• The Transactions of The Korean Institute of Electrical Engineers
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• v.66 no.6
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• pp.955-961
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• 2017

In this paper, we propose a parallel approximate string matching algorithm with k-mismatches for multiple fixed-length patterns (PMASM) in DNA sequences. PMASM is developed from parallel single pattern approximate string matching algorithms to effectively calculate the Hamming distances for multiple patterns with a fixed-length. In the preprocessing phase of PMASM, all target patterns are binary encoded and stored into a look-up memory. With each input character from the input string, the Hamming distances between a substring and all patterns can be updated at the same time based on the binary encoding information in the look-up memory. Moreover, PMASM adopts graphics processing units (GPUs) to process the data computations in parallel. This paper presents three kinds of PMASM implementation methods in GPUs: thread PMASM, block-thread PMASM, and shared-mem PMASM methods. The shared-mem PMASM method gives an example to effectively make use of the GPU parallel capacity. Moreover, it also exploits special features of the CUDA (Compute Unified Device Architecture) memory structure to optimize the performance. In the experiments with DNA sequences, the proposed PMASM on GPU is 385, 77, and 64 times faster than the traditional naive algorithm, the shift-add algorithm and the single thread PMASM implementation on CPU. With the same NVIDIA GPU model, the performance of the proposed approach is enhanced up to 44% and 21%, compared with the naive, and the shift-add algorithms.

• Proceedings of the Korean Information Science Society Conference
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• 2007.06c
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• pp.171-176
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• 2007

Parsing 작업의 결과인 Parse Tree 정보는 문장에 관한 구조적 정보를 가지고 있는 Tree 정보로 이 정보를 이용하여 정보 검색에 활용하는 알고리즘을 제안한다. 제안하는 알고리즘은 XML 기술과 스트링 매칭 기법을 이용하였으며, 사용한 스트링 매칭 기법은 Approximate String Matching 기법이다. Query 정보와 문서 정보를 Parsing하여 얻은 Parse Tree를 XML 형태의 정보로 변환한 후, 두 정보를 가지고 Approximate String Matching 기법을 적용하여 Query 정보와 문서 정보 간의 유사도를 계산한다. 제안하는 알고리즘의 장점은 구조 기반의 정보 검색 기능이 가능하고 비슷한 정보에 대한 검색 기능이 가능하며 비슷한 구조에 대한 검색 기능이 가능하다는 것이다.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.10 no.8
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• pp.1986-1992
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• 2009

A user often searches a data by inputting a variant such as the abbreviation or substring of a word, or a misspelled word. The simple approach to the searching for variants is to build a variants dictionary. However, it entails enormous cost and time and can not handle variants by misspelling. Approximate searching, searching by approximate string matching, is a good approach to the searching. A problem in the approach is that it cannot handle variants by abbreviations. This paper propose a method for searching various variants including abbreviations and misspelled words, by using the trie indexing. First, this paper shows a variant matching method with the calculation of path weighted-metric. In addition, it provides variant searching algorithm to reduce the search time.

• ETRI Journal
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• v.31 no.5
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• pp.545-553
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• 2009

String matching is a fundamental element of an important category of modern packet processing applications which involve scanning the content flowing through a network for thousands of strings at the line rate. To keep pace with high network speeds, specialized hardware-based solutions are needed which should be efficient enough to maintain scalability in terms of speed and the number of strings. In this paper, a novel architecture based upon a recently proposed data structure called the Bloomier filter is proposed which can successfully support scalability. The Bloomier filter is a compact data structure for encoding arbitrary functions, and it supports approximate evaluation queries. By eliminating the Bloomier filter's false positives in a space efficient way, a simple yet powerful exact string matching architecture is proposed that can handle several thousand strings at high rates and is amenable to on-chip realization. The proposed scheme is implemented in reconfigurable hardware and we compare it with existing solutions. The results show that the proposed approach achieves better performance compared to other existing architectures measured in terms of throughput per logic cells per character as a metric.

• Journal of KIISE
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• v.43 no.10
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• pp.1073-1078
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• 2016

(${\delta}$, ${\gamma}$)-matching for strings over integer alphabets can be applied to such fields as musical melody and share prices on stock markets. In this paper, we define ${\delta}$-approximate periods and ${\gamma}$-approximate periods of strings over integer alphabets. We also present two $O(n^2)$-time algorithms, each of which finds minimum ${\delta}$-approximate periods and minimum ${\gamma}$-approximate periods, respectively. Then, we provide the experimental results of execution times of both algorithms.

