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Comparison Architecture for Large Number of Genomic Sequences

  • Choi, Hae-won;Ryoo, Myung-Chun;Park, Joon-Ho
    • Journal of Information Technology and Architecture
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    • v.9 no.1
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    • pp.11-19
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    • 2012
  • Generally, a suffix tree is an efficient data structure since it reveals the detailed internal structures of given sequences within linear time. However, it is difficult to implement a suffix tree for a large number of sequences because of memory size constraints. Therefore, in order to compare multi-mega base genomic sequence sets using suffix trees, there is a need to re-construct the suffix tree algorithms. We introduce a new method for constructing a suffix tree on secondary storage of a large number of sequences. Our algorithm divides three files, in a designated sequence, into parts, storing references to the locations of edges in hash tables. To execute experiments, we used 1,300,000 sequences around 300Mbyte in EST to generate a suffix tree on disk.

Estimation of Carbon Stock in the Chir Pine (Pinus roxburghii Sarg.) Plantation Forest of Kathmandu Valley, Central Nepal

  • Sharma, Krishna Prasad;Bhatta, Suresh Prashad;Khatri, Ganga Bahadur;Pajiyar, Avinash;Joshi, Daya Krishna
    • Journal of Forest and Environmental Science
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    • v.36 no.1
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    • pp.37-46
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    • 2020
  • Vegetation carbon sequestration and regeneration are the two major parameters of forest research. In this study, we analyzed the vegetation carbon stock and regeneration of community-managed pine plantation of Kathmandu, central Nepal. Vegetation data were collected from 40 circular plots of 10 m radius (for the tree) and 1m radius (for seedling) applying a stratified random sampling and nested quadrat method. The carbon stock was estimated by Chave allometric model and estimated carbon stock was converted into CO2 equivalents. Density-diameter (d-d) curve was also prepared to check the regeneration status and stability of the plantation. A d-d curve indicates the good regeneration status of the forest with a stable population in each size class. Diversity of trees was very low, only two tree species Pinus roxburghii and Eucalyptus citriodora occurred in the sample plots. Pine was the dominant tree in terms of density, basal area, biomass, carbon stock and CO2 stock than the eucalyptus. The basal area, carbon stock and CO2 stock of forest was 33±1.0 ㎡ ha-1, 108±5.0 Mg ha-1 and 394±18 Mg ha-1, respectively. Seedling and tree density of the plantation was 4,965 ha-1 and 339 ha-1 respectively. The forest carbon stock showed a positive relationship with biomass, tree diameter, height and basal area but no relationship with tree density. Canopy cover and tree diameter have a negative effect on seedling density and regeneration. In conclusion, the community forest has a stable population in each size class, sequestering a significant amount of carbon and CO2 emitted from densely populated Kathmandu metro city as the forest biomass hence have a potentiality to mitigate the global climate change.

Cut tree approach for facility layout problem

  • Kim, Chae-Bogk
    • Korean Management Science Review
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    • v.11 no.3
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    • pp.55-65
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    • 1994
  • Given the flow matrix, plant size and department sizes, the algorithms in this paper provide the layout with rectilinear distance. To construct automated facility design, cut tree approach is employed. A branch and bound computer code developed by Tillinghast is modifided to find the feasible fits of departments without shape distortion in the plant rectangle.

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Performance and Convergence Analysis of Tree-LDPC codes on the Min-Sum Iterative Decoding Algorithm (Min-Sum 반복 복호 알고리즘을 사용한 Tree-LDPC의 성능과 수렴 분석)

  • Noh Kwang-seok;Heo Jun;Chung Kyuhyuk
    • The Journal of Korean Institute of Communications and Information Sciences
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    • v.31 no.1C
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    • pp.20-25
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    • 2006
  • In this paper, the performance of Tree-LDPC code is presented based on the min-sum algorithm with scaling and the asymptotic performance in the water fall region is shown by density evolution. We presents that the Tree-LDPC code show a significant performance gain by scaling with the optimal scaling factor which is obtained by density evolution methods. We also show that the performance of min-sum with scaling is as good as the performance of sum-product while the decoding complexity of min-sum algorithm is much lower than that of sum-product algorithm. The Tree-LDPC decoder is implemented on a FPGA chip with a small interleaver size.

