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4th International Conference on Smart and Sustainable Technologies (SpliTech)

作者： Markic, Ivan Stula, Maja Zoric, Marija Cent Insurance Co Ltd Mostar Bosnia & Herceg Fac Elect Engn Mech Engn & Naval Architecture Spl Dept Elect & Comp Split Croatia

ISBN: (纸本)9789532900910

In this article we shortly present new string pattern matching algorithm. The algorithm uses novel technique for skipping unnecessary comparisons in pattern searching phase. The pattern searching is applied in almost all branches of science such as bioinformatics, information security, text mining, etc. In the context of continuous increase of data, efficient algorithms are necessary to ensure that one can find a pattern in a sequence in a fast and accurate manner. pattern searching solves the problem of finding a pattern exhibiting certain properties within a given sequence of symbols. Concept of the new algorithm presented in this article is based on a character index in a pattern, aiming at, but not limited to patterns in DNA sequences.

关键词： string pattern matching genome DNA biological data exact string matching

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Loop Grammars to Identify RNA Structural patterns 10

Loop Grammars to Identify RNA Structural Patterns

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12th International Joint Conference on Biomedical Engineering Systems and Technologies / 10th International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS)

作者： Quadrini, Michela Merelli, Emanuela Piergallini, Riccardo Univ Camerino Sch Sci & Technol Via Madonna Carceri 9 I-62032 Camerino Italy

ISBN: (纸本)9789897583537

The biological functions of an RNA molecule are largely determined by molecular configuration. Understanding the link between the structure and the biological functions has been considered one of the challenges in biology. In this study, we face the problem of identifying a given structural pattern into an RNA pseudoknotfree secondary structure. We introduce a context-free grammar, Loop Grammar, that formalizes the primary and secondary structure of an RNA molecule as a composition of loops. Such composition is expressed as to concatenation or nesting of the simplest structural elements, hairpins, generated during the folding process when a bond between two nonconsecutive nucleotides is established. Then, we formalize the concatenation and nesting on Fatgraphs, oriented surfaces with boundary, and we define a Surface Loop Grammar, whose algebraic expressions uniquely identify such surfaces associated with given RNA structures. The terms of the Loop Grammar allow us to face the problems of identifying substructures considering both the primary and secondary structures, while the strings generated by Surface Loop Grammar permit to identify a given structural pattern in a secondary structure in terms of relations among hairpins. Both use the string pattern matching.

关键词： RNA Secondary Structures Relations Hairpins string pattern matching

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In-place algorithms for exact and approximate shortest unique substring problems

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THEORETICAL COMPUTER SCIENCE 2017年 690卷 12-25页

作者： Hon, Wing-Kai Thankachan, Sharma V. Xu, Bojian Natl Tsing Hua Univ Dept Comp Sci Hsinchu 300 Taiwan Univ Cent Florida Dept Comp Sci Orlando FL 32816 USA Eastern Washington Univ Dept Comp Sci Cheney WA 99004 USA

We revisit the exact shortest unique substring (SUS) finding problem, and propose its approximate version where mismatches are allowed, due to its applications in subfields such as computational biology, We design a generic in-place framework that fits to solve both the exact and approximate k-mismatch SUS finding, using the minimum 2n memory words, each of inverted right perpendicular log(2)(n)inverted left perpendicular bits, plus n bytes space, where n is the input string size. By using the in-place framework, we can find the exact and approximate k-mismatch SUS for every string position using a total of O(n) and O(n(2)) time, respectively, regardless of the value of k. Our framework does not involve any compressed or succinct data structures and thus is practical and easy to implement. Experimental study shows that the peak memory usage of our proposal is consistently 9n bytes for any string of size n, validating the claim that our solution is in-place. Further, our proposal uses much less memory and is much faster than the currently best work that has implementation for exact SUS finding. (C) 2017 Elsevier B.V. All rights reserved.

关键词： string pattern matching Shortest unique substring In-place algorithms

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Concluding pattern of Web Page Based on string pattern matching

Concluding Pattern of Web Page Based on String Pattern Match...

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International Conference on Web Information Systems and Mining (WISM 2011)

作者： Cai, Yiqing Wang, Xinjun Lu, Chunsheng Yan, Zhongmin Peng, Zhaohui Shandong Univ Sch Comp Sci & Technol Jinan 250100 Peoples R China Informat Ctr Minist Human Resources & Social Secu Beijing Peoples R China

ISBN: (纸本)9783642239816

Presently, each Web site has its own topics and formats to arrange the page structure and present information. Therefore, there is a great need for value-added service that extracts information from multiple sources. Data extraction from HTML is usually performed by software modules called wrappers. In many studies of constructing wrapper, concluding the pattern of the Web site is a importance task in the beginning. This paper studies the problem of concluding pattern from a Web page that contains several nested structure and repeated structure. In our method, the algorithm bases on string pattern matching can discover the nested structure and the repeated structure in a Web page. Then a regular expression will be generated as the pattern of the Web site.

