Efficient Text Pattern Matching

Lecturer:

Jan Holub (gar.)

Tutor:

Jakub Jaroš

Supervisor:

Department of Computer Science

Synopsis:

Students get knowledge of efficient algorithms for text pattern matching. They learn to use so called succinct data structures that are efficient in both access time and memory complexity. They will be able to use the knowledge in design of applications that utilize pattern matching.

Requirements:

Syllabus of lectures:

1. Introduction, basic definitions.

2. Border array and exact pattern matching.

3. Exact pattern matching algorithms.

4. FFT in pattern matching.

5. Text full index: Suffix array.

6. Text full index: Suffix tree, LCP construction.

7. Text full index: Factor, suffix automata, on-line construction.

8. Succinct data structure: rank & select.

9. Succinct data structure: wavelet tree.

10. FM-Index.

11. Dictionary representation, spell checking.

12. Approximate pattern matching.

13. Pattern matching in bioinformatcs and musicology.

Syllabus of tutorials:

Study Objective:

The pattern matching is a key task in most applications. Its importance is increasing with enlargement of the mass of information collected. Efficient algorithms and data structures for pattern matching are therefore crucial in information processing, but also in other fields like security (e.g., intrusion detection, virus scans). This module provides an extensive overview of such algorithms and data structures.

Study materials:

1. Crochemore, C., Rytter, W. ''Jewels of Stringology''. World Scientific Publishing Company, 2003. ISBN 9810248970.

2. Navarro, G., Raffinot, M. ''Flexible Pattern Matching in Strings''. Cambridge University Press, 2008. ISBN 0521039932.

Note:

Time-table for winter 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	roomT9:347 Holub J. 09:15–10:45 (lecture parallel1) Dejvice NBFIT učebnaroomT9:347 Jaroš J. 12:45–14:15 ODD WEEK (lecture parallel1 parallel nr.101) Dejvice NBFIT učebna
Tue
Fri
Thu
Fri

Time-table for summer semester 2011/2012:

Time-table is not available yet

The course is a part of the following study plans:

• Branch System Programming, Version for Students who Enrolled in 2010, Presented in Czech (compulsory course of the branch)
• Branch System Programming, Presented in Czech, Version for Students who Enrolled in 2011 (compulsory course of the branch)
• Branch System Programming, Presented in Czech, Version for Students who Enrolled in 2012 (compulsory course of the branch)