• Smart Media Journal
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• v.9 no.2
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• pp.33-38
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• 2020

Order preserving matching refers to the problem of reporting substrings of a given text where there exists order isomorphism with the pattern. In this paper, we propose a new algorithm based on filtering and evaluation. The proposed algorithm is simple and easy to implement, and runs in linear time on average. Experimental results show that it works efficiently with real world data.

• KIPS Transactions on Computer and Communication Systems
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• v.2 no.2
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• pp.67-74
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• 2013

Approximate string matching problems have been studied in diverse fields. Recently, fast approximate string matching algorithms are being used to reduce the time and costs for the next generation sequencing. To measure the amounts of errors between two strings, we use a distance function such as the edit distance. Given two strings X(|X| = m) and Y(|Y| = n) over an alphabet ${\Sigma}$, the edit distance between X and Y is the minimum number of edit operations to convert X into Y. The edit distance between X and Y can be computed using the well-known dynamic programming technique in O(mn) time and space. The edit distance also can be computed using the Four-Russians' algorithm whose preprocessing step runs in $O((3{\mid}{\Sigma}{\mid})^{2t}t^2)$ time and $O((3{\mid}{\Sigma}{\mid})^{2t}t)$ space and the computation step runs in O(mn/t) time and O(mn) space where t represents the size of the block. In this paper, we present a parallelized version of the computation step of the Four-Russians' algorithm. Our algorithm computes the edit distance between X and Y in O(m+n) time using m/t threads. Then we implemented both the sequential version and our parallelized version of the Four-Russians' algorithm using CUDA to compare the execution times. When t = 1 and t = 2, our algorithm runs about 10 times and 3 times faster than the sequential algorithm, respectively.

• ETRI Journal
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• v.38 no.3
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• pp.518-528
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• 2016

The searching of an extensive document database for documents that are locally similar to a given query document, and the subsequent detection of similar regions between such documents, is considered as an essential task in the fields of information retrieval and data management. In this paper, we present a framework for such a task. The proposed framework employs the method of short-read mapping, which is used in bioinformatics to reveal similarities between genomic sequences. In this paper, documents are considered biological objects; consequently, edit operations between locally similar documents are viewed as an evolutionary process. Accordingly, we are able to apply the method of evolution tracing in the detection of similar regions between documents. In addition, we propose heuristic methods to address issues associated with the different stages of the proposed framework, for example, a frequency-based fragment ordering method and a locality-aware interval aggregation method. Extensive experiments covering various scenarios related to the search of an extensive document database for documents that are locally similar to a given query document are considered, and the results indicate that the proposed framework outperforms existing methods.

• KIPS Transactions on Computer and Communication Systems
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• v.4 no.7
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• pp.213-218
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• 2015

Given two strings X and Y (|X|=m, |Y|=n) over an alphabet ${\Sigma}$, the extended edit distance between X and Y can be computed using dynamic programming in O(mn) time and space. Recently, a parallel algorithm that takes O(m+n) time and O(mn) space using m threads to compute the extended edit distance between X and Y was presented. In this paper, we present an improved parallel algorithm using the shared memory on GPU. The experimental results show that our parallel algorithm runs about 19~25 times faster than the previous parallel algorithm.

• Journal of KIISE:Software and Applications
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• v.36 no.4
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• pp.329-334
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• 2009

The ontology alignment has two kinds of major problems. First, the features used for ontology alignment are usually defined by experts, but it is highly possible for some critical features to be excluded from the feature set. Second, the semantic and the structural similarities are usually computed independently, and then they are combined in an ad-hoc way where the weights are determined heuristically. This paper proposes the modified parse tree kernel (MPTK) for ontology alignment. In order to compute the similarity between entities in the ontologies, a tree is adopted as a representation of an ontology. After transforming an ontology into a set of trees, their similarity is computed using MPTK without explicit enumeration of features. In computing the similarity between trees, the approximate string matching is adopted to naturally reflect not only the structural information but also the semantic information. According to a series of experiments with a standard data set, the kernel method outperforms other structural similarities such as GMO. In addition, the proposed method shows the state-of-the-art performance in the ontology alignment.