• 경영과학
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• 제24권2호
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• pp.157-176
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• 2007

Fuzzy cognitive map(FCM) has long been used as an effective way of constructing the human's decision making process explicitly. By taking advantage of this feature, FCM has been extensively used in providing what-if solutions to a wide variety of business decision making problems. In contrast, the goal-seeking analysis mechanism by using the FCM is rarely observed in literature, which remains a research void in the fields of FCM. In this sense, this study proposes a new type of the FCM-based goal-seeking analysis which is based on utilizing the genetic algorithm. Its main recipe lies in the fact that the what-if analysis as well as goal-seeking analysis are enabled very effectively by incorporating the genetic algorithm into the FCM-driven inference process. To prove the empirical validity of the proposed approach, valid questionnaires were gathered from a number of experts on software sales, and analyzed statistically. Results showed that the proposed approach is robust and significant.

• Journal of Information Processing Systems
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• 제13권5호
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• pp.1089-1102
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• 2017

In software systems, it has been observed that a fault is often caused by an interaction between a small number of input parameters. Even for moderately sized software systems, exhaustive testing is practically impossible to achieve. This is either due to time or cost constraints. Combinatorial (t-way) testing provides a technique to select a subset of exhaustive test cases covering all of the t-way interactions, without much of a loss to the fault detection capability. In this paper, an approach is proposed to generate 2-way (pairwise) test sets using genetic algorithms. The performance of the algorithm is improved by creating an initial solution using the overlap coefficient (a similarity matrix). Two mutation strategies have also been modified to improve their efficiency. Furthermore, the mutation operator is improved by using a combination of three mutation strategies. A comparative survey of the techniques to generate t-way test sets using genetic algorithms was also conducted. It has been shown experimentally that the proposed approach generates faster results by achieving higher percentage coverage in a fewer number of generations. Additionally, the size of the mixed covering arrays was reduced in one of the six benchmark problems examined.

• International Journal of Computer Science & Network Security
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• 제21권12호
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• pp.175-182
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• 2021

Deadlock is a situation in which two or more processes competing for resources are waiting for the others to finish, and neither ever does. There are two different forms of systems, multi-unit and single-unit resource systems. The difference is the number of instances (or units) of each type of resource. Deadlock problem can be modeled as a constrained combinatorial problem that seeks to find a possible scheduling for the processes through which the system can avoid entering a deadlock state. To solve deadlock problem, several algorithms and techniques have been introduced, but the use of metaheuristics is one of the powerful methods to solve it. Genetic algorithms have been effective in solving many optimization issues, including deadlock Problem. In this paper, an improved parallel framework of the genetic algorithm is introduced and adapted effectively and efficiently to deadlock problem. The proposed modified method is implemented in java and tested on a specific dataset. The experiment shows that proposed approach can produce optimal solutions in terms of burst time and the number of feasible solutions in each advanced generation. Further, the proposed approach enables all types of crossovers to work with high performance.

• Asian-Australasian Journal of Animal Sciences
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• 제22권1호
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• pp.124-130
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• 2009

Estimating genetic interaction effects in animal genomics would be one of the most challenging studies because the phenotypic variation for economically important traits might be largely explained by interaction effects among multiple nucleotide sequence variants under various environmental exposures. Genetic improvement of economic animals would be expected by understanding multi-locus genetic interaction effects associated with economic traits. Most analyses in animal breeding and genetics, however, have excluded the possibility of genetic interaction effects in their analytical models. This review discusses a historical estimation of the genetic interaction and difficulties in analyzing the interaction effects. Furthermore, two recently developed methods for assessing genetic interactions are introduced to animal genomics. One is the restricted partition method, as a nonparametric grouping-based approach, that iteratively utilizes grouping of genotypes with the smallest difference into a new group, and the other is the Bayesian method that draws inferences about the genetic interaction effects based on their marginal posterior distributions and attains the marginalization of the joint posterior distribution through Gibbs sampling as a Markov chain Monte Carlo. Further developing appropriate and efficient methods for assessing genetic interactions would be urgent to achieve accurate understanding of genetic architecture for complex traits of economic animals.

