Identification of the Optimal Number of Clusters in Textual Data

2022 ◽  
pp. 215-225
Author(s):  
Tanjina Das ◽  
Srikanta Paitnaik ◽  
Smita Prava Mishra
Keyword(s):  
Optimal Number ◽  
Number Of Clusters ◽  
Textual Data ◽  
Optimal Number Of Clusters

Method for determining optimal number of clusters in K-means clustering algorithm

2010 ◽  
Vol 30 (8) ◽  
pp. 1995-1998 ◽  
Author(s):  
Shi-bing ZHOU ◽  
Zhen-yuan XU ◽  
Xu-qing TANG
Keyword(s):  
Clustering Algorithm ◽  
Optimal Number ◽  
Number Of Clusters ◽  
Optimal Number Of Clusters

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.

Interval Type 2 Fuzzy Fireworks Algorithm for Clustering

2020 ◽  
pp. 195-211
Author(s):  
Juan Barraza ◽  
Fevrier Valdez ◽  
Patricia Melin ◽  
Claudia I. Gonzalez
Keyword(s):  
Fuzzy Inference ◽  
Optimization Method ◽  
Optimal Number ◽  
Dynamic Adjustment ◽  
Number Of Clusters ◽  
Inference System ◽  
Fireworks Algorithm ◽  
Interval Type ◽  
Optimal Number Of Clusters

This chapter presents Interval Type 2 Fuzzy Fireworks Algorithm for clustering (IT2FWAC). It is an optimization method for finding the optimal number of clusters based on the centroid features which uses the Fireworks Algorithm (FWA), but with a dynamic adjustment of parameters using an Interval Type 2 Fuzzy Inference System (IT2FIS). Three variations of the IT2FWAC are proposed to find the optimal number of clusters for different datasets: IT2FWAC -I, IT2FWAC -II, and IT2FWAC –III. They are explained in detail.

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