상대적 계층적 군집 방법을 이용한 마이크로어레이 자료의 군집분석

우숙영,이재원,전명식 한국데이터정보과학회 2014 한국데이터정보과학회지 Vol.25 No.5

Hierarchical clustering analysis helps easily exploring massive microarray data and understanding biological phenomena with dendrogram. But, because hierarchical clustering algorithms only consider the absolute similarity, it is difficult to illustrate a relative dissimilarity, which consider not only the distance between a pair of clusters, but also how distant are they from the rest of the clusters. In this study, we introduced the relative hierarchical clustering method proposed by Mollineda and Vidal(2000) and compared hierarchical clustering method and relative hierarchical method using the simulated data and the real data in the various situations. The evaluation of the quality of two hierarchical methods was performed using percentage of incorrectly grouped points (PIGP), homogeneity and separation. 계층적 군집 분석은 분석 결과를 덴드로그램으로 쉽게 표시할 수 있어서 방대한 양의 마이크로어레이 자료를 탐색하기에 유용하며, 군집된 결과를 이용하여 생물학적 현상을 이해하는데 도움을 준다. 하지만, 계층적 군집방법은 두 군집간의 절대값 거리만을 고려하여 병합하기 때문에 군집 간의 상대적 비유사성은 설명하지 못하는 단점이 있다. 본 연구에서는 상대적 계층적 군집 방법을 소개하고, 마이크로어레이 자료와 같이 다양한 군집의 모양을 가진 모의실험 자료들과 실제 마이크로어레이 자료를 사용하여 상대적 계층적 군집방법과 기존의 계층적 군집 방법을 비교하였다. 두 계층적 군집 방법의 질적 평가는 오분류율, 동질성, 이질성 지표를 이용하여 수행하였다.

Performance Analysis of Clustering using Partitioning and Hierarchical Clustering Techniques

S. C. Punitha,P. Ranjith Jeba Thangaiah,M. Punithavalli 보안공학연구지원센터 2014 International Journal of Database Theory and Appli Vol.7 No.6

Text clustering is the method of combining text or documents which are similar and dissimilar to one another. In several text tasks, this text mining is used such as extraction of information and concept/entity, summarization of documents, modeling of relation with entity, categorization/classification and clustering. This text mining categorizes only digital documents or text and it is a method of data mining. It is the method of combining text document into category and applied in various applications such as retrieval of information, web or corporate information systems. Clustering is also called unsupervised learning because like other document classification, no labeled documents are providing in clustering; hence, clustering is also known as unsupervised learning. A new method called Hierarchical Agglomerative Clustering (HAC) which manages clusters as tree like structure that make possible for browsing. In this HAC method, the nodes in the tree can be viewed as parent-child relationship i.e. topic-subtopic relationship in a hierarchy. HAC method starts with each example in its own cluster and iteratively combines them to form larger and larger clusters. The main focus of this work is to present a performance analysis of various techniques available for document clustering.

Clustering Approaches to Identifying Gene Expression Patterns from DNA Microarray Data

Do, Jinhwan,Choi, Dongkug Korean Society for Molecular Biology 2008 Molecules and cells Vol.25 No.2

The analysis of microarray data is essential for large amounts of gene expression data. In this review we focus on clustering techniques. The biological rationale for this approach is the fact that many co-expressed genes are co-regulated, and identifying co-expressed genes could aid in functional annotation of novel genes, de novo identification of transcription factor binding sites and elucidation of complex biological pathways. Co-expressed genes are usually identified in microarray experiments by clustering techniques. There are many such methods, and the results obtained even for the same datasets may vary considerably depending on the algorithms and metrics for dissimilarity measures used, as well as on user-selectable parameters such as desired number of clusters and initial values. Therefore, biologists who want to interpret microarray data should be aware of the weakness and strengths of the clustering methods used. In this review, we survey the basic principles of clustering of DNA microarray data from crisp clustering algorithms such as hierarchical clustering, K-means and self-organizing maps, to complex clustering algorithms like fuzzy clustering.

Clustering Approaches to Identifying Gene Expression Patterns from DNA Microarray Data

도진환,최동국 한국분자세포생물학회 2008 Molecules and cells Vol.25 No.2

The analysis of microarray data is essential for large amounts of gene expression data. In this review we focus on clustering techniques. The biological rationale for this approach is the fact that many coexpressed genes are co-regulated, and identifying coexpressed genes could aid in functional annotation of novel genes, de novo identification of transcription factor binding sites and elucidation of complex biological pathways. Co-expressed genes are usually identified in microarray experiments by clustering techniques. There are many such methods, and the results obtained even for the same datasets may vary considerably depending on the algorithms and metrics for dissimilarity measures used, as well as on userselectable parameters such as desired number of clusters and initial values. Therefore, biologists who want to interpret microarray data should be aware of the weakness and strengths of the clustering methods used. In this review, we survey the basic principles of clustering of DNA microarray data from crisp clustering algorithms such as hierarchical clustering, K-means and self-organizing maps, to complex clustering algorithms like fuzzy clustering.

