• Journal of Physiology & Pathology in Korean Medicine
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• v.18 no.5
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• pp.1291-1300
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• 2004

Baicalin, a biologically active flavonoid form the roots of Scutallaria baicalensis (Skullcap), have been reported to not only function as anti-oxidants but also cause anticancer effect. We investigated the mechanism of baicalin-induced cytotoxicity and the macro scale gene expression analysis in leukemia cell line, HL-60 cells. Baicalin (10 μM) were used to treat the cells for 6h, 12h, 24h, 48h and 72h. In a human cDNAchip study of 65,000 genes evaluated 6, 12, 24, 48. 72 hours after treated with Baicalin in HL-60 cells. Hierarchical cluster against the genes which showed expression changes by more than two fold. One hundred one genes were grouped into 6 clusters according to their profile of expression by a hierarchical clustering algorithm. For genes differentially expressed in response to baicalin treatment, we tested functional classes based on Gene Ontology (GO) terms. This study provides the most comprehensive available survey of gene expression changes in response to baicalin treatment in HL-60 cell line.

• Journal of the Institute of Convergence Signal Processing
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• v.7 no.4
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• pp.201-206
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• 2006

Genetic Algorithms have been known to provide near optimal solutions for various optimization problems in engineering. In this paper, we study the effect of gene order in genetic algorithms on the defining length of the schema with high fitness values. Its effect on the performance of genetic algorithms was also analyzed through two well known problems. A few gene reordering methods were proposed for graph partitioning and knapsack problems. Experimental results showed that genetic algorithms with gene reordering could find solutions of better qualities compared to the ones without gene reordering. It is very important to find proper reordering method for a given problem to improve the performance of genetic algorithms.

• Proceedings of the Korean Society of Computer Information Conference
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• 2009.01a
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• pp.41-44
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• 2009

데이터 마이닝의 대표적인 기법인 군집화는 군집내의 유사성을 최대화하고, 군집들간의 유사성을 최소화 시키도록 데이터의 집합을 분할하는 것이다. 대용량의 데이터베이스에서 최적의 효율화를 내기 위해서는 원시데이터에 대한 접근 횟수를 줄이고, 이것을 알고리즘 적용 대상이 데이터 구조의 크기를 줄이는 군집화 기법에 많은 관심이 보이고 있다. 본 논문에서는 유전자 알고리즘을 이용하여 자동으로 군집의 개수를 결정하는 군집화 알고리즘을 제안하는 적합도 함수는 보다 양질의 군집을 찾아내는 것으로 평가 되었다. 또한 유전자 알고리즘 중 8가지를 세부 분석하여 평가하였다.

• Journal of Microbiology and Biotechnology
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• v.16 no.5
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• pp.748-756
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• 2006

We propose a genome-scale clustering approach to identify whole genome relationships using the functional groups given by the Kyoto Encyclopedia of Genes and Genomes Orthology (KO) database. The metabolic capabilities of each organism were defined by the number of genes in each functional category. The archaeal, bacterial, and eukaryotic genomes were compared by simultaneously applying a two-step clustering method, comprised of a self-organizing tree algorithm followed by unsupervised hierarchical clustering. The clustering results were consistent with various phenotypic characteristics of the organisms analyzed and, additionally, showed a different aspect of the relationship between genomes that have previously been established through rRNA-based comparisons. The proposed approach to collect and cluster the metabolic functional capabilities of organisms should make it a useful tool in predicting relationships among organisms.

• Journal of Institute of Control, Robotics and Systems
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• v.16 no.3
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• pp.227-232
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• 2010

In this paper we consider the multi-robot system that collects target objects spread in an unexplored environment. The robots cooperate each other to improve the capability and the efficiency. The robots attract or intimidate each other as behaviors of bacterial swarms or particles with electrical moments. The interactions would increase the working efficiency in some environments but it would decrease the efficiency in some other environments. Therefore, the system needs to adapt to the working environment by adjusting the strengths of the interactions. The strengths of the interactions are expressed as sets of gene codes that mean the weights of each kind of attracting or intimidating vectors. The proposed system adjusts the gene codes using evolutional strategy. The proposed approach has been validated by computer simulation. The results of this paper show that our inter-swarm interacting strategy and optimizing algorithm improves the working efficiency, adaptively to the characteristics of environments.

• Bioinformatics and Biosystems
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• v.2 no.1
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• pp.24-27
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• 2007

Human cell regulatory mechanism is one of suspicious problems among biologists. Here we tried to uncover the human breast cancer cell regulatory mechanism from gene expression data (Marc J. Van de vijver, et. al., 2002) using a module network algorithm which is suggested by Segal, et. al.(2003) Finally, we derived a module network which consists of 50 modules and 10 tree depths. Moreover, to validate this candidate network, we applied a GO enrichment test and known transcription factor-target relationships from Transfac(R) (V. Matys, et. al, 2006) and HPRD database (Peri, S. et al., 2003).

