• Journal of the Korea Knowledge Information Technology Society
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• v.13 no.5
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• pp.607-614
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• 2018

Oryeong-san is a prescription widely used for diseases where water is stagnant because it has the effect of circulating the water in the body and releasing it into the urine. In order to investigate the mechanisms of oryeong-san, we in this paper construct and analysis the compound-target network of medicinal materials constituting oryeong-san based on a systems pharmacology approach. First, the targets related to the 475 chemical compounds of oryeong-san were searched in the STITCH database, and the search results for the interactions between compounds and targets were downloaded as XML files. The compound-target network of oryeong-san is visualized and explored using Gephi 0.8.2, which is an open-source software for graphs and networks. In the network, nodes are compounds and targets, and edges are interactions between the nodes. The edge is weighted according to the reliability of the interaction. In order to analysis the compound-target network, it is clustered using MCL algorithm, which is able to cluster the weighted network. A total of 130 clusters were created, and the number of nodes in the cluster with the largest number of nodes was 32. In the clustered network, it was revealed that the active compounds of medicinal materials were associated with the targets for regulating the blood pressure in the kidney. In the future, we will clarify the mechanisms of oryeong-san by linking the information on disease databases and the network of this research.

• Journal of KIISE:Software and Applications
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• v.29 no.1_2
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• pp.10-19
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• 2002

In searching and locating a collection of components on the Web, users require a Web browser. Since the Web libraries tend to grow rapidly, there needs to be an effective way to organize and manage such large libraries. Traditional Web-based library(retrieval) systems provide various classification scheme and retrieval services to store and retrieve components. However, these systems do not include invaluable services, for example, enabling users to grasp the overall contents of the library at the beginning of retrieval. This paper discusses a Web-based library system, which provides the efficient management of object-oriented components and a set of services beyond simple component store and retrieval. These services consist of component comprehension through a reverse engineering process, automated summary extraction, and comprehension-based retrieval. Also, The performance of an automated cluster-based classification scheme adopted on the system is evaluated and compared with the cluster-based classification scheme adopted on the system is evaluated and compared with the performance of two other systems using traditional classification scheme.

• Journal of Korea Spatial Information System Society
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• v.8 no.2 s.17
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• pp.75-89
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• 2006

LBS (Location-Based Service) systems have become a serious subject for research and development since recent rapid advances in wireless communication technologies and position measurement technologies such as global positioning system. The architecture named the GALIS (Gracefully Aging Location Information System) has been suggested which is a cluster-based distributed computing system architecture to overcome performance losses and to efficiently handle a large volume of data, at least millions. The GALIS consists of SLDS and LLDS. The SLDS manages current location information of moving objects and the LLDS manages past location information of moving objects. In this thesis, we implement a monitoring technique for the GALIS prototype, to allow dynamic load balancing among multiple computing nodes by keeping track of the load of each node in real-time during the location data management and spatio-temporal query processing. We also propose a buffering technique which efficiently manages the query results having overlapped query regions to improve query processing performance of the GALIS. The proposed scheme reduces query processing time by eliminating unnecessary query execution on the overlapped regions with the previous queries.

• Bioinformatics and Biosystems
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• v.1 no.2
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• pp.99-102
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• 2006

The Basic Local Alignment Search Tool (BLAST) is one of the most established software in bioinformatics research and it compares a query sequence against the libraries of known sequences in order to investigate sequence similarity. Expressed Sequence Tags (ESTs) are single-pass sequence reads from mRNA (or cDNA) and represent the expression for a given cDNA library and the snapshot of genes expressed in a given tissue and/or at a given developmental stage. Therefore, ESTs can be very valuable information for functional genomics and bioinformatics researches. Although major bio database (DB) websites including NCBI are providing BLAST services and EST data, local DB and search system is demanding for better performance and security issue. Here we present animal EST DBs and local BLAST search system. The animal ESTs DB in NCBI Genbank were divided by animal species using the Perl script we developed. and we also built the new extended DB search systems fur the new data (Local Animal BLAST Search System: http://bioinfo.kohost.net), which was constructed on the high-capacity PC Cluster system fur the best performance. The new local DB contains 650,046 sequences for Bos taurus(cattle), 368,120 sequences for Sus scrofa (pig), 693,005 sequences for Gallus gallus (fowl), respectively.