A Cell-based Indexing for Managing Current Location Information of Moving Objects (이동객체의 현재 위치정보 관리를 위한 셀 기반 색인 기법)

  • Lee, Eung-Jae;Lee, Yang-Koo;Ryu, Keun-Ho
    • The KIPS Transactions:PartD
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    • v.11D no.6
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    • pp.1221-1230
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    • 2004
  • In mobile environments, the locations of moving objects such as vehicles, airplanes and users of wireless devices continuously change over time. For efficiently processing moving object information, the database system should be able to deal with large volume of data, and manage indexing efficiently. However, previous research on indexing method mainly focused on query performance, and did not pay attention to update operation for moving objects. In this paper, we propose a novel moving object indexing method, named ACAR-Tree. For processing efficiently frequently updating of moving object location information as well as query performance, the proposed method is based on fixed grid structure with auxiliary R-Tree. This hybrid structure is able to overcome the poor update performance of R-Tree which is caused by reorganizing of R-Tree. Also, the proposed method is able to efficiently deal with skewed-. or gaussian distribution of data using auxiliary R-Tree. The experimental results using various data size and distribution of data show that the proposed method has reduced the size of index and improve the update and query performance compared with R-Tree indexing method.

Digital Hologram Watermarking using Quad-tree Fresnelet Transform (Quad-tree Fresnelet 변환을 이용한 디지털 홀로그램 워터마킹)

  • Seo, Young Ho;Koo, Ja Myung;Lee, Yoon Hyuk;Kim, Dong Wook
    • Journal of Korea Society of Digital Industry and Information Management
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    • v.9 no.3
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    • pp.79-89
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    • 2013
  • This paper proposes a watermarking scheme to protect ownership of a digital hologram, an ultra-high value-added content. It performs pre-defined levels of quad-tree Fresnelet transforms. The relationship among the same-positional-blocks is extracted as the digital pre-watermark. For the relationship, we use properties of a digital hologram that a hologram pixel retains all the information of the object and that the same size of partial holograms reconstructs the same size of object but different in their view points. Also we mix a set of private data with the pre-watermark and the result is encrypted by a block cipher algorithm with a private key. Experimental results showed that the proposed scheme is very robust for the various malicious and non-malicious attacks. Also because it extracts the watermarking data instead of inserting, the watermarking process does not harm the original hologram data. So, it is expected to be used effectively for invisible and robust watermark for digital holograms.

Ethnobotany of Wild Baobab (Adansonia digitata L.): A Way Forward for Species Domestication and Conservation in Sudan

  • Gurashi, N.A.;Kordofani, M.A.Y.;Adam, Y.O.
    • Journal of Forest and Environmental Science
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    • v.33 no.4
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    • pp.270-280
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    • 2017
  • Selection of superior phenotypes of fruit trees and products based on established criteria by local people is a prerequisite for future species domestication and conservation. Thus the study objective was to identify the local people's perceptions and preferences on baobab trees and products. A sample of 142 respondents was randomly selected using structured interviews in Blue Nile and North Kordofan, Sudan in 2013. Descriptive analysis was employed using SPSS and Excel programs. The study results indicated that local people use the morphological characteristics of the tree (leaves, fruits, seeds, kernels and bark) to differentiate individual trees. Based on the perceptions, local people recorded trees with delicious leaves, white pulp color, big fruit size and mature capsule size, and high pulp yield as criteria for differentiating between baobab trees in the study areas. In contrast, the undesirable traits were connected to trees with acidic pulp, slimy pulp, bitter leaves, and low pulp yield. The study concluded that the ethnobotanical knowledge of the baobab tree and its products may play an important role in tree domestication and improvement in Sudan. However, further research on tree genetics is needed to complement the ethnobotanical knowledge for baobab resources domestication and conservation.

