The 2-Interval Pattern Matching Problems and Its Application to ncRNA Scanning

2009 ◽  
pp. 79-89
Author(s):  
Thomas K. F. Wong ◽  
S. M. Yiu ◽  
T. W. Lam ◽  
Wing-Kin Sung
Keyword(s):  
Pattern Matching ◽  
Matching Problems

scholarly journals A Parameterized Study of Maximum Generalized Pattern Matching Problems

Algorithmica ◽  
2015 ◽  
Vol 75 (1) ◽  
pp. 1-26 ◽  
Author(s):  
Sebastian Ordyniak ◽  
Alexandru Popa
Keyword(s):  
Pattern Matching ◽  
Matching Problems ◽  
Generalized Pattern Matching

A Criteria Transformation Approach to Pattern Matching based on Non-Linear Parameter Optimization

2015 ◽  
Vol 24 (2) ◽  
pp. 249-263 ◽  
Author(s):  
Christian John ◽  
Dietmar Tutsch ◽  
Thomas Lepich ◽  
Bernard Beitz ◽  
Reinhard Möller
Keyword(s):  
Pattern Matching ◽  
Parameter Optimization ◽  
Optimization Procedure ◽  
Optimization Method ◽  
Object Oriented Programming ◽  
Information Modeling ◽  
Linear Parameter ◽  
Matching Problems ◽  
Wide Range ◽  
Non Linear

AbstractThis paper presents a concept for pattern matching based on a parameter optimization system for approximative numerical calculation of some parameter combination under soft and hard constraints. The concept uses a non-linear parameter optimization method with an iterative variation of parameters. The paper focuses on the information modeling process to migrate problem-domain specific criteria into optimization-compatible objects suitable for a standardized parameter optimization procedure. A step-by-step transformation process is presented and implemented in object-oriented programming: classes and interfaces. The method is applicable to a wide range of pattern-matching problems due to its flexibility and extensibility.

A Fast Engine for Multi-String Pattern Matching

2017 ◽  
Vol 31 (12) ◽  
pp. 1750039 ◽  
Author(s):  
Zhan Peng ◽  
Yuping Wang ◽  
Wei Yue
Keyword(s):  
Data Structure ◽  
Pattern Matching ◽  
Large Scale ◽  
String Matching ◽  
Memory Consumption ◽  
Matching Problems ◽  
Text String ◽  
Tree Node ◽  
String Pattern ◽  
Better Than

Multi-string matching (MSM) is a core technique searching a text string for all occurrences of some string patterns. It is widely used in many applications. However, as the number of string patterns increases, most of the existing algorithms suffer from two issues: the long matching time, and the high memory consumption. To address these issues, in this paper, a fast matching engine is proposed for large-scale string matching problems. Our engine includes a filter module and a verification module. The filter module is based on several bitmaps which are responsible for quickly filtering out the invalid positions in the text, while for each potential matched position, the verification module confirms true pattern occurrence. In particular, we design a compact data structure called Adaptive Matching Tree (AMT) for the verification module, in which each tree node only saves some pattern fragments of the whole pattern set and the inner structure of each tree node is chosen adaptively according to the features of the corresponding pattern fragments. This makes the engine time and space efficient. The experiments indicate that, our matching engine performs better than the compared algorithms, especially for large pattern sets.

Research on an Single Pattern Matching Algorithm

2012 ◽  
Vol 433-440 ◽  
pp. 4468-4474
Author(s):  
Qiang Zheng
Keyword(s):  
Pattern Matching ◽  
High Performance ◽  
String Matching ◽  
Matching Algorithm ◽  
Matching Problems ◽  
Cross Border ◽  
Protection Method ◽  
Single Pattern ◽  
Low Efficiency ◽  
The Cost

The design of exact single pattern string matching algorithm with high performance is the basis of all string matching problems. To overcome the defects of low efficiency of pattern matching, this paper improves one of the fastest exact single pattern matching algorithms known on English text, which is SBNDM2。The simplest form of the BNDM core loop is obtained, in which there are only 5 instructions per-character read by amending the relationship between position in the pattern and bit in the bit mask. And a cross-border protection method is added to the algorithm in order to reduce the cost of cross-border inspection. Two algorithms named S2BNDM and S2BNDM′ are presented. The experimental results indicate that both S2BNDM and S2BNDM′are faster than SBNDM2 in any case.

scholarly journals A Note on Linear Time Simulation of Deterministic Two-Way Pushdown Automata

1977 ◽  
Vol 6 (75) ◽  
Author(s):  
Neil D. Jones
Keyword(s):  
Pattern Matching ◽  
Data Structures ◽  
Linear Time ◽  
Random Access ◽  
Simulation Algorithm ◽  
Pushdown Automaton ◽  
Matching Problems ◽  
Time Result ◽  
Time Simulation ◽  
Pushdown Automata

<p>Cook has shown that any deterministic two-way pushdown automaton could be simulated by a uniform-cost random access machine in time O(n) for inputs of length n. The result was of interest because such a machine is a natural model for a variety of backtracking algorithms, particularly as used in pattern matching problems. The linear time result was surprising because of the fact that such machines may run as many as 2n steps before halting; similar problems with 'combinatorial explosions' are well known to occur in applications of backtracking. Cook's result inspired the development of a number of efficient pattern matching algorithms.</p><p>However, it is impractical to use Cook's algorithm directly to do pattern matching, since it involves a large constant time factor and much storage. The purpose of this note is to present an alternate, simpler simulation algorithm which involves consideration only of the configurations actually reached by the automaton. It can be expected to run faster and use less storage (depending on the data structures used), thus bringing Cook's result a step closer to practical utility.</p>

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