• Bioinformatics and Biosystems
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• v.2 no.1
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• pp.7-11
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• 2007

Methods for making scoring matrix based on phylogenetic tree for all possible exchanges of one amino acid with another. PFMT(Phylogenetic focused Mutation Tendency) matrix is different BLOSUM62 and PAM160 which are the most used scoring matrixes. This matrix calculates possibility of substitution from common ancestor to high spices. PFMT matrix scores substitution frequency in COGs databases which contain 152 KOGs's dataset. PFMT matrix usefully is able to compare between query sequence and sequences of more higher species and show detailed substitution relation of 20 amino acids.

• The Journal of the Korea institute of electronic communication sciences
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• v.7 no.1
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• pp.117-124
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• 2012

In this paper, we propose a simple H parity check matrix from the CPM(circulant permutation matrix), which can easily avoid the cycle-4, and approach to flexible code rates and lengths. As a result, the operations of the submatrices will become the multiplications between several CPMs, the calculations of the LDPC(low density parity check) encoding could be simplest. Also we consider the fast encoding problem for LDPC codes. The proposed constructions could lead to fast encoding based on the simplest matrices operations for both regular and irregular LDPC codes.

• Journal of the Institute of Electronics Engineers of Korea TC
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• v.42 no.8 s.338
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• pp.1-10
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• 2005

In this paper, the explicit low density codes construction from the generalized permutation matrices related to algebra theory is investigated, and we design several Jacket inverse block matrices on the recursive formula and permutation matrices. The results show that the proposed scheme is a simple and fast way to obtain the low density codes, and we also Proved that the structured low density parity check (LDPC) codes, such as the $\pi-rotation$ LDPC codes are the low density Jacket inverse block matrices too.

• Journal of KIISE:Software and Applications
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• v.34 no.7
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• pp.595-602
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• 2007

This paper proposes a method that discriminates signal peptide and predicts the cleavage site of the secretory proteins cleaved by the signal peptidase I. The preprocessing stage uses hydrophobicity scales of amino acids in order to predict the presence of signal sequence and the cleavage site. The preprocessing enhances the performance of the prediction method by eliminating the non-secretory proteins in the early stage of prediction. for the effective use of support vector machine for the signal sequence prediction, the biologically relevant distance between the amino acid sequences is defined by using the hydrophobicity and substitution matrix; the hydrophobicity can be used to Predict the location of amino acid in a cell and the substitution matrix represents the evolutionary relationships of amino acids. The proposed method showed 98.9% discrimination rates from signal sequences and 88% correct rate of the cleavage site prediction on Swiss-Prot release 50 protein database using the 5-fold-cross-validation. In the comparison tests, the proposed method has performed significantly better than other prediction methods.

• The Journal of the Korea institute of electronic communication sciences
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• v.9 no.4
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• pp.403-408
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• 2014

In this paper, we consider the encoding scheme of low density codes. In particular, we propose the fast encoding algorithm of the low density codes using circulant permutation matrices, The fast encoding algorithm is similar to the fast Hadamard transform, and the results show that the proposed scheme is a simple and fast encoding algorithm of the low density codes.

• Review of KIISC
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• v.3 no.1
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• pp.26-30
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• 1993

본 논문에서는Akl-Meijer가 설계한 랜덤 치환 발생기를 일반화한 알고리즘을 제안한다. Akl과 Meijer는 사이즈가 m인 치환(Permutation)과 0과 m!-1사이의 정수를 일대일 대응시키는 Knuth의 알고리즘을 이용하여, 선형 합동법 Y=X+C mod m! (C는 상수)에서 발생되는 난수와 일대일 대응되는 치환을 발생하는 치환 발생 알고리즘을 설계하였으며, 이를 응용하여, 이진 난수 발생기를 제시하였다. 본 논문에서는 선형 합동법 Y=AX+C mod m!(A, C는 상수)에서 발생되는 난수와 일대일 대응되는 치환 계산과정을 상삼각 행렬(Upper triangular matrix) 의 곱으로 변환하여 고속으로 계산하는 알고리즘을 제시한후, 이 알고리즘의 출력 치환을 n 개 결합하여 치환을 발생하는 랜덤치환 발생기를 설계한다. 또한 이의 암호적인 응용으로, 치환 발생기를 이용한 이진 난수 발생기를 제시한다.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.32 no.4C
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• pp.440-446
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• 2007

This paper addresses a new representation of DFT matrix via the Jacket transform based on the element inverse processing. We simply represent the inverse of the DFT matrix following on the factorization way of the Jacket transform, and the results show that the inverse of DFT matrix is only simply related to its sparse matrix and the permutations. The decomposed DFT matrix via Jacket matrix has a strong geometric structure that exhibits a block modulating property. This means that the DFT matrix decomposed via the Jacket matrix can be interpreted as a block modulating process.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.31 no.2C
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• pp.123-129
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• 2006

In this paper, we concentrate on reducing the complexity for efficient encoder. We design structural LDPC code using circulant matrix and permutation matrix and eIRA code. It is possible to design low complex encoder by using shift register and differential encoder and interleaver than general LDPC encoder that use matrix multiplication operation. The code designed by this structure shows similar performance as random code. And the proposed codes can considerably reduce a number of XOR gates.

• The Journal of the Korea institute of electronic communication sciences
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• v.7 no.2
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• pp.317-325
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• 2012

In this paper, we consider the encoding scheme of Low Density Parity Check codes. In particular, using the Jacket Pattern and circulant permutation matrices, we propose the simple encoding scheme of Richardson's lower triangular matrix. These encoding scheme can be extended to a flexible code rate. Based on the simple matrix process, also we can design low complex and simple encoders for the flexible code rates.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.35 no.2B
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• pp.325-333
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• 2010

Most communication systems including Wibro use quasi-cyclic LDPC codes composed of circulants. However, it is very difficult to design quasi-cyclic(QC) LDPC codes with optimal degree distribution satisfying conditions on layered decoding and girth due to the restriction of the size of its base matrix. In this paper, we propose a good solution by introducing superposition matrices to QC LDPC codes. We derive the conditions on checking girth of QC LDPC codes with superposition matrices, and propose new decoder to support layered decoding both for original QC LDPC codes and their modifications with superposition matrices. Simulation results show considerable improvements to convergence speed and error-correcting performance of proposed scheme which adopts QC LDPC codes with superposition matrices.