• KIPS Transactions on Software and Data Engineering
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• v.2 no.2
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• pp.119-122
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• 2013

Repetitive strings such as periods have been studied vigorously in so diverse fields as data compression, computer-assisted music analysis, bioinformatics, and etc. In bioinformatics, periods are highly related to repetitive patterns in DNA sequences so called tandem repeats. In some cases, quite similar but not the same patterns are repeated and thus we need approximate string matching algorithms to study tandem repeats in DNA sequences. In this paper, we propose a new definition of approximate periods of strings based on distance sum. Given two strings $p({\mid}p{\mid}=m)$ and $x({\mid}x{\mid}=n)$, we propose an algorithm that computes the minimum approximate period distance based on distance sum. Our algorithm runs in $O(mn^2)$ time for the weighted edit distance, and runs in O(mn) time for the edit distance, and runs in O(n) time for the Hamming distance.

• KSII Transactions on Internet and Information Systems (TIIS)
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• v.14 no.5
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• pp.2258-2274
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• 2020

In this paper we first propose a new cryptosystem based on our data hiding scheme (2,9,8) introduced in 2019 with high security, where encrypting and hiding are done at once, the ciphertext does not depend on the input image size as existing hybrid techniques of cryptography and steganography. We then exploit our automata approach presented in 2019 to design two algorithms for exact and approximate pattern matching on secret data encrypted by our cryptosystem. Theoretical analyses remark that these algorithms both have O(n) time complexity in the worst case, where for the approximate algorithm, we assume that it uses ⌈(1-ε)m)⌉ processors, where ε, m and n are the error of our string similarity measure and lengths of the pattern and secret data, respectively. In searchable encryption, our cryptosystem is used by users and our pattern matching algorithms are performed by cloud providers.

• Journal of KIISE
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• v.44 no.8
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• pp.760-766
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• 2017

Repetitive strings have been studied in diverse fields such as data compression, bioinformatics and so on. Recently, two problems of approximate periods of strings over integer alphabets were introduced, finding minimum ${\delta}-approximate$ periods and finding minimum ${\gamma}-approximate$ periods. Both problems can be solved in $O(n^2)$ time when n is the length of the string. In this paper, we present two parallel algorithms for solving the above two problems in O(n) time using $O(n^2)$ threads, respectively. The experimental results show that our parallel algorithms for finding minimum ${\delta}-approximate$ (resp. ${\gamma}-approximate$) periods run approximately 19.7 (resp. 40.08) times faster than the sequential algorithms when n = 10,000.

• Journal of KIISE:Computer Systems and Theory
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• v.29 no.1
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• pp.16-21
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• 2002

Repetitive strings have been studied in such diverse fields as molecular biology data compression etc. Some important regularities that have been studied are perods, covers seeds and squares. A natural extension of the repetition problems is to allow errors. Among the four notions above aproximate squares and approximate periodes have been studied. In this paper, we introduce the notion of approximate covers which is an approximate version of covers. Given two strings P(｜P｜=m) and T(｜T｜=n) we propose and algorithm with finds the minimum distance t such that P is a t-approximate cover of T. The algorithm take O(m,n) time for the edit distance and $O(mn^2)$ time of finding a string which is an approximate cover of T is minimum distance is NP-complete.

• Journal of KIISE:Software and Applications
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• v.37 no.10
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• pp.788-801
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• 2010

Advancing of mobile device is remarkable, so the research on mobile input device is getting more important issue. There are lots of input devices such as keypad, QWERTY keypad, touch and speech recognizer, but they are not as convenient as typical keyboard-based desktop input devices so input strings usually contain many typing errors. These input errors are not trouble with communication among person, but it has very critical problem with searching in database, such as dictionary and address book, we can not obtain correct results. Especially, Hangeul has more than 10,000 different characters because one Hangeul character is made by combination of consonants and vowels, frequency of error is higher than English. Generally, suffix tree is the most widely used data structure to deal with errors of query, but it is not enough for variety errors. In this paper, we propose fast approximate Korean word searching system, which allows variety typing errors. This system includes several algorithms for applying general approximate string searching to Hangeul. And we present profanity filters by using proposed system. This system filters over than 90% of coined profanities.