• Genomics & Informatics
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• 제14권4호
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• pp.187-195
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• 2016

In genetic association studies with high-dimensional genomic data, multiple group testing procedures are often required in order to identify disease/trait-related genes or genetic regions, where multiple genetic sites or variants are located within the same gene or genetic region. However, statistical testing procedures based on an individual test suffer from multiple testing issues such as the control of family-wise error rate and dependent tests. Moreover, detecting only a few of genes associated with a phenotype outcome among tens of thousands of genes is of main interest in genetic association studies. In this reason regularization procedures, where a phenotype outcome regresses on all genomic markers and then regression coefficients are estimated based on a penalized likelihood, have been considered as a good alternative approach to analysis of high-dimensional genomic data. But, selection performance of regularization procedures has been rarely compared with that of statistical group testing procedures. In this article, we performed extensive simulation studies where commonly used group testing procedures such as principal component analysis, Hotelling's $T^2$ test, and permutation test are compared with group lasso (least absolute selection and shrinkage operator) in terms of true positive selection. Also, we applied all methods considered in simulation studies to identify genes associated with ovarian cancer from over 20,000 genetic sites generated from Illumina Infinium HumanMethylation27K Beadchip. We found a big discrepancy of selected genes between multiple group testing procedures and group lasso.

• Genomics & Informatics
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• 제14권4호
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• pp.255-264
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• 2016

The plethora of genome sequence information of bacteria in recent times has ushered in many novel strategies for antibacterial drug discovery and facilitated medical science to take up the challenge of the increasing resistance of pathogenic bacteria to current antibiotics. In this study, we adopted subtractive genomics approach to analyze the whole genome sequence of the Fusobacterium nucleatum, a human oral pathogen having association with colorectal cancer. Our study divulged 1,499 proteins of F. nucleatum, which have no homolog's in human genome. These proteins were subjected to screening further by using the Database of Essential Genes (DEG) that resulted in the identification of 32 vitally important proteins for the bacterium. Subsequent analysis of the identified pivotal proteins, using the Kyoto Encyclopedia of Genes and Genomes (KEGG) Automated Annotation Server (KAAS) resulted in sorting 3 key enzymes of F. nucleatum that may be good candidates as potential drug targets, since they are unique for the bacterium and absent in humans. In addition, we have demonstrated the three dimensional structure of these three proteins. Finally, determination of ligand binding sites of the 2 key proteins as well as screening for functional inhibitors that best fitted with the ligands sites were conducted to discover effective novel therapeutic compounds against F. nucleatum.

• 식물조직배양학회지
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• 제27권4호
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• pp.259-268
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• 2000

Senescence is a sequence of biochemical and physiological events that lead to death of a cell, organ, or whole organism. Senescence is now clearly regarded as a genetically determined and evolutionarilly acquired developmental process comprising the final stage of development. However, in spite of the biological and practical importance, genetic mechanism of senescence has been very limited. Through forward and reverse genetic approaches, we are trying to reveal the molecular and genetic mechanism of senescence in plants, employing leaf organs of Arabidopsis as a model system. Using forward genetic approach, we have initially isolated several delayed senescence mutants either from T-DNA insertional lines or chemical-mutagenized lines. In the case of ore 4 and ore 9 mutants, the mutated genes were identified. The recent progress on characterization of mutants and identification of the mutated genes will be reported. We are also screening mutations from other various sources of mutant pools, such as activation tagging lines and promoter trap lines. Two dominant senescence-delayed mutants were isolated from the activation tagging pool. Cloning of the genes responsible for this phenotype is in progress. For reverse genetic approach, the genes that induced during leaf senescence were first isolated by differential screening method. We are currently using PCR-based suppression subtractive hybridization, designed to enrich a cDNA library for rare differentially expressed transcripts. Using this method, we have identified over 35 new sequences that are upregulated at leaf senescence stage. We are investigating the function of these novel genes by systemically generating antisense lines.

