scholarly journals A Novel Cluster Ensemble based on a Single Clustering Algorithm

2021 ◽  
Author(s):  
Tahseen Khan ◽  
Wenhong Tian ◽  
Mustafa R. Kadhim ◽  
Rajkumar Buyya
Keyword(s):  
Clustering Algorithm ◽  
Cluster Ensemble

Cluster Ensemble and Multi-Objective Clustering Methods

2008 ◽  
pp. 325-343 ◽  
Author(s):  
Katti Faceli ◽  
Andre C.P.L.F. de Carvalho ◽  
Marcilio C.P. de Souto
Keyword(s):  
Clustering Algorithm ◽  
Clustering Algorithms ◽  
Ensemble Methods ◽  
Data Exploration ◽  
Clustering Methods ◽  
Clustering Ensemble ◽  
Cluster Ensemble ◽  
Multi Objective ◽  
Ensemble Algorithm ◽  
New Algorithms

Clustering is an important tool for data exploration. Several clustering algorithms exist, and new algorithms are frequently proposed in the literature. These algorithms have been very successful in a large number of real-world problems. However, there is no clustering algorithm, optimizing only a single criterion, able to reveal all types of structures (homogeneous or heterogeneous) present in a dataset. In order to deal with this problem, several multi-objective clustering and cluster ensemble methods have been proposed in the literature, including our multi-objective clustering ensemble algorithm. In this chapter, we present an overview of these methods, which, to a great extent, are based on the combination of various aspects of traditional clustering algorithms.

scholarly journals Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis

2019 ◽  
Vol 20 (S19) ◽  
Author(s):  
Thomas A. Geddes ◽  
Taiyun Kim ◽  
Lihao Nan ◽  
James G. Burchfield ◽  
Jean Y. H. Yang ◽  
...  
Keyword(s):  
Data Analysis ◽  
Single Cell ◽  
Clustering Algorithm ◽  
Dimensional Space ◽  
Clustering Algorithms ◽  
Random Projection ◽  
Computational Technique ◽  
Cell Type ◽  
Cluster Ensemble ◽  
Cell Type Specific

Abstract Background Single-cell RNA-sequencing (scRNA-seq) is a transformative technology, allowing global transcriptomes of individual cells to be profiled with high accuracy. An essential task in scRNA-seq data analysis is the identification of cell types from complex samples or tissues profiled in an experiment. To this end, clustering has become a key computational technique for grouping cells based on their transcriptome profiles, enabling subsequent cell type identification from each cluster of cells. Due to the high feature-dimensionality of the transcriptome (i.e. the large number of measured genes in each cell) and because only a small fraction of genes are cell type-specific and therefore informative for generating cell type-specific clusters, clustering directly on the original feature/gene dimension may lead to uninformative clusters and hinder correct cell type identification. Results Here, we propose an autoencoder-based cluster ensemble framework in which we first take random subspace projections from the data, then compress each random projection to a low-dimensional space using an autoencoder artificial neural network, and finally apply ensemble clustering across all encoded datasets to generate clusters of cells. We employ four evaluation metrics to benchmark clustering performance and our experiments demonstrate that the proposed autoencoder-based cluster ensemble can lead to substantially improved cell type-specific clusters when applied with both the standard k-means clustering algorithm and a state-of-the-art kernel-based clustering algorithm (SIMLR) designed specifically for scRNA-seq data. Compared to directly using these clustering algorithms on the original datasets, the performance improvement in some cases is up to 100%, depending on the evaluation metric used. Conclusions Our results suggest that the proposed framework can facilitate more accurate cell type identification as well as other downstream analyses. The code for creating the proposed autoencoder-based cluster ensemble framework is freely available from https://github.com/gedcom/scCCESS

scholarly journals Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis

2019 ◽  
Author(s):  
Thomas A Geddes ◽  
Taiyun Kim ◽  
Lihao Nan ◽  
James G Burchfield ◽  
Jean YH Yang ◽  
...  
Keyword(s):  
Data Analysis ◽  
Single Cell ◽  
Clustering Algorithm ◽  
Dimensional Space ◽  
Clustering Algorithms ◽  
Evaluation Metrics ◽  
Computational Technique ◽  
Cell Type ◽  
Cluster Ensemble ◽  
Cell Type Specific

