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Genome-wide analyses of the Jeju, Thoroughbred, and Jeju crossbred horse populations using the high density SNP array

  • Kim, Nam Young;Seong, Ha-Seung;Kim, Dae Cheol;Park, Nam Geon;Yang, Byoung Chul;Son, Jun Kyu;Shin, Sang Min;Woo, Jae Hoon;Shin, Moon Cheol;Yoo, Ji Hyun;Choi, Jung-Woo
    • Genes and Genomics
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    • v.40 no.11
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    • pp.1249-1258
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    • 2018
  • The Jeju horse is an indigenous Korean horse breed that is currently registered with the Food and Agriculture Organization of the United Nations. However, there is severe lack of genomic studies on Jeju horse. This study was conducted to investigate genetic characteristics of horses including Jeju horse, Thoroughbred and Jeju crossbred (Jeju${\times}$Thoroughbred) populations. We compared the genomes of three horse populations using the Equine SNP70 Beadchip array. Short-range Linkage disequilibrium was the highest in Thoroughbred, whereas $r^2$ values were lowest in Jeju horse. Expected heterozygosity was the highest in Jeju crossbred (0.351), followed by the Thoroughbred (0.337) and Jeju horse (0.311). The level of inbreeding was slightly higher in Thoroughbred (-0.009) than in Jeju crossbred (-0.035) and Jeju horse (-0.038). $F_{ST}$ value was the highest between Jeju horse and Thoroughbred (0.113), whereas Jeju crossbred and Thoroughbred showed the lowest value (0.031). The genetic relationship was further assessed by principal component analysis, suggesting that Jeju crossbred is more genetically similar to Thoroughbred than Jeju horse population. Additionally, we detected potential selection signatures, for example, in loci located on LCORL/NCAPG and PROP1 genes that are known to influence body. Genome-wide analyses of the three horse populations showed that all the breeds had somewhat a low level of inbreeding within each population. In the population structure analysis, we found that Jeju crossbred was genetically closer to Thoroughbred than Jeju horse. Furthermore, we identified several signatures of selection which might be associated with traits of interest. To our current knowledge, this study is the first genomic research, analyzing genetic relationships of Jeju horse, Thoroughbred and Jeju crossbred.

Intrusion Detection Method Using Unsupervised Learning-Based Embedding and Autoencoder (비지도 학습 기반의 임베딩과 오토인코더를 사용한 침입 탐지 방법)

  • Junwoo Lee;Kangseok Kim
    • KIPS Transactions on Software and Data Engineering
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    • v.12 no.8
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    • pp.355-364
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    • 2023
  • As advanced cyber threats continue to increase in recent years, it is difficult to detect new types of cyber attacks with existing pattern or signature-based intrusion detection method. Therefore, research on anomaly detection methods using data learning-based artificial intelligence technology is increasing. In addition, supervised learning-based anomaly detection methods are difficult to use in real environments because they require sufficient labeled data for learning. Research on an unsupervised learning-based method that learns from normal data and detects an anomaly by finding a pattern in the data itself has been actively conducted. Therefore, this study aims to extract a latent vector that preserves useful sequence information from sequence log data and develop an anomaly detection learning model using the extracted latent vector. Word2Vec was used to create a dense vector representation corresponding to the characteristics of each sequence, and an unsupervised autoencoder was developed to extract latent vectors from sequence data expressed as dense vectors. The developed autoencoder model is a recurrent neural network GRU (Gated Recurrent Unit) based denoising autoencoder suitable for sequence data, a one-dimensional convolutional neural network-based autoencoder to solve the limited short-term memory problem that GRU can have, and an autoencoder combining GRU and one-dimensional convolution was used. The data used in the experiment is time-series-based NGIDS (Next Generation IDS Dataset) data, and as a result of the experiment, an autoencoder that combines GRU and one-dimensional convolution is better than a model using a GRU-based autoencoder or a one-dimensional convolution-based autoencoder. It was efficient in terms of learning time for extracting useful latent patterns from training data, and showed stable performance with smaller fluctuations in anomaly detection performance.

