• Journal of the Korea Academia-Industrial cooperation Society
• /
• v.13 no.9
• /
• pp.3952-3961
• /
• 2012

Developing computational methods for identifying cell cycle-regulated genes has been one of important topics in systems biology. Most of previous methods consider the periodic characteristics of expression signals to identify the cell cycle-regulated genes. However, we assume that cell cycle-regulated genes are relatively active having relatively many interactions with each other based on the underlying cellular network. Thus, we are motivated to apply the theory of multivariate phase synchronization to the cell cycle expression analysis. In this study, we apply the method known as "Self-Organizing Maps with statistical Phase Synchronization (SOMPS)", which is the combination of self-organizing map and multivariate phase synchronization, producing several subsets of genes that are expected to have interactions with each other in their subset (Kim, 2008). Our evaluation experiments show that the SOMPS algorithm is able to detect cell cycle-regulated genes as much as one of recently reported method that performs better than most existing methods.

• The Journal of Korean Institute of Communications and Information Sciences
• /
• v.27 no.12C
• /
• pp.1215-1227
• /
• 2002

This paper presents a genetic algorithmic approach to shortest path (SP) routing problem. Variable-length chromosomes (strings) and their genes (parameters) have been used for encoding the problem. The crossover operation that exchanges partial chromosomes (partial-routes) at positionally independent crossing sites and the mutation operation maintain the genetic diversity of the population. The proposed algorithm can cure all the infeasible chromosomes with a simple repair function. Crossover and mutation together provide a search capability that results in improved quality of solution and enhanced rate of convergence. Computer simulations show that the proposed algorithm exhibits a much better quality of solution (route optimality) and a much higher rate of convergence than other algorithms. The results are relatively independent of problem types (network sizes and topologies) for almost all source-destination pairs.

• Journal of Biomedical Engineering Research
• /
• v.25 no.6
• /
• pp.617-621
• /
• 2004

In recent, researchers in the field of Bioinformatics need to analyze thousands of genome sequences efficiently according to introduce of new analysis methods and technologies such as genome expression microchip. This rapid growth in the field of bio-engineering needs computing resources to analyze rapidly for genome sequences, but it does not introduce the computing resources due to an enormous investment expense. The core factor of this study is integrated environment based PC-Cluster system & high speed access rate up to 155Mbps, continuous collection system for bio-information at home and abroad. The results of the study are establishment & stabilization of information and communication infrastructure, establishment & stabilization of high performance computer network up to 155Mbps, development of PC-Cluster system with 32 nodes, a parallel BLAST on Cluster system, which can provides scalable speedup in terms of response time, and development of collection & search system for bio-information.

• Journal of KIISE:Software and Applications
• /
• v.32 no.4
• /
• pp.247-257
• /
• 2005

Generally, the network topology design problem is characterized as a kind of NP-hard combinatorial optimization problem, which is difficult to solve with the classical method because it has exponentially increasing complexity with the augmented network size. In this paper, we propose the efficient approach with two phase that is comprised of evolutionary computation approach based on Prufer number(PN), which can efficiently represent the spanning tree, and a heuristic method considering 2-connectivity, to solve the highly reliable network topology design problem minimizing the construction cost subject to network reliability: firstly, to find the spanning tree, genetic algorithm that is the most widely known type of evolutionary computation approach, is used; secondly, a heuristic method is employed, in order to search the optimal network topology based on the spanning tree obtained in the first Phase, considering 2-connectivity. Lastly, the performance of our approach is provided from the results of numerical examples.

• Journal of Institute of Control, Robotics and Systems
• /
• v.10 no.12
• /
• pp.1189-1195
• /
• 2004

This paper investigates construction of gene (interaction) networks from gene expression time-series data based on evolutionary computation. To illustrate the proposed approach in a comprehensive way, we first assume an artificial gene network and then compare it with the reconstructed network from the gene expression time-series data generated by the artificial network. Next, we employ real gene expression time-series data (Spellman's yeast data) to construct a gene network by applying the proposed approach. From these experiments, we find that the proposed approach can be used as a useful tool for discovering the structure of a gene network as well as the corresponding relations among genes. The constructed gene network can further provide biologists with information to generate/test new hypotheses and ultimately to unravel the gene functions.

