• Proceedings of the Korean Information Science Society Conference
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• 1998.10c
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• pp.51-53
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• 1998

3개 이상의 DNA 혹은 단백질의 염기서열을 정렬하는 복수 염기서열 정렬(multiple sequence alignment)방법은 염기서열들 사이의 진화관계, gene regulation, 단백질의 구조와 기능에 관한 연구에 필수적인 도구이다. 복수 염기서열 정렬문제는 NP-complete 문제군에 속하며, 이 문제를 해결하기 위하여 가장 유용하게 사용되는 알고리즘으로는 dynamic programming이 있다. Dynamic programming은 주어진 입력 염기서열 군들에 대한 최적의 정렬을 생산할 수 있다. 그러나 dynamic programming의 단점은 오랜 실행시간이 요구되며, 때로는 dynamic programming의 속성 때문에 이 알고리즘을 사용하여도 주어진 입력 염기서열 군들에 대한 최적의 정렬을 얻어내지 못하는 경우가 있다. 본 연구에서는 이러한 dynamic programming의 문제를 해결하기 위하여 genetic algorithm을 복수 염기서열 정렬문제에 적용하였다. 본 논문에서는 genetic algorithm의 design과 적용방법을 기술하였다. 본 연구에서 제안된 genetic algorithm을 사용하여 dynamic programming의 단점이었던 오랜 실행시간을 줄일 수 있었으며, dynamic programming이 제공하지 못하는 최적의 염기서열 정렬을 제공할 수 있었다.

• Proceedings of the Korean Information Science Society Conference
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• 2012.06b
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• pp.264-266
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• 2012

인터넷 상에서의 변형 단어들을 처리하는 문제는 정보 검색, 기계 번역, 웹 마이닝, 욕설 및 스팸 필터링과 같은 다양한 분야에서 사용될 수 있다. 특히 단어의 변형 추이를 파악하는 등 데이터 수집 및 분석을 위해서는 주어진 단어가 어떤 변형 단어의 집합으로 이루어진 부류에 포함되는지 여부를 파악해야 할 필요성이 있다. 본 논문에서는 같은 부류에 속한 변형 단어 집합에 대하여 다중 서열 정렬(multiple sequence alignment)을 수행함으로써 해당 집합을 하나의 대표 문자열로 취급하는 변환 기법을 제안하고, 이를 이용해 주어진 단어가 해당 부류에 속하는지 여부를 효과적으로 분류하는 기법을 소개한다. 실험결과 제안 기법의 분류 성능은 민감도 93.4% 수준에서 89.1%의 특이도를 보여 전수 비교를 통한 분류에 비하여 결코 성능은 하락하지 않으면서 분류 속도는 16.5배 향상되었음을 확인할 수 있었다.

• Proceedings of the Korean Information Science Society Conference
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• 1999.10a
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• pp.661-663
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• 1999

복수 염기서열 정렬(multiple sequence alignment)은 염기서열들 사이의 진화관계, 단백질의 구조와 기능에 관한 연구에 필수적인 도구이다. 다이나믹 프로그래밍(dynamic programming) 방법은 대부분의 경우에 있어 최적의 염기서열 정렬 결과를 제공할 수 있다. 그러나 그것이 사용하는 갭 비용함수 때문에 특별한 경우에 최적의 염기서열 정렬을 만들어 내지 못한다. 본 논문에서는 다이나믹 프로그래밍에 의해 획득된 염기서열을 개선하기 위한 휴리스틱 방법을 제안한 후, 실제 단백질 데이터를 가지고 성능 분석을 한다.

• Journal of KIISE:Databases
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• v.34 no.5
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• pp.396-408
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• 2007

After the Human Genome Project finished the sequencing of a human DNA sequence, the concerns on protein functions are increasing. Since the structures of proteins are conserved in divergent evolution, their functions are determined by their structures rather than by their amino acid sequences. Therefore, if similarities between two protein structures are observed, we could expect them to have common biological functions. So far, a lot of researches on protein structure alignment have been performed. However, most of them use RMSD(Root Mean Square Deviation) as a similarity measure with which it is hard to judge the similarity level of two protein structures intuitively. In addition, they retrieve only one result having the highest alignment score with which it is hard to satisfy various users of different purpose. To overcome these limitations, we propose a novel protein structure alignment algorithm based on MRPD(Maximum of Residue Pair Distance) and SG (Similarity Graph). MRPD is more intuitive similarity measure by which fast tittering of unpromising pairs of protein pairs is possible, and SG is a compact representation method for multiple alignment results with which users can choose the most plausible one among various users' needs by providing multiple alignment results without compromising the time to align protein structures.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.37B no.10
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• pp.938-946
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• 2012

Interference alignment (IA) is a data transmission technique that achieves the maximum degrees-of-freedom (DoF) in the multiuser interference channel for high signal-to-noise ratios (SNRs). However, most prior works on IA are based on the unrealistic assumption that perfect and global channel-state information (CSI) is available at all transmitters and receivers. In this paper, we propose the efficient design of feedback framework for IA that substantially suppresses the feedback overhead. While the feedback overhead in the conventional IA quadratically increases with K, the proposed feedback scheme supports the sequential exchange of computed IA precoders between transmitters and receivers and reduces the feedback overhead that linearly scales with K. Moreover, we analyze the residual interference due to the quantization error in limited feedback and propose the ordered IA algorithm that selects IA pair to minimize the sum residual interference in given channel realizations.

• KSBB Journal
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• v.20 no.2 s.91
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• pp.71-75
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• 2005

Alignment of 2D-gel images of biological samples can visualize the difference of expression profiles and also inform us candidates of protein spots to be further analyzed. However, comparison of two proteome images between the case and control does not always successfully identify differentially expressed proteins because of sample-to-sample variation, poor reproducibility of 2D-gel electrophoresis and inconsistent electrophoresis conditions. Multiple alignment of 2D-gel image must be preceded before visualizing the difference of expression profiles or clustering proteome images. Thus, a software for the alignment of multiple 2D-Gel images and their clustering was developed by applying various algorithms and statistical methods. Microsoft Visual C++ was used to implement the algorithms in this work. Multiresoultion-multilevel algorithm was found out to be suitable for fast alignment and for largely distorted images. Clustering of 10 different proteome images of Fetal Alcohol Syndrome, was carried out by implementing a k-means algorithm and it gave a phylogenetic tree of proteomic distance map of the samples. However, the phylogenetic tree does not discriminate the case and control. The whole image clustering shows that the proteomic distance is more dependent to age and sex.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.38A no.7
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• pp.560-570
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• 2013

In this paper, we propose transceiver design strategies for the two-cell multiple-input multiple-output (MIMO) interfering broadcast channel where inter-cell interference (ICI) exists in addition to inter-user interference (IUI). We first formulate the generalized zero-forcing interference alignment (ZF-IA) method based on the alignment of IUI and ICI in multi-dimensional subspace. We then devise a minimum weighted-mean-square-error (WMSE) method based on "regularizing" the precoders and decoders of the generalized ZF-IA scheme. In contrast to the existing weighted-sum-rate-maximizing transceiver, our method does not require an iterative calculation of the optimal weights. Because of this, the proposed scheme, while not designed specially to maximize the sum-rate, is computationally efficient and achieves a faster convergence compared to the known weighed-sum-rate maximizing scheme. Through analysis and simulation, we show the effectiveness of the proposed regularized ZF-IA scheme.

• Journal of Institute of Control, Robotics and Systems
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• v.11 no.10
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• pp.851-856
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• 2005

The DNA and protein data of diverse species have been daily discovered and deposited in the public archives according to each established format. Database systems in the public archives provide not only an easy-to-use, flexible interface to the public, but also in silico analysis tools of unidentified sequence data. Of such in silico analysis tools, multiple sequence alignment [1] methods relying on pairwise alignment and Smith-Waterman algorithm [2] enable us to identify unknown DNA, protein sequences or phylogenetic relation among several species. However, in the existing multiple alignment method as the number of sequences increases, the runtime increases exponentially. In order to remedy this problem, we adopted a parallel processing suffix tree algorithm that is able to search for common subsequences at one time without pairwise alignment. Also, the cross-matching subsequences triggering inexact-matching among the searched common subsequences might be produced. So, the cross-matching masking process was suggested in this paper. To identify the function of the clusters generated by suffix tree clustering, BLAST was combined with a clustering tool. Our clustering and annotating tool is summarized as the following steps: (1) construction of suffix tree; (2) masking of cross-matching pairs; (3) clustering of gene sequences and (4) annotating gene clusters by BLAST search. The system was successfully evaluated with 22 gene sequences in the pyrubate pathway of bacteria, clustering 7 clusters and finding out representative common subsequences of each cluster

• The Journal of Korean Institute of Communications and Information Sciences
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• v.40 no.12
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• pp.2389-2391
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• 2015

The feasibility condition of interference alignment (IA) for full-duplex (FD) multiple-input multipleoutput (MIMO) cellular networks is considered. The necessary and sufficient condition on the IA feasibility is established, characterizing the achievable sum degrees of freedom (DoF). The results demonstrate that FD operation with appropriate IA is able to improve the sum DoF on the conventional half-duplex operation.

• Journal of Information Display
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• v.9 no.2
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• pp.22-27
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• 2008

We propose an optical configuration of a vertical alignment (VA) liquid crystal (LC) cell to eliminate the light leakage in the diagonal direction. VA LC cell has an excellent contrast ratio in the normal direction due to the no phase-retardation. However, change of the phase-retardation occurs in all directions, which causes the light leakage and deteriorates the characteristics of the dark state. We designed the LC cell structure composed of multiple combinations with two A-plates and two C-plates in order to achieve wide viewing property on the Poincare sphere. From calculations, we show that the proposed structure can improve the viewing angle characteristics by compensating for the light leakage in all directions.