关键词： hierarchical preorder traversal string pattern of Web site string pattern matching nested structure the repeated structure concluding pattern

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An In-place Framework for Exact and Approximate Shortest Unique Substring Queries 26th

An In-place Framework for Exact and Approximate Shortest Uni...

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26th International Symposium on Algorithms and Computation (ISAAC)

作者： Hon, Wing-Kai Thankachan, Sharma V. Xu, Bojian Natl Tsing Hua Univ Dept Comp Sci Hsinchu 30043 Taiwan Georgia Inst Technol Sch Computat Sci & Engn Atlanta GA 30332 USA Eastern Washington Univ Dept Comp Sci Cheney WA 99004 USA

ISBN: (纸本)9783662489710;9783662489703

关键词： string pattern matching Shortest unique substring In-place algorithms

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Inverted Lists string pattern matching

Inverted Lists String Pattern Matching

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2nd IEEE International Conference on Computer Science and Information Technology

作者： Khancome, Chouvalit Boonjing, Veera KMITL Fac Sci Dept Math & Comp Sci Ladkrabang Bankok Thailand

ISBN: (纸本)9781424445189

This paper presents two algorithms of string pattern matching. These algorithms employ the inverted lists to accommodate the string pattern to be searched for. The first solution scans the text in a single pass for all occurrences of string pattern. The second solution, which improves the first one, takes the comparison times equal to the length of pattern plus the number of comparisons that lead to be mismatched.

关键词： string pattern matching inverted lists (IVL) inverted index

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AN IMPROVED PREFIX-FREE REGULAR-EXPRESSION matching

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INTERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTER SCIENCE 2013年第5期24卷 679-687页

作者： Han, Yo-Sub Yonsei Univ Dept Comp Sci Seoul 120794 South Korea

We revisit the regular-expression matching problem with respect to prefix-freeness of the pattern. It is known that a prefix-free pattern gives only a linear number of matching substrings in the size of an input text. We improve the previous algorithm and suggest an efficient algorithm that finds all pairs (start, end) of start and end positions of all matching substrings with a singles can of the input when the pattern is a prefix-free regular expression.

关键词： string pattern matching regular-expression matching prefix-free regular expressions

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IE Internet Information Forensics Technology in Unallocated Disk Space

IE Internet Information Forensics Technology in Unallocated ...

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1st International Symposium on Computer Network and Multimedia Technology

作者： Chen Haiping Luo Delin Gao Qinquan Qian Zhicong Wu Shunxiang Xiamen Univ Dept Automat Xiamen Peoples R China

ISBN: (纸本)9781424452729

This paper presents the main content of IE (Internet Explore) Internet record data, what fields are of forensic interest and what information the available tools can extract. It shows that remnants may still be found in unallocated disk space even the IE Internet record normal file data is deleted. This paper proposes a string pattern matching algorithm to find IE Internet record data in unallocated space based on known internal record structures. The system developed can recover deleted IE records and it may be an approach to obtain evidence in unallocated disk space.

关键词： forensics IE Internet records string pattern matching

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A pre-processing algorithm for string pattern matching

A pre-processing algorithm for string pattern matching

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International Conference on Algorithmic Mathematics and Computer Science (AMCS 05)

作者： Boxer, L Niagara Univ Dept Comp & Informat Sci Niagara Univ NY 14109 USA

We introduce an algorithm that can be run in sublinear time and has, under certain circumstances, a high probability of greatly reducing the amount of data from the text that must be considered in order to solve strin... 详细信息

ISBN: (纸本)1932415637

关键词： string pattern matching analysis of algorithms

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Efficient implementation of Aho-Corasick pattern matching automata using Unicode

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SOFTWARE-PRACTICE & EXPERIENCE 2007年第6期37卷 669-690页

作者： Nieminen, Janne Kilpelainen, Pekka Univ Kuopio Dept Comp Sci FI-70211 Kuopio Finland

We study different efficient implementations of an Aho-Corasick pattern matching automaton when searching for patterns in Unicode text. Much of the previous research has been based on the assumption of a relatively small alphabet, for example the 7-bit ASCII. Our aim is to examine the differences in performance arising from the use of a large alphabet, such as Unicode that is widely used today. The main concern is the representation of the transition function of the pattern matching automaton. We examine and compare array, linked list, hashing, balanced tree, perfect hashing, hybrid, triple-array, and doublearray representations. For perfect hashing, we present an algorithm that constructs the hash tables in expected linear time and linear space. We implement the Aho-Corasick automaton in Java using the different transition function representations, and we evaluate their performance. Triple-array and doublearray performed best in our experiments, with perfect hashing, hashing, and balanced tree coming next. We discovered that the array implementation has a slow preprocessing time when using the Unicode alphabet. It seems that the use of a large alphabet can slow down the preprocessing time of the automaton considerably depending on the transition function representation used. Copyright (C) 2006 John Wiley & Sons, Ltd.

关键词： string pattern matching Aho-Corasick implementation transition function

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