AbstractBackgroundSingle-cell RNA-sequencing (scRNA-seq) is a transformative technology, allowing global transcriptomes of individual cells to be profiled with high accuracy. An essential task in scRNA-seq data analysis is the identification of cell types from complex samples or tissues profiled in an experiment. To this end, clustering has become a key computational technique for grouping cells based on their transcriptome profiles, enabling subsequent cell type identification from each cluster of cells. Due to the high feature-dimensionality of the transcriptome (i.e. the large number of measured genes in each cell) and because only a small fraction of genes are cell type-specific and therefore informative for generating cell type-specific clusters, clustering directly on the original feature/gene dimension may lead to uninformative clusters and hinder correct cell type identification.ResultsHere, we propose an autoencoder-based cluster ensemble framework in which we first take random subspace projections from the data, then compress each random projection to a low-dimensional space using an autoencoder artificial neural network, and finally apply ensemble clustering across all encoded datasets for generating clusters of cells. We employ four evaluation metrics to benchmark clustering performance and our experiments demonstrate that the proposed autoencoder-based cluster ensemble can lead to substantially improved cell type-specific clusters when applied with both the standard k-means clustering algorithm and a state-of-the-art kernel-based clustering algorithm (SIMLR) designed specifically for scRNA-seq data. Compared to directly using these clustering algorithms on the original datasets, the performance improvement in some cases is up to 100%, depending on the evaluation metrics used.ConclusionsOur results suggest that the proposed framework can facilitate more accurate cell type identification as well as other downstream analyses. The code for creating the proposed autoencoder-based cluster ensemble framework is freely available from https://github.com/gedcom/autoencoder_cluster_ensemble

scholarly journals A Random Walk Based Cluster Ensemble Approach for Data Integration and Cancer Subtyping

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 66
Author(s):  
Chao Yang ◽  
Yu-Tian Wang ◽  
Chun-Hou Zheng
Keyword(s):  
Breast Cancer ◽  
Random Walk ◽  
Clustering Algorithm ◽  
Molecular Taxonomy ◽  
Biological Significance ◽  
Ensemble Methods ◽  
The Cancer Genome Atlas ◽  
Cluster Ensemble ◽  
Association Matrix ◽  
The Relationship

Availability of diverse types of high-throughput data increases the opportunities for researchers to develop computational methods to provide a more comprehensive view for the mechanism and therapy of cancer. One fundamental goal for oncology is to divide patients into subtypes with clinical and biological significance. Cluster ensemble fits this task exactly. It can improve the performance and robustness of clustering results by combining multiple basic clustering results. However, many existing cluster ensemble methods use a co-association matrix to summarize the co-occurrence statistics of the instance-cluster, where the relationship in the integration is only encapsulated at a rough level. Moreover, the relationship among clusters is completely ignored. Finding these missing associations could greatly expand the ability of cluster ensemble methods for cancer subtyping. In this paper, we propose the RWCE (Random Walk based Cluster Ensemble) to consider similarity among clusters. We first obtained a refined similarity between clusters by using random walk and a scaled exponential similarity kernel. Then, after being modeled as a bipartite graph, a more informative instance-cluster association matrix filled with the aforementioned cluster similarity was fed into a spectral clustering algorithm to get the final clustering result. We applied our method on six cancer types from The Cancer Genome Atlas (TCGA) and breast cancer from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC). Experimental results show that our method is competitive against existing methods. Further case study demonstrates that our method has the potential to find subtypes with clinical and biological significance.

scholarly journals Fuzzyc-Means and Cluster Ensemble with Random Projection for Big Data Clustering

2016 ◽  
Vol 2016 ◽  
pp. 1-13 ◽  
Author(s):  
Mao Ye ◽  
Wenfen Liu ◽  
Jianghong Wei ◽  
Xuexian Hu
Keyword(s):  
Big Data ◽  
Clustering Algorithm ◽  
State Of The Art ◽  
Random Projection ◽  
Aggregation Method ◽  
Data Set ◽  
Cluster Ensemble ◽  
Positive Effects ◽  
Fcm Clustering ◽  
Value Decomposition

Because of its positive effects on dealing with the curse of dimensionality in big data, random projection for dimensionality reduction has become a popular method recently. In this paper, an academic analysis of influences of random projection on the variability of data set and the dependence of dimensions has been proposed. Together with the theoretical analysis, a new fuzzyc-means (FCM) clustering algorithm with random projection has been presented. Empirical results verify that the new algorithm not only preserves the accuracy of original FCM clustering, but also is more efficient than original clustering and clustering with singular value decomposition. At the same time, a new cluster ensemble approach based on FCM clustering with random projection is also proposed. The new aggregation method can efficiently compute the spectral embedding of data with cluster centers based representation which scales linearly with data size. Experimental results reveal the efficiency, effectiveness, and robustness of our algorithm compared to the state-of-the-art methods.

Distributed Entropy Energy-Efficient Clustering algorithm for cluster head selection (DEEEC)

2020 ◽  
Vol 39 (6) ◽  
pp. 8139-8147
Author(s):  
Ranganathan Arun ◽  
Rangaswamy Balamurugan
Keyword(s):  
Energy Efficient ◽  
Clustering Algorithm ◽  
Cluster Head ◽  
Residual Energy ◽  
Energy Utilization ◽  
Sensor Nodes ◽  
Second Stage ◽  
Energy Efficient Clustering ◽  
Two Stages ◽  
Ch Selection

In Wireless Sensor Networks (WSN) the energy of Sensor nodes is not certainly sufficient. In order to optimize the endurance of WSN, it is essential to minimize the utilization of energy. