scholarly journals PENERAPAN k-MODES CLUSTERING DENGAN VALIDASI DUNN INDEX PADA PENGELOMPOKAN KARAKTERISTIK CALON TKI MENGGUNAKAN R-GUI

2021 ◽  
Vol 10 (3) ◽  
pp. 359-366
Author(s):  
Hanik Malikhatin ◽  
Agus Rusgiyono ◽  
Di Asih I Maruddani
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Categorical Data ◽  
Optimal Number ◽  
Class I ◽  
Number Of Clusters ◽  
The Government ◽  
Index Value ◽  
Cluster 2 ◽  
Optimal Number Of Clusters

Prospective TKI workers who apply for passports at the Immigration Office Class I Non TPI Pati have countries destinations and choose different PPTKIS agencies. Therefore, the grouping of characteristics prospective TKI needed so that can be used as a reference for the government in an effort to improve the protection of TKI in destination countries and carry out stricter supervision of PPTKIS who manage TKI. The purpose of this research is to classify the characteristics of prospective TKI workers with the optimal number of clusters. The method used is k-Modes Clustering with values of k = 2, 3, 4, and 5. This method can agglomerate categorical data. The optimal number of clusters can be determined using the Dunn Index. For grouping data easily, then compiled a Graphical User Interface (GUI) based application with RStudio. Based on the analysis, the optimal number of clusters is two clusters with a Dunn Index value of 0,4. Cluster 1 consists of mostly male TKI workers (51,04%), aged ≥ 20 years old (91,93%), with the destination Malaysia country (47%), and choosing PPTKIS Surya Jaya Utama Abadi (37,51%), while cluster 2, mostly of male TKI workers (94,10%), aged ≥ 20 years old (82,31%), with the destination Korea Selatan country (77,95%), and choosing PPTKIS BNP2TKI (99,78%). 

scholarly journals Internal evaluation criteria for categorical data in hierarchical clustering

2018 ◽  
Vol 15 (2) ◽  
Author(s):  
Zdeněk Šulc ◽  
Jana Cibulková ◽  
Jiří Procházka ◽  
Hana Řezanková
Keyword(s):  
Hierarchical Clustering ◽  
Categorical Data ◽  
Likelihood Function ◽  
Evaluation Criteria ◽  
Optimal Number ◽  
Number Of Clusters ◽  
Internal Evaluation ◽  
Correct Number ◽  
Cluster Quality ◽  
Optimal Number Of Clusters

The paper compares 11 internal evaluation criteria for hierarchical clustering of categorical data regarding a correct number of clusters determination. The criteria are divided into three groups based on a way of treating the cluster quality. The variability-based criteria use the within-cluster variability, the likelihood-based criteria maximize the likelihood function, and the distance-based criteria use distances within and between clusters. The aim is to determine which evaluation criteria perform well and under what conditions. Different analysis settings, such as the used method of hierarchical clustering, and various dataset properties, such as the number of variables or the minimal between-cluster distances, are examined. The experiment is conducted on 810 generated datasets, where the evaluation criteria are assessed regarding the optimal number of clusters determination and mean absolute errors. The results indicate that the likelihood-based BIC1 and variability-based BK criteria perform relatively well in determining the optimal number of clusters and that some criteria, usually the distance-based ones, should be avoided.

Clustering Count-based RNA Methylation Data Using a Nonparametric Generative Model

2018 ◽  
Vol 14 (1) ◽  
pp. 11-23 ◽  
Author(s):  
Lin Zhang ◽  
Yanling He ◽  
Huaizhi Wang ◽  
Hui Liu ◽  
Yufei Huang ◽  
...  
Keyword(s):  
Clustering Analysis ◽  
Methylation Level ◽  
Optimal Number ◽  
Generative Model ◽  
Methylation Data ◽  
Sequencing Data ◽  
Number Of Clusters ◽  
Rna Methylation ◽  
Clustering Effect ◽  
Optimal Number Of Clusters

Background: RNA methylome has been discovered as an important layer of gene regulation and can be profiled directly with count-based measurements from high-throughput sequencing data. Although the detailed regulatory circuit of the epitranscriptome remains uncharted, clustering effect in methylation status among different RNA methylation sites can be identified from transcriptome-wide RNA methylation profiles and may reflect the epitranscriptomic regulation. Count-based RNA methylation sequencing data has unique features, such as low reads coverage, which calls for novel clustering approaches. <P><P> Objective: Besides the low reads coverage, it is also necessary to keep the integer property to approach clustering analysis of count-based RNA methylation sequencing data. <P><P> Method: We proposed a nonparametric generative model together with its Gibbs sampling solution for clustering analysis. The proposed approach implements a beta-binomial mixture model to capture the clustering effect in methylation level with the original count-based measurements rather than an estimated continuous methylation level. Besides, it adopts a nonparametric Dirichlet process to automatically determine an optimal number of clusters so as to avoid the common model selection problem in clustering analysis. <P><P> Results: When tested on the simulated system, the method demonstrated improved clustering performance over hierarchical clustering, K-means, MClust, NMF and EMclust. It also revealed on real dataset two novel RNA N6-methyladenosine (m6A) co-methylation patterns that may be induced directly by METTL14 and WTAP, which are two known regulatory components of the RNA m6A methyltransferase complex. <P><P> Conclusion: Our proposed DPBBM method not only properly handles the count-based measurements of RNA methylation data from sites of very low reads coverage, but also learns an optimal number of clusters adaptively from the data analyzed. <P><P> Availability: The source code and documents of DPBBM R package are freely available through the Comprehensive R Archive Network (CRAN): https://cran.r-project.org/web/packages/DPBBM/.

Investigating cluster validation metrics for optimal number of clusters determination

2021 ◽  
pp. 1-16
Author(s):  
Aikaterini Karanikola ◽  
Charalampos M. Liapis ◽  
Sotiris Kotsiantis
Keyword(s):  
Real World ◽  
Optimal Number ◽  
Cluster Validation ◽  
Clustering Methods ◽  
Number Of Clusters ◽  
Validity Indices ◽  
Selection Of ◽  
Specific Distance ◽  
Optimal Number Of Clusters

In short, clustering is the process of partitioning a given set of objects into groups containing highly related instances. This relation is determined by a specific distance metric with which the intra-cluster similarity is estimated. Finding an optimal number of such partitions is usually the key step in the entire process, yet a rather difficult one. Selecting an unsuitable number of clusters might lead to incorrect conclusions and, consequently, to wrong decisions: the term “optimal” is quite ambiguous. Furthermore, various inherent characteristics of the datasets, such as clusters that overlap or clusters containing subclusters, will most often increase the level of difficulty of the task. Thus, the methods used to detect similarities and the parameter selection of the partition algorithm have a major impact on the quality of the groups and the identification of their optimal number. Given that each dataset constitutes a rather distinct case, validity indices are indicators introduced to address the problem of selecting such an optimal number of clusters. In this work, an extensive set of well-known validity indices, based on the approach of the so-called relative criteria, are examined comparatively. A total of 26 cluster validation measures were investigated in two distinct case studies: one in real-world and one in artificially generated data. To ensure a certain degree of difficulty, both real-world and generated data were selected to exhibit variations and inhomogeneity. Each of the indices is being deployed under the schemes of 9 different clustering methods, which incorporate 5 different distance metrics. All results are presented in various explanatory forms.

Sign in / Sign up

Export Citation Format

Share Document