Indexes to Find the Optimal Number of Clusters in a Hierarchical Clustering

Author(s):  
José David Martín-Fernández ◽  
José María Luna-Romera ◽  
Beatriz Pontes ◽  
José C. Riquelme-Santos
2019 ◽  
Vol 2019 ◽  
pp. 1-11 ◽  
Author(s):  
Hui Huang ◽  
Yan Ma

The Bag-of-Words (BoW) model is a well-known image categorization technique. However, in conventional BoW, neither the vocabulary size nor the visual words can be determined automatically. To overcome these problems, a hybrid clustering approach that combines improved hierarchical clustering with a K-means algorithm is proposed. We present a cluster validity index for the hierarchical clustering algorithm to adaptively determine when the algorithm should terminate and the optimal number of clusters. Furthermore, we improve the max-min distance method to optimize the initial cluster centers. The optimal number of clusters and initial cluster centers are fed into K-means, and finally the vocabulary size and visual words are obtained. The proposed approach is extensively evaluated on two visual datasets. The experimental results show that the proposed method outperforms the conventional BoW model in terms of categorization and demonstrate the feasibility and effectiveness of our approach.


2018 ◽  
Vol 15 (2) ◽  
Author(s):  
Zdeněk Šulc ◽  
Jana Cibulková ◽  
Jiří Procházka ◽  
Hana Řezanková

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.


2018 ◽  
Vol 14 (1) ◽  
pp. 11-23 ◽  
Author(s):  
Lin Zhang ◽  
Yanling He ◽  
Huaizhi Wang ◽  
Hui Liu ◽  
Yufei Huang ◽  
...  

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/.


2021 ◽  
pp. 1-16
Author(s):  
Aikaterini Karanikola ◽  
Charalampos M. Liapis ◽  
Sotiris Kotsiantis

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.


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