• Genomics & Informatics
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• v.18 no.1
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• pp.11.1-11.3
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• 2020

In genome-wide association studies, pathway-based analysis has been widely performed to enhance interpretation of single-nucleotide polymorphism association results. We proposed a novel method of hierarchical structural component model (HisCoM) for pathway analysis of common variants (HisCoM for pathway analysis of common variants [HisCoM-PCA]) which was used to identify pathways associated with traits. HisCoM-PCA is based on principal component analysis (PCA) for dimensional reduction of single nucleotide polymorphisms in each gene, and the HisCoM for pathway analysis. In this study, we developed a HisCoM-PCA software for the hierarchical pathway analysis of common variants. HisCoM-PCA software has several features. Various principle component scores selection criteria in PCA step can be specified by users who want to summarize common variants at each gene-level by different threshold values. In addition, multiple public pathway databases and customized pathway information can be used to perform pathway analysis. We expect that HisCoM-PCA software will be useful for users to perform powerful pathway analysis.

• Bulletin of the Korean Chemical Society
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• v.24 no.9
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• pp.1345-1350
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• 2003

Principal component analysis based two-dimensional (PCA-2D) correlation analysis is applied to FTIR spectra of polystyrene/methyl ethyl ketone/toluene solution mixture during the solvent evaporation. Substantial amount of artificial noise were added to the experimental data to demonstrate the practical noise-suppressing benefit of PCA-2D technique. 2D correlation analysis of the reconstructed data matrix from PCA loading vectors and scores successfully extracted only the most important features of synchronicity and asynchronicity without interference from noise or insignificant minor components. 2D correlation spectra constructed with only one principal component yield strictly synchronous response with no discernible a asynchronous features, while those involving at least two or more principal components generated meaningful asynchronous 2D correlation spectra. Deliberate manipulation of the rank of the reconstructed data matrix, by choosing the appropriate number and type of PCs, yields potentially more refined 2D correlation spectra.

• Proceedings of the Korean Information Science Society Conference
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• 2002.04a
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• pp.247-249
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• 2002

본 논문에서는 주성분 분석(principal component analysis; 이하 PCA) 및 독립성분분석(independent component analysis; 이하 ICA)을 이용, 이차원 영상을 분류하여 다중해상도에서 영상간의 거리를 측정하여 PCA 와 ICA 중에서 어느 것이 영상간의 상대적 식별을 용이하게 하는지 모의 실험을 통하여 확인하고자 한다. 모의 실험 결과로부터, ICA가 PCA에 비하여 영상간의 상대적 식별이 용이하여 빨리 수렴이 되는 것을 모의 실험을 통하여 확인하였다.

• Proceedings of the Korea Contents Association Conference
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• 2003.11a
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• pp.213-217
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• 2003

In this paper, we analysize the noise robustness of MLPs(Multilayer perceptrons). Also, as a preprocessing stage of MLPs to improve noise robustness, we consider the ICA(independent component analysis) and PCA(principle component analysis). After analyzing the noise redunction effect using PCA or ICA, we verify the noise robustness of MLPs through handwritten-digit recognition simulations.

• Proceedings of the Korean Statistical Society Conference
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• 2004.11a
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• pp.79-84
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• 2004

We use principal component analysis (PCA) to identify exons of a gene and further analyze their internal structures. The PCA is conducted on the short-time Fourier transform (STFT) based on the 64 codon sequences and the 4 nucleotide sequences. By comparing to independent component analysis (ICA), we can differentiate between the exon and intron regions, and how they are correlated in terms of the square magnitudes of STFTs. The experiment is done on the gene F56F11.4 in the chromosome III of C. elegans. For this data, the nucleotide based PCA identifies the exon and intron regions clearly. The codon based PCA reveals a weak internal structure in some exon regions, but not the others. The result of ICA shows that the nucleotides thymine (T) and guanine (G) have almost all the information of the exon and intron regions for this data. We hypothesize the existence of complex exon structures that deserve more detailed analysis.

• Proceedings of the Korea Water Resources Association Conference
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• 2018.05a
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• pp.276-276
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• 2018

In this paper the potential of the Principle Component Analysis(PCA) technique that can be used to detect leaks in water pipe network blocks was evaluated. For this purpose the PCA was conducted to evaluate the relevance of the calculated outliers of a PCA model utilizing the recorded pipe flows and the recorded pipe leak incidents of a case study water distribution system. The PCA technique was enhanced by applying the computational algorithms developed in this study. The algorithms were designed to extract a partial set of flow data from the original 24 hour flow data so that the variability of the flows in the determined partial data set are minimal. The relevance of the calculated outliers of a PCA model and the recorded pipe leak incidents was analyzed. The results showed that the effectiveness of detecting leaks may improve by applying the developed algorithm. However, the analysis suggested that further development on the algorithm is needed to enhance the applicability of the PCA in detecting leaks in real-world water pipe networks.

