be able to apply the gained knowledge in the design of applications required text pattern matching, such as data streaming, DNA sequencing, etc.

Requirements:

Basics of formal language theory, language translations, and finite automata.

Syllabus of lectures:

1. Text systems, basic notions, taxonomy of text pattern matching problems.

2. Forward pattern matching, models of searching algorithms.

3. Nondeterministic search automata.

4. Simulation of nondeterministic search automata, bit parallelism, dynamic programming.

5. Prefix and suffix automata.

6. Factor automata, factor oracle, suffix oracle.

7. Borders and periods in texts.

8. Repetitions in texts, exact and approximate.

9. Simulation of nondeterministic search automata, fail function, the MP a KMP algorithms.

10. Simulation of nondeterministic search automata, fail function, the AC algorithm.

11. Backward single pattern matching, the BM algorithm, the CW algorithm.

12. State-of-the-art in text pattern matching (e.g., matching in a multidimensional text, searching in a compressed text).

Syllabus of tutorials:

1. Finite automata, basic operations with finite automata. Taxonomy of pattern matching problems for exact and approximate matching.

2. Nondeterministic search finite automata. Deterministic search finite automata and their complexity.

3. Simulation of nondeterministic search finite automata, bit parallelism, dynamic programming, MP & KMP algorithms, AC algorithm.

4. Construction of prefix and suffix automata. Construction of factor automata, factor & suffix oracles.

5. Computation of borders and periods of text. Searching exact and approximate repetitions in text.

6. Backward pattern matching - BM & CW algorithms.

Study Objective:

The module deals with automata models of algorithms for text searching. The main topics are text pattern matching and repetitions. In both cases, both exact and inexact pattern matchings are considered. The fundamental formal tool for description of the algorithms is the finite automaton. The knowledge gained in this module can be applied in analysis and design of algorithms for text pattern matching.

Study materials:

1. Melichar, B., Holub, J., Polcar, T. ''Text searching algorithms''. Volume I and II, Lecture notes. Prague, CTU, 2008.

2. Melichar, B., et al. ''Text searching algorithms''. Seminars. Prague, CTU, 2008.

Note:

Further information:

No time-table has been prepared for this course

The course is a part of the following study plans:

• Knowledge Engineering, in Czech, Presented in Czech, for Students who Enrolled in 2015 (elective course)
• Master Informatics, Presented in Czech, Version for Students who Enrolled in 2015 (elective course)
• Knowledge Engineering, in Czech, Presented in Czech, Version 2016 and and 2017 (elective course)
• Computer Systems and Networks, Presented in Czech, Version 2016 to 2019 (elective course)
• Design and Programming of Embedded Systems, in Czech, Version 2016 to 2019 (elective course)
• Specialization Web and Software Engineering, in Czech, Version 2016 to 2019 (elective course)
• Specialization Software Engineering, in Czech, Version 2016 to 2019 (elective course)
• Specialization Web Engineering, Presented in Czech, Version 2016 to 2019 (elective course)
• Master Informatics, Presented in Czech, Version 2016 to 2019 (VO)
• Specialization System Programming, Presented in Czech, Version 2016 to 2019 (elective course)
• Specialization Computer Science, Presented in Czech, Version 2016-2017 (compulsory course of the branch)
• Knowledge Engineering, in Czech, Presented in Czech, Version 2018 to 2019 (elective course)