• The KIPS Transactions:PartB
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• v.12B no.4 s.100
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• pp.429-436
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• 2005

A simple stereo matching algorithm using population-based incremental learning(PBIL) is proposed in this paper to decrease the general problem of genetic algorithms, such as memory consumption and inefficiency of search. PBIL is a variation of genetic algorithms using stochastic search and competitive teaming based on a probability vector. The structure of PBIL is simpler than that of other genetic algorithm families, such as serial and parallel ones, due to the use of a probability vector. The PBIL strategy is simplified and adapted for stereo matching circumstances. Thus, gene pool, chromosome crossover, and gene mutation we removed, while the evolution rule, that fitter chromosomes should have higher survival probabilities, is preserved. As a result, memory space is decreased, matching rules are simplified and computation cost is reduced. In addition, a scheme controlling the distance of neighbors for disparity smoothness is inserted to obtain a wide-area consistency of disparities, like a result of coarse-to-fine matchers. Because of this scheme, the proposed algorithm can produce a stable disparity map with a small fixed-size window. Finally, an alterative version of the proposed algorithm without using probability vector is also presented for simpler set-ups.

• The Korean Journal of Applied Statistics
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• v.20 no.1
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• pp.167-181
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• 2007

Many clustering algorithms and cluster validation techniques for high-dimensional gene expression data have been suggested. The evaluations of these cluster validation techniques have, however, seldom been implemented. In this paper we compared various cluster validity indices for low-dimensional simulation data and real gene expression data, and found that Dunn's index is the most effective and robust, Silhouette index is next and Davies-Bouldin index is the bottom among the internal measures. Jaccard index is much more effective than Goodman-Kruskal index and adjusted Rand index among the external measures.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.2
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• pp.835-838
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• 2016

Background: Lung cancer remains one of the most common cancers in the world, both in terms of new cases (about 13% of total per year) and deaths (nearly one cancer death in five), because of the high case fatality. Errors in lung cancer type or malignant growth determination lead to degraded treatment efficacy, because anticancer strategy depends on tumor morphology. Materials and Methods: We have made an attempt to evaluate effectiveness of machine learning algorithms in the task of lung cancer classification based on gene expression levels. We processed four publicly available data sets. The Dana-Farber Cancer Institute data set contains 203 samples and the task was to classify four cancer types and sound tissue samples. With the University of Michigan data set of 96 samples, the task was to execute a binary classification of adenocarcinoma and non-neoplastic tissues. The University of Toronto data set contains 39 samples and the task was to detect recurrence, while with the Brigham and Women's Hospital data set of 181 samples it was to make a binary classification of malignant pleural mesothelioma and adenocarcinoma. We used the k-nearest neighbor algorithm (k=1, k=5, k=10), naive Bayes classifier with assumption of both a normal distribution of attributes and a distribution through histograms, support vector machine and C4.5 decision tree. Effectiveness of machine learning algorithms was evaluated with the Matthews correlation coefficient. Results: The support vector machine method showed best results among data sets from the Dana-Farber Cancer Institute and Brigham and Women's Hospital. All algorithms with the exception of the C4.5 decision tree showed maximum potential effectiveness in the University of Michigan data set. However, the C4.5 decision tree showed best results for the University of Toronto data set. Conclusions: Machine learning algorithms can be used for lung cancer morphology classification and similar tasks based on gene expression level evaluation.

• Genomics & Informatics
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• v.10 no.2
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• pp.123-127
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• 2012

Gene set analysis (GSA) is useful in interpreting a genome-wide association study (GWAS) result in terms of biological mechanism. We compared the performance of two different GSA implementations that accept GWAS p-values of single nucleotide polymorphisms (SNPs) or gene-by-gene summaries thereof, GSA-SNP and i-GSEA4GWAS, under the same settings of inputs and parameters. GSA runs were made with two sets of p-values from a Korean type 2 diabetes mellitus GWAS study: 259,188 and 1,152,947 SNPs of the original and imputed genotype datasets, respectively. When Gene Ontology terms were used as gene sets, i-GSEA4GWAS produced 283 and 1,070 hits for the unimputed and imputed datasets, respectively. On the other hand, GSA-SNP reported 94 and 38 hits, respectively, for both datasets. Similar, but to a lesser degree, trends were observed with Kyoto Encyclopedia of Genes and Genomes (KEGG) gene sets as well. The huge number of hits by i-GSEA4GWAS for the imputed dataset was probably an artifact due to the scaling step in the algorithm. The decrease in hits by GSA-SNP for the imputed dataset may be due to the fact that it relies on Z-statistics, which is sensitive to variations in the background level of associations. Judicious evaluation of the GSA outcomes, perhaps based on multiple programs, is recommended.