Automata in Text Pattern Matching

Lecturer:

Bořivoj Melichar (gar.)

Tutor:

Ondřej Guth

Supervisor:

Department of 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:

Time-table for winter semester 2011/2012:

Time-table is not available yet

Time-table for summer semester 2011/2012:

	06:00–08:0008:00–10:0010:00–12:0012:00–14:0014:00–16:0016:00–18:0018:00–20:0020:00–22:0022:00–24:00
Mon
Tue	roomT9:344 Melichar B. 11:00–12:30 (lecture parallel1) Dejvice NBFIT ucebna
Fri
Thu
Fri	roomT9:302 Guth O. 11:00–12:30 ODD WEEK (lecture parallel1 parallel nr.101) Dejvice NBFIT učebna

The course is a part of the following study plans:

• Computer Science, Presented in English, Version for Students, who Enrolled in 2010 and 2011 (compulsory course of the branch)
• Master Informatics, Presented in English - Version for Students who Enrolled in 2010 (VO)
• Master Informatics, Presented in English - Version for Students who Enrolled in 2011 (VO)
• Master Informatics, Presented in English - Version for Students who Enrolled in 2012 (VO)
• Computer Science, Presented in English - Version for Students who Enrolled in 2012 (compulsory course of the branch)