• Proceedings of the Korean Society of Machine Tool Engineers Conference
• /
• 2004.04a
• /
• pp.430-438
• /
• 2004

Among the optimization method, GA (genetic algorithm) is a very powerful searching method enough to compete with design sensitivity analysis method. GA is very easy to apply, since it dose not require any design sensitivity information. However, GA has been computationally not efficient due to huge repetitive computation. In this study, parallel computation is adopted to Improve computational efficiency, Paralleled GA is introduced on a clustered LINUX based personal computer system.

• 한국HCI학회:학술대회논문집
• /
• 2007.02a
• /
• pp.932-937
• /
• 2007

생의학 분야 문헌의 양이 빠르게 증가함에 따라, 생의학 연구자들이 필요로 하는 정보를 얻기가 어렵게 되었다. 이를 해결하기 위해, 인간-컴퓨터 상호작용 분야에서는 생의학 문헌 검색 시스템, 또는 생의학 문헌의 정보 추출 시스템 등에 대한 연구가 진행되고 있다. 본 논문에서는 생의학 문헌으로부터 정보를 자동으로 추출하기 위한 관계정보 추출 시스템에 대해 소개한다. 소개하는 시스템은 크게 요약 수집 모듈, 관계 추출 모듈, 관계 가시화 모듈로 구성되어 있다. 우선, 요약 수집 모듈에서는 특정 주제의 문헌들을 검색 및 수집한다. 그리고, 관계 추출 모듈에서는 수집된 문헌들에 대해서, 단백질/유전자 등의 생물학 개체를 인식하고, 구문분석을 통하여 인식된 개체들 사이의 관계를 추출한다. 마지막으로, 관계 가시화 모듈에서는 추출된 관계를 통합하여 네트워크 형태로 가시화한다. 이 시스템은 생물학 실험 이전의 문헌 기반 타당성 검사, 단백질-단백질 상호작용 또는 특정 질병과 유전자의 조절관계 분석, 또는 대용량 문헌 처리를 통한 패스웨이 데이터베이스 구축 등에 활용될 수 있다.

• Proceedings of the Korean Information Science Society Conference
• /
• 2006.06a
• /
• pp.55-57
• /
• 2006

k-medoid 클러스터링 알고리즘은 고정된 클러스터 수(k)를 가지고 실험하기 때문에 데이터에 대한 사전 지식이 없으면 올바른 분석이 어렵고, 클러스터 수를 변경하면서 여러 번 반복 실험하여 실험 결과에 대한 타당성을 조사해야 하기 때문에 데이터의 크기가 커질수록 시간 비용이 증가하는 단점이 생긴다. 본 논문에서는 k-medoid 클러스터링 알고리즘 분석에 있어서 가장 어려운 문제 중 하나인 적절한 클러스터 수 k를 사회 네트워크 분석 방법 중 매개중심 값을 이용하여 찾는 새로운 방법을 제안하고 이를 실제 마이크로 어레이 데이터에 적용하여 유전자 알고리즘에 기반한 k-medoid 클러스터링을 수행함으로써 좀 더 정확한 클러스터링 결과를 보인다.

• Journal of the Korean Society for Precision Engineering
• /
• v.20 no.4
• /
• pp.189-196
• /
• 2003

Among the optimization method, GA (genetic algorithm) is a very powerful searching method enough to compete with design sensitivity analysis method. GA is very easy to apply, since it dose not require any design sensitivity information. However, GA has been computationally not efficient due to huge repetitive computation. In this study, parallel computation is adopted to improve computational efficiency. Paralleled GA is introduced on a clustered LINUX based personal computer system.

• Journal of the Korea Society of Computer and Information
• /
• v.8 no.3
• /
• pp.150-155
• /
• 2003

Multicasting, the transmission of data to a group, can be solved from constructing multicast tree, that is, the whole network is partitioned to some clusters and the clusters are constructed by multicast tree. This paper proposes an algorithm that reduces the multicast routing costs using a clustering method. Multicast tree is constructed by minimum-cost Steiner tree. It is important to solve the mnimum-cost Steiner tree problem in the multicast routing problems. Hence, this paper proposes a genetic algorithm for multicast routing problems using clustering method.