• Proceedings of the Korean Environmental Sciences Society Conference
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• 2003.11a
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• pp.33-36
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• 2003

Principal component analysis (PCA) was used to improve image classification by the unsupervised classification techniques, the K-means. To do this, I selected a Landsat TM scene of Jeju Island, Korea and proposed two methods for PCA： unstandardized PCA (UPCA) and standardized PCA (SPCA). The estimated accuracy of the image classification of Jeju area was computed by error matrix. The error matrix was derived from three unsupervised classification methods. Error matrices indicated that classifications done on the first three principal components for UPCA and SPCA of the scene were more accurate than those done on the seven bands of TM data and that also the results of UPCA and SPCA were better than those of the raw Landsat TM data. The classification of TM data by the K-means algorithm was particularly poor at distinguishing different land covers on the island. From the classification results, we also found that the principal component based classifications had characteristics independent of the unsupervised techniques (numerical algorithms) while the TM data based classifications were very dependent upon the techniques. This means that PCA data has uniform characteristics for image classification that are less affected by choice of classification scheme. In the results, we also found that UPCA results are better than SPCA since UPCA has wider range of digital number of an image.

• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 2000.11a
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• pp.305-309
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• 2000

In this paper, we presents a new methodology for face recognition after analysing conventional ICA(Independent Component Analysis) based approach. In the literature we found that ICA based methods have followed the same procedure without any exception, first PCA(Principal Component Analysis) has been used for feature extraction, next ICA learning method has been applied for feature enhancement in the reduced dimension. However, it is contradiction that features are extracted using higher order moments depend on variance, the second order statistics. It is not considered that a necessary component can be located in the discarded feature space. In the new methodology, features are extracted using the magnitude of kurtosis(4-th order central moment or cumulant). This corresponds to the PCA based feature extraction using eigenvalue(2nd order central moment or variance). The synergy effect of PCA and ICA can be achieved if PCA is used for noise reduction filter. ICA methodology is analysed using SVD(Singular Value Decomposition). PCA does whitening and noise reduction. ICA performs the feature extraction. Simulation results show the effectiveness of the methodology compared to the conventional ICA approach.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.14 no.5
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• pp.1093-1102
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• 2010

Principal component analysis (PCA) is a well-known method for dimension reduction while maintaining most of the variation in data. Although PCA has been applied to many areas successfully, it is sensitive to outliers. Several variants of PCA have been proposed to resolve the problem and, among the variants, robust fuzzy PCA (RF-PCA) demonstrated promising results. RF-PCA uses fuzzy memberships to reduce the noise sensitivity. However, there are also problems in RF-PCA and the convergence property is one of them. RF-PCA uses two different objective functions to update memberships and principal components, which is the main reason of the lack of convergence property. The difference between two functions also slows the convergence and deteriorates the solutions of RF-PCA. In this paper, a variant of RF-PCA, called RF-PCA2, is proposed. RF-PCA2 uses an integrated objective function both for memberships and principal components. By using alternating optimization, RF-PCA2 is guaranteed to converge on a local optimum. Furthermore, RF-PCA2 converges faster than RF-PCA and the solutions found are more similar to the desired solutions than those of RF-PCA. Experimental results also support this.

• Journal of the Korea Society of Computer and Information
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• v.16 no.4
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• pp.15-22
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• 2011

Principal component analysis (PCA) is a well-known method for dimensionality reduction and feature extraction while maintaining most of the variation in data. Although PCA has been applied in many areas successfully, it is sensitive to outliers and only valid for Gaussian distributions. Several variants of PCA have been proposed to resolve noise sensitivity and, among the variants, improved robust fuzzy PCA (RF-PCA2) demonstrated promising results. RF-PCA, however, is still a linear algorithm that cannot accommodate non-Gaussian distributions. In this paper, a non-linear algorithm that combines RF-PCA2 and kernel PCA (K-PCA), called improved robust kernel fuzzy PCA (RKF-PCA2), is introduced. The kernel methods make it to accommodate non-Gaussian distributions. RKF-PCA2 inherits noise robustness from RF-PCA2 and non-linearity from K-PCA. RKF-PCA2 outperforms previous methods in handling non-Gaussian distributions in a noise robust way. Experimental results also support this.