Proposal of a hierarchical topology and spatial reuse superframe for enhancing throughput of a cluster‐based WBAN

Pham Thanh Hiep,Nguyen Nhu Thang,Guanghao Sun,Nguyen Huy Hoang 한국전자통신연구원 2019 ETRI Journal Vol.41 No.5

A cluster topology was proposed with the assumption of zero noise to improve the performance of wireless body area networks (WBANs). However, in WBANs, the transmission power should be reduced as low as possible to avoid the effect of electromagnetic waves on the human body and to extend the lifetime of a battery. Therefore, in this work, we consider a bit error rate for a cluster‐based WBAN and analyze the performance of the system while the transmission of sensors and cluster headers (CHs) is controlled. Moreover, a hierarchical topology is proposed for the cluster‐based WBAN to further improve the throughput of the system; this proposed system is called as the hierarchical cluster WBAN. The hierarchical cluster WBAN is combined with a transmission control scheme, that is, complete control, spatial reuse superframe, to increase the throughput. The proposed system is analyzed and evaluated based on several factors of the system model, such as signal‐to‐noise ratio, number of clusters, and number of sensors. The calculation result indicates that the proposed hierarchical cluster WBAN outperforms the cluster‐based WBAN in all analyzed scenarios.

The Cluster Head Preferred Hierarchical Clustering Routing Protocol Based on G-Means in Wireless Sensor Networks

Tianshu Wang,Gongxuan Zhang,Xichen Yang,Yang Lv 보안공학연구지원센터 2015 International Journal of Future Generation Communi Vol.8 No.3

In hierarchical structures determined by traditional routing protocols of wireless sensor networks, clustering is not structured and the networks prone to generate scatters, leading to some nodes die quickly. So this paper presents a cluster head preferred hierarchical clustering routing protocol based on G-Means (GHPHC). It uses G-Means algorithm to detect each clustering structure, so that each cluster is Gaussian distribution and it avoids the generation of scatters. At the same time, the cluster head preferred algorithm proposed in this paper gives the corresponding weight for each node of all clusters, thus select a suitable cluster head node for every cluster. Experimental results show that compared to traditional routing protocols, the death rate of nodes in a wireless sensor network which uses GHPHC protocol is more slow, and has a longer life cycle.

OPAC에서 탐색결과의 클러스터링에 관한 연구

노정순 한국문헌정보학회 2004 한국문헌정보학회지 Vol.38 No.1

This study evaluated the applicability of the static hierarchic clustering model to clustering query results in OPAC. Two clustering methods(Between Average Linkage(BAL) and Complete Linkage(CL)) and two similarity coefficients(Dice and Jaccard) were tested on the query results retrieved from 16 title-based keyword searchings. The precision of optimal clusters was improved more than 100% compared with title-word searching. There was no difference between similarity coefficients but clustering methods in optimal cluster effectiveness. CL method is better in precision ratio but BAL is better in recall ratio at the optimal top-level and bottom-level clusters. However the differences are not significant except higher recall ratio of BAL at the top-level cluster. Small number of clusters and long chain of hierarchy for optimal cluster resulted from BAL could not be desirable and efficient. 본 연구는 한글 OPAC에서 문헌의 분류와 된 탐색결과를 클러스터링하는데도 효과적인지를 규명하기 위해 수행되었다. 서명에 출현하는 단어와 색인자가 부여한 통제어를 통합한 색인어를 이진빈도로 가중치를 주어, 다이스와 자카드 계수, 집단간 평균연결과 완전연결 클러스터링 기법이 테스트되었다. 16개의 서명단어 탐색으로 검색된 문헌을 클러스터링한 결과 최적으로 선택된 클러스터의정확률은 유사도 계수나 클러스터링 기법에 관계없이 서명단어탐색보다 100%이상 향상되었다. 1단계와 최종단계 클러로 유의한 수준은 아니었다. 1단계 클러스터에서 집단간 평균연결이 보다 높은 재현율을 보인 것은 유의하였다. 다이스와 자카드 사이에 차이는 없었다. 최종클러스터가 선택되기까지 집단간 평균연결은 너무 긴 계층군집 단계를 필요로하여 탐색효율 측면에서 바람직해 보이지 않았다.