Performance Evaluation of the FP-tree and the DHP Algorithms for Association Rule Mining (FP-tree와 DHP 연관 규칙 탐사 알고리즘의 실험적 성능 비교)

  • Lee, Hyung-Bong;Kim, Jin-Ho
    • Journal of KIISE:Databases
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    • v.35 no.3
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    • pp.199-207
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    • 2008
  • The FP-tree(Frequency Pattern Tree) mining association rules algorithm was proposed to improve mining performance by reducing DB scan overhead dramatically, and it is recognized that the performance of it is better than that of any other algorithms based on different approaches. But the FP-tree algorithm needs a few more memory because it has to store all transactions including frequent itemsets of the DB. This paper implements a FP-tree algorithm on a general purpose UNK system and compares it with the DHP(Direct Hashing and Pruning) algorithm which uses hash tree and direct hash table from the point of memory usage and execution time. The results show surprisingly that the FP-tree algorithm is poor than the DHP algorithm in some cases even if the system memory is sufficient for the FP-tree. The characteristics of the test data are as follows. The site of DB is look, the number of total items is $1K{\sim}7K$, avenrage length of transactions is $5{\sim}10$, avergage size of maximal frequent itemsets is $2{\sim}12$(these are typical attributes of data for large-scale convenience stores).

Calculation of Tree Height and Canopy Crown from Drone Images Using Segmentation

  • Lim, Ye Seul;La, Phu Hien;Park, Jong Soo;Lee, Mi Hee;Pyeon, Mu Wook;Kim, Jee-In
    • Journal of the Korean Society of Surveying, Geodesy, Photogrammetry and Cartography
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    • v.33 no.6
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    • pp.605-614
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    • 2015
  • Drone imaging, which is more cost-effective and controllable compared to airborne LiDAR, requires a low-cost camera and is used for capturing color images. From the overlapped color images, we produced two high-resolution digital surface models over different test areas. After segmentation, we performed tree identification according to the method proposed by , and computed the tree height and the canopy crown size. Compared with the field measurements, the computed results for the tree height in test area 1 (coniferous trees) were found to be accurate, while the results in test area 2 (deciduous coniferous trees) were found to be underestimated. The RMSE of the tree height was 0.84 m, and the width of the canopy crown was 1.51 m in test area 1. Further, the RMSE of the tree height was 2.45 m, and the width of the canopy crown was 1.53 m in test area 2. The experiment results validated the use of drone images for the extraction of a tree structure.

Seral Changes in Floristic Composition during Abandoned Field Succession after Shifting Cultivation (화전 후 묵밭의 식생 천이 진행에 따른 종조성의 변화)

  • Lee, Kyu Song;Joon-Ho Kim
    • The Korean Journal of Ecology
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    • v.18 no.2
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    • pp.275-283
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    • 1995
  • Seral changes in floristic composition during abandoned field succession after shifting cultivation was investigated in eastern Kangwon-Do, Korea. According to the DCA ordination based on the floristic composition, sere of the dominant species was shown as follows: Digitaria sanguinalis, Persicaria spp., Commelina communis etc. in the annual stage (0∼1 years); Erigeron spp., Artemisia spp., Rubus crataegus etc. in the Erigeron-Artemisia stage (2∼6 years); Pinus densiflora, Salix spp., Miscanthus sinensis, Arundinella hirta etc. in the shrub - earlier tree stage (10∼25 years); P. densiflora, Quercus mongolica, Spodiopogon sibiricus etc. in the mid-tree stage (25∼50 years); Q. mongolica, Tripterigium regelii, Lespedeza maximowiczii, Carex siderosticta etc. in the latter tree stage (50∼80 years). In mid-tree stage, size-frequency distribution of P. densiflora was plotted as a platycurtic curve and that of Q. mongolica as a reverse J-shaped curve, which meant P. densiflora was thinned through interspecific competition and Q. mongolica was regenerated by itself in the later tree stage.

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