• The Journal of the Korea Contents Association
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• v.8 no.1
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• pp.259-271
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• 2008

We propose a protein function finding algorithm that is able to predict specific molecular function for unannotated proteins through domain analysis from protein-protein network. To do this, we first construct protein-protein interaction(PPI) network in Saccharomyces cerevisiae from MIPS databases. The PPI network(proteins; 3,637, interactions; 10,391) shows the characteristics of a scale-free network and a hierarchical network that proteins with a number of interactions occur in small and the inherent modularity of protein clusters. Protein-protein interaction databases obtained from a Y2H(Yeast Two Hybrid) screen or a composite data set include random false positives. To filter the database, we reconstruct the PPI networks based on the cellular localization. And then we analyze Hub proteins and the network structure in the reconstructed network and define structural modules from the network. We analyze protein domains from the structural modules and derive functional modules from them. From the derived functional modules with high certainty, we find tentative functions for unannotated proteins.

• Proceedings of the Korean Society of Computational and Applied Mathematics Conference
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• 2003.09a
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• pp.11-11
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• 2003

오늘날 단일 슈퍼컴퓨터로는 처리가 불가능한 거대한 문제들의 해법이 시도되고 있는데, 이들은 지리적으로 분산된 슈퍼컴퓨터, 데이터베이스, 과학장비 및 디스플레이 장치 등을 초고속 통신망으로 연결한 GRID 환경에서 효과적으로 실행시킬 수 있다. GRID는 1990년대 중반 과학 및 공학용 분산 컴퓨팅의 연구 과정에서 등장한 것으로, 점차 응용분야가 넓어지고 있다. 그러나 GRID 같은 분산 환경은 기존의 단일 병렬 시스템과는 많은 점에서 다르며 이전의 기술들을 그대로 적용하기에는 무리가 있다. 기존 병렬 시스템에서는 주로 동기 알고리즘(synchronous algorithm)이 사용되는데, 직렬 연산과 같은 결과를 얻기 위해 동기화(synchronization)가 필요하며, 부하 균형이 필수적이다. 그러나 부하 균형은 이질 클러스터(heterogeneous cluster)처럼 프로세서들의 성능이 서로 다르거나, 지리적으로 분산된 계산자원을 사용하는 GRID 환경에서는 이기종의 문제뿐 아니라 네트워크를 통한 메시지의 전송 지연 등으로 유휴시간이 길어질 수밖에 없다. 이처럼 동기화의 필요성에 의한 연산의 지연을 해결하는 하나의 방안으로 비동기 반복법(asynchronous iteration)이 나왔으며, 지금도 활발히 연구되고 있다. 이는 알고리즘의 동기점을 가능한 한 제거함으로써 빠른 프로세서의 유휴 시간을 줄이는 것이 목적이다. 즉 비동기 알고리즘에서는, 각 프로세서는 다른 프로세서로부터 갱신된 데이터가 올 때까지 기다리지 않고 계속 다음 작업을 수행해 나간다. 따라서 동시에 갱신된 데이터를 교환한 후 다음 단계로 진행하는 동기 알고리즘에 비해, 미처 갱신되지 않은 데이터를 사용하는 경우가 많으므로 전체적으로는 연산량 대비의 수렴 속도는 느릴 수 있다 그러나 각 프로세서는 거의 유휴 시간이 없이 연산을 수행하므로 wall clock time은 동기 알고리즘보다 적게 걸리며, 때로는 50%까지 빠른 결과도 보고되고 있다 그러나 현재까지의 연구는 모두 어떤 수렴조건을 만족하는 선형 시스템의 해법에 국한되어 있으며 비교적 구현하기 쉬운 공유 메모리 시스템에서의 연구만 보고되어 있다. 본 연구에서는 행렬의 주요 고유쌍을 구하는 데 있어 비동기 반복법의 적용 가능성을 타진하기 위해 우선 이론적으로 단순한 멱승법을 사용하여 실험하였고 그 결과 순수한 비동기 반복법은 수렴하기 어렵다는 결론을 얻었다 그리하여 동기 알고리즘에 비동기적 요소를 추가한 혼합 병렬 알고리즘을 제안하고, MPI(Message Passing Interface)를 사용하여 수원대학교의 Hydra cluster에서 구현하였다. 그 결과 특정 노드의 성능이 다른 것에 비해 현저하게 떨어질 때 전체적인 알고리즘의 수렴 속도가 떨어지는 것을 상당히 완화할 수 있음이 밝혀졌다.