Keyword Network Analysis for Technology Forecasting (기술예측을 위한 특허 키워드 네트워크 분석)

  • Choi, Jin-Ho;Kim, Hee-Su;Im, Nam-Gyu
    • Journal of Intelligence and Information Systems
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    • v.17 no.4
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    • pp.227-240
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    • 2011
  • New concepts and ideas often result from extensive recombination of existing concepts or ideas. Both researchers and developers build on existing concepts and ideas in published papers or registered patents to develop new theories and technologies that in turn serve as a basis for further development. As the importance of patent increases, so does that of patent analysis. Patent analysis is largely divided into network-based and keyword-based analyses. The former lacks its ability to analyze information technology in details while the letter is unable to identify the relationship between such technologies. In order to overcome the limitations of network-based and keyword-based analyses, this study, which blends those two methods, suggests the keyword network based analysis methodology. In this study, we collected significant technology information in each patent that is related to Light Emitting Diode (LED) through text mining, built a keyword network, and then executed a community network analysis on the collected data. The results of analysis are as the following. First, the patent keyword network indicated very low density and exceptionally high clustering coefficient. Technically, density is obtained by dividing the number of ties in a network by the number of all possible ties. The value ranges between 0 and 1, with higher values indicating denser networks and lower values indicating sparser networks. In real-world networks, the density varies depending on the size of a network; increasing the size of a network generally leads to a decrease in the density. The clustering coefficient is a network-level measure that illustrates the tendency of nodes to cluster in densely interconnected modules. This measure is to show the small-world property in which a network can be highly clustered even though it has a small average distance between nodes in spite of the large number of nodes. Therefore, high density in patent keyword network means that nodes in the patent keyword network are connected sporadically, and high clustering coefficient shows that nodes in the network are closely connected one another. Second, the cumulative degree distribution of the patent keyword network, as any other knowledge network like citation network or collaboration network, followed a clear power-law distribution. A well-known mechanism of this pattern is the preferential attachment mechanism, whereby a node with more links is likely to attain further new links in the evolution of the corresponding network. Unlike general normal distributions, the power-law distribution does not have a representative scale. This means that one cannot pick a representative or an average because there is always a considerable probability of finding much larger values. Networks with power-law distributions are therefore often referred to as scale-free networks. The presence of heavy-tailed scale-free distribution represents the fundamental signature of an emergent collective behavior of the actors who contribute to forming the network. In our context, the more frequently a patent keyword is used, the more often it is selected by researchers and is associated with other keywords or concepts to constitute and convey new patents or technologies. The evidence of power-law distribution implies that the preferential attachment mechanism suggests the origin of heavy-tailed distributions in a wide range of growing patent keyword network. Third, we found that among keywords that flew into a particular field, the vast majority of keywords with new links join existing keywords in the associated community in forming the concept of a new patent. This finding resulted in the same outcomes for both the short-term period (4-year) and long-term period (10-year) analyses. Furthermore, using the keyword combination information that was derived from the methodology suggested by our study enables one to forecast which concepts combine to form a new patent dimension and refer to those concepts when developing a new patent.

Investigation of Intertidal Zone using TerraSAR-X (TerraSAR-X를 이용한 조간대 관측)

  • Park, Jeong-Won;Lee, Yoon-Kyung;Won, Joong-Sun
    • Korean Journal of Remote Sensing
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    • v.25 no.4
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    • pp.383-389
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    • 2009
  • The main objective of the research is a feasibility study on the intertidal zone using a X-band radar satellite, TerraSAR-X. The TerraSAR-X data have been acquired in the west coast of Korea where large tidal flats, Ganghwa and Yeongjong tidal flats, are developed. Investigations include: 1) waterline and backscattering characteristics of the high resolution X-band images in tidal flats; 2) polarimetric signature of halophytes (or salt marsh plants), specifically Suaeda japonica; and 3) phase and coherence of interferometric pairs. Waterlines from TerraSAR-X data satisfy the requirement of horizontal accuracy of 60 m that corresponds to 20 cm in average height difference while current other spaceborne SAR systems could not meet the requirement. HH-polarization was the best for extraction of waterline, and its geometric position is reliable due to the short wavelength and accurate orbit control of the TerraSAR-X. A halophyte or salt marsh plant, Suaeda japonica, is an indicator of local sea level change. From X-band ground radar measurements, a dual polarization of VV/VH-pol. is anticipated to be the best for detection of the plant with about 9 dB difference at 35 degree incidence angle. However, TerraSAR-X HH/TV dual polarization was turned to be more effective for salt marsh monitoring. The HH-HV value was the maximum of about 7.9 dB at 31.6 degree incidence angle, which is fairly consistent with the results of X-band ground radar measurement. The boundary of salt marsh is effectively traceable specifically by TerraSAR-X cross-polarization data. While interferometric phase is not coherent within normal tidal flat, areas of salt marsh where the landization is preceded show coherent interferometric phases regardless of seasons or tide conditions. Although TerraSAR-X interferometry may not be effective to directly measure height or changes in tidal flat surface, TanDEM-X or other future X-band SAR tandem missions within one-day interval would be useful for mapping tidal flat topography.