Comparisons on Clustering Methods: Use of LMS Log Variables on Academic Courses

( Il-hyun Jo ),( Yeonjeong Park ),( Jongwoo Song ) 한국교육공학회 2017 Educational Technology International Vol.18 No.2

Academic analytics guides university decision-makers to assign limited resources more effectively. Especially, diverse academic courses clustered by the usage patterns and levels on Learning Management System(LMS) help understanding instructors’ pedagogical approach and the integration level of technologies. Further, the clustering results can contribute deciding proper range and levels of financial and technical supports. However, in spite of diverse analytic methodologies, clustering analysis methods often provide different results. The purpose of this study is to present implications by using three different clustering analysis including Gaussian Mixture Model, K-Means clustering, and Hierarchical clustering. As a case, we have clustered academic courses based on the usage levels and patterns of LMS in higher education using those three clustering techniques. In this study, 2,639 courses opened during 2013 fall semester in a large private university located in South Korea were analyzed with 13 observation variables that represent the characteristics of academic courses. The results of analysis show that the strengths and weakness of each clustering analysis and suggest that academic leaders and university staff should look into the usage levels and patterns of LMS with more elaborated view and take an integrated approach with different analytic methods for their strategic decision on development of LMS.

Magnetoencephalography Interictal Spike Clustering in Relation with Surgical Outcome of Cortical Dysplasia

Jeong, Woorim,Chung, Chun Kee,Kim, June Sic The Korean Neurosurgical Society 2012 Journal of Korean neurosurgical society Vol.52 No.5

Objective : The aim of this study was to devise an objective clustering method for magnetoencephalography (MEG) interictal spike sources, and to identify the prognostic value of the new clustering method in adult epilepsy patients with cortical dysplasia (CD). Methods : We retrospectively analyzed 25 adult patients with histologically proven CD, who underwent MEG examination and surgical resection for intractable epilepsy. The mean postoperative follow-up period was 3.1 years. A hierarchical clustering method was adopted for MEG interictal spike source clustering. Clustered sources were then tested for their prognostic value toward surgical outcome. Results : Postoperative seizure outcome was Engel class I in 6 (24%), class II in 3 (12%), class III in 12 (48%), and class IV in 4 (16%) patients. With respect to MEG spike clustering, 12 of 25 (48%) patients showed 1 cluster, 2 (8%) showed 2 or more clusters within the same lobe, 10 (40%) showed 2 or more clusters in a different lobe, and 1 (4%) patient had only scattered spikes with no clustering. Patients who showed focal clustering achieved better surgical outcome than distributed cases (p=0.017). Conclusion : This is the first study that introduces an objective method to classify the distribution of MEG interictal spike sources. By using a hierarchical clustering method, we found that the presence of focal clustered spikes predicts a better postoperative outcome in epilepsy patients with CD.

계층 발생 프레임워크를 이용한 군집 계층 시각화

신동화(DongHwa Shin),이세희(Sehi L’Yi),서진욱(Jinwook Seo) 한국정보과학회 2015 정보과학회 컴퓨팅의 실제 논문지 Vol.21 No.6

군집화 알고리즘은 그 종류에 따라 만들어낼 수 있는 군집의 종류와 보여줄 수 있는 정보의 수준이 차이가 난다. 밀도기반 군집화 알고리즘은 데이터 분포 상의 임의의 모양을 가진 군집을 잘 잡아내지만 보여줄 수 있는 계층정보가 매우 적거나 없는 수준이고, 반면 계층적 군집화 알고리즘은 자세한 계층 정보를 보여주지만 구 모양의 군집 외에는 잘 잡아내지 못한다. 이 논문에서는 이러한 두 군집화 방식의 대표적 알고리즘인 OPTICS와 응집 계층 군집화 알고리즘의 장점만을 취하는 계층 발생 프레임워크를 제시하고 이와 더불어 효과적 데이터 분석을 위한 여러 시각화, 상호작용 기법을 지원하는 시각적 분석 애플리케이션을 제공한다. There are many types of clustering algorithms such as centroid, hierarchical, or density-based methods. Each algorithm has unique data grouping principles, which creates different varieties of clusters. Ordering Points To Identify the Clustering Structure (OPTICS) is a well-known density-based algorithm to analyze arbitrary shaped and varying density clusters, but the obtained clusters only correlate loosely. Hierarchical agglomerative clustering (HAC) reveals a hierarchical structure of clusters, but is unable to clearly find non-convex shaped clusters. In this paper, we provide a novel hierarchy generation framework and application which can aid users by combining the advantages of the two clustering methods.