• Journal of KIISE:Software and Applications
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• v.35 no.8
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• pp.501-511
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• 2008

Probe design is one of the essential tasks in successful DNA microarray experiments. The requirements for probes vary as the purpose or type of microarray experiments. In general, most previous works use the simple filtering approach with the fixed threshold value for each requirement. Here, we formulate the probe design as a multiobjective optimization problem with the two objectives and solve it using ${\epsilon}$-multiobjective evolutionary algorithm. The suggested approach was applied in designing probes for 19 types of Human Papillomavirus and 52 genes in Arabidopsis Calmodulin multigene family and successfully produced more target specific probes compared to well known probe design tools such as OligoArray and OligoWiz.

• Journal of KIISE:Software and Applications
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• v.32 no.12
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• pp.1217-1228
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• 2005

Recently, since DNA computing has been widely studied for various applications, DNA sequence design which is the most basic and important step for DNA computing has been highlighted. In previous works, DNA sequence design has been formulated as a multi-objective optimization task, and solved by elitist non-dominated sorting genetic algorithm (NSGA-II). However, NSGA-II needed lots of computational time. Therefore, we use an $\varepsilon$- multiobjective evolutionarv algorithm ($\varepsilon$-MOEA) to overcome the drawbacks of NSGA-II in this paper. To compare the performance of two algorithms in detail, we apply both algorithms to the DTLZ2 benchmark function. $\varepsilon$-MOEA outperformed NSGA-II in both convergence and diversity, $70\%$ and $73\%$ respectively. Especially, $\varepsilon$-MOEA finds optimal solutions using small computational time. Based on these results, we redesign the DNA sequences generated by the previous DNA sequence design tools and the DNA sequences for the 7-travelling salesman problem (TSP). The experimental results show that $\varepsilon$-MOEA outperforms the most cases. Especially, for 7-TSP, $\varepsilon$-MOEA achieves the comparative results two tines faster while finding $22\%$ improved diversity and $92\%$ improved convergence in final solutions using the same time.

• Proceedings of the Korean Information Science Society Conference
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• 2006.06a
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• pp.82-84
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• 2006

최근의 생물학적인 연구에 DNA microarray가 널리 쓰이고 있기 때문에, 이러한 DNA microarray를 구성하는데 필요한 probe design 작업의 중요성이 점차 커져가고 있다. 이 논문에서는 probe design 문제를 thermodynamic fitness function이 2개인 multi-objective optimization 작업으로 변환한 뒤, ${\epsilon}$-multiobjective evolutionary algorithm을 이용하여 probe set을 찾는다. 또한, probe 탐색공간의 크기를 줄이기 위하여 각 DNA sequence의 primer 영역을 찾는 작업을 진행하며, 사용자가 직접 프로그램을 테스트할 수 있는 웹사이트를 제공한다. 실험 대상으로는 mycoides를 선택하였으며, 이 논문에서 제안된 방법을 사용하여 성공적으로 probe set을 발견할 수 있었다.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.27 no.2B
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• pp.137-144
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• 2002

In this paper, we optimize the base station placement and transmission power using genetic approach. A new representation describing base station placement and transmit power with real number is proposed, and new genetic operators are introduced. This new representation can describe the locations, powers, and number of base stations, Considering coverage, power and economy efficiency, we also suggest a weighted objective function. Our algorithm is applied to an obvious optimization problem, and then it is verified. Moreover, our approach is tried in inhomogeneous traffic distribution. Simulation result proves that the algorithm enables to fad near optimal solution according to the weighted objective function.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.34 no.8A
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• pp.618-624
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• 2009

In the evolution from wireless sensor networks(WSNs) to ubiquitous sensor networks(USNs), technologies that can support intensive data-traffic loads, large number of users, improved interoperability, and extreme longevity are required. Therefore, efficient communication time coordination control and low power consumption becomes one of the most important design goals for USN MAC protocols. So far several time division multiplexed (TDM) MAC protocols have been proposed. However, since the pros and cons of existing protocols are not easy to analyze, it becomes a challenging task to design improved TOM MAC protocols. Based on this objective, this paper provides a novel protocol analysis along with a message complexity derivation and comparison of the existing TDM MAC protocols.