• Genomics & Informatics
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• 제21권3호
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• pp.42.1-42.23
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• 2023

Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, one of the most deadly infections in humans. The emergence of multidrug-resistant and extensively drug-resistant Mtb strains presents a global challenge. Mtb has shown resistance to many frontline antibiotics, including rifampicin, kanamycin, isoniazid, and capreomycin. The only licensed vaccine, Bacille Calmette-Guerin, does not efficiently protect against adult pulmonary tuberculosis. Therefore, it is urgently necessary to develop new vaccines to prevent infections caused by these strains. We used a subtractive proteomics approach on 23 virulent Mtb strains and identified a conserved membrane protein (MmpL4, NP_214964.1) as both a potential drug target and vaccine candidate. MmpL4 is a non-homologous essential protein in the host and is involved in the pathogen-specific pathway. Furthermore, MmpL4 shows no homology with anti-targets and has limited homology to human gut microflora, potentially reducing the likelihood of adverse effects and cross-reactivity if therapeutics specific to this protein are developed. Subsequently, we constructed a highly soluble, safe, antigenic, and stable multi-subunit vaccine from the MmpL4 protein using immunoinformatics. Molecular dynamics simulations revealed the stability of the vaccine-bound Tolllike receptor-4 complex on a nanosecond scale, and immune simulations indicated strong primary and secondary immune responses in the host. Therefore, our study identifies a new target that could expedite the design of effective therapeutics, and the designed vaccine should be validated. Future directions include an extensive molecular interaction analysis, in silico cloning, wet-lab experiments, and evaluation and comparison of the designed candidate as both a DNA vaccine and protein vaccine.

• Genomics & Informatics
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• 제21권4호
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• pp.48.1-48.8
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• 2023

Liver cancer is the fourth leading cause of death worldwide. Well-known risk factors include hepatitis B virus and hepatitis C virus, along with exposure to aflatoxins, excessive alcohol consumption, obesity, and type 2 diabetes. Genomic variants play a crucial role in mediating the associations between these risk factors and liver cancer. However, the specific variants involved in this process remain under-explored. This study utilized a bioinformatics approach to identify genetic variants associated with liver cancer from various continents. Single-nucleotide polymorphisms associated with liver cancer were retrieved from the genome-wide association studies catalog. Prioritization was then performed using functional annotation with HaploReg v4.1 and the Ensembl database. The prevalence and allele frequencies of each variant were evaluated using Pearson correlation coefficients. Two variants, rs2294915 and rs2896019, encoded by the PNPLA3 gene, were found to be highly expressed in the liver tissue, as well as in the skin, cell-cultured fibroblasts, and adipose-subcutaneous tissue, all of which contribute to the risk of liver cancer. We further found that these two SNPs (rs2294915 and rs2896019) were positively correlated with the prevalence rate. Positive associations with the prevalence rate were more frequent in East Asian and African populations. We highlight the utility of this population-specific PNPLA3 genetic variant for genetic association studies and for the early prognosis and treatment of liver cancer. This study highlights the potential of integrating genomic databases with bioinformatic analysis to identify genetic variations involved in the pathogenesis of liver cancer. The genetic variants investigated in this study are likely to predispose to liver cancer and could affect its progression and aggressiveness. We recommend future research prioritizing the validation of these variations in clinical settings.

• 한국전자통신학회논문지
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• 제19권2호
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• pp.417-426
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• 2024

일반적으로 머신러닝을 수행하기 위해서는 딥러닝 모델에 대한 사전 지식과 경험이 필요하고, 데이터를 연산하기 위해 고성능 하드웨어와 많은 시간이 필요하게 된다. 이러한 이유로 머신러닝은 임베디드 프로세서에서 실행하기에는 많은 제약이 있다.본 논문에서는 이러한 문제를 해결하기 위해 머신러닝의 과정 중 콘볼루션 연산(Convolution operation)에 유전 알고리즘을 적용하여 선택적 콘볼루션 연산(Selective convolution operation)과 학습 방법을 제안한다. 선택적 콘볼루션 연산에서는 유전 알고리즘에 의해 추출된 픽셀에 대해서만 콘볼루션을 수행하는 방식이다. 이 방식은 유전 알고리즘에서 지정한 비율만큼 픽셀을 선택하여 연산하는 방식으로 연산량을 지정된 비율만큼 줄일 수 있다. 본 논문에서는 유전 알고리즘을 적용한 머신러닝 연산의 심화학습을 진행하여 해당 세대의 적합도가 목표치에 도달하는지 확인하고 기존 방식의 연산량과 비교한다. 적합도가 충분히 수렴할 수 있도록 세대를 반복하여 학습하고, 적합도가 높은 모델을 유전 알고리즘의 교배와 돌연변이를 통해 다음 세대의 연산에 활용한다.