• Journal of Intelligence and Information Systems
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• v.8 no.2
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• pp.177-187
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• 2002

Spatial data mining is a process to discover interesting relationships and characteristics those exist implicitly in a spatial database. Many spatial clustering algorithms have been developed. But, there are few approaches that focus simultaneously on clustering spatial data and assigning weight to non-spatial attributes of objects. In this paper, we propose a new spatial clustering algorithm, called DBSCAN-W, which is an extension of the existing density-based clustering algorithm DBSCAN. DBSCAN algorithm considers only the location of objects for clustering objects, whereas DBSCAN-W considers not only the location of each object but also its non-spatial attributes relevant to a given application. In DBSCAN-W, each datum has a region represented as a circle of various radius, where the radius means the degree of the importance of the object in the application. We showed that DBSCAN-W is effective in generating clusters reflecting the users requirements through experiments.

• Journal of KIISE:Computing Practices and Letters
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• v.16 no.11
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• pp.1031-1040
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• 2010

Hash join is one of the core algorithms in databases management systems. If a hash join cannot complete in one-pass because the available memory is insufficient (i.e., hash table overflow), however, it may incur a few sequential writes and excessive random reads. With harddisk as the tempoary storage for hash joins, the I/O time would be dominated by slow random reads in its probing phase. Meanwhile, flash memory based SSDs (flash SSDs) are becoming popular, and we will witness in the foreseeable future that flash SSDs replace harddisks in enterprise databases. In contrast to harddisk, flash SSD without any mechanical component has fast latency in random reads, and thus it can boost hash join performance. In this paper, we investigate several important and practical issues when flash SSD is used as tempoary storage for hash join. First, we reveal the va patterns of hash join in detail and explain why flash SSD can outperform harddisk by more than an order of magnitude. Second, we present and analyze the impact of cluster size (i.e., va unit in hash join) on performance. Finally, we emperically demonstrate that, while a commerical query optimizer is error-prone in predicting the execution time with harddisk as temporary storage, it can precisely estimate the execution time with flash SSD. In summary, we show that, when used as temporary storage for hash join, flash SSD will provide more reliable cost estimation as well as fast performance.

• Journal of the Korea Convergence Society
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• v.7 no.5
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• pp.1-6
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• 2016

Many studies have been carried out for the development of big data utilization and analysis technology recently. There is a tendency that government agencies and companies to introduce a Hadoop of a processing platform for analyzing big data is increasing gradually. Increased interest with respect to the processing and analysis of these big data collection technology of data has become a major issue in parallel to it. However, study of the collection technology as compared to the study of data analysis techniques, it is insignificant situation. Therefore, in this paper, to build on the Hadoop cluster is a big data analysis platform, through the Apache sqoop, stylized from relational databases, to collect the data. In addition, to provide a sensor through the Apache flume, a system to collect on the basis of the data file of the Web application, the non-structured data such as log files to stream. The collection of data through these convergence would be able to utilize as a basic material of big data analysis.

• The Journal of the Korea Contents Association
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• v.14 no.11
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• pp.467-475
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• 2014

With the development of genomics, wearable device and IT/NT, a vast amount of bio-medical data are generated recently. Also, healthcare industries based on big-data are booming and big-data technology based on bio-medical data is rising rapidly as a core technology for improving the national health and aged society. A pathway is the biological deep knowledge that represents the relations of dynamics and interaction among proteins, genes and cells by a network. A pathway is wildly being used as an important part of a bio-medical big-data analysis. However, a pathway analysis requires a lot of time and effort because a pathway is very diverse and high volume. Also, multidimensional analysis systems for various pathways are nonexistent even now. In this paper, we proposed a pathway analysis system that collects user interest pathways from KEGG pathway database that supports the most widely used pathways, constructs a network based on a hierarchy structure of pathways and analyzes the relations of dynamics and interaction among pathways by clustering and selecting core pathways from the network. Finally, to verify the superiority of our pathway analysis system, we evaluate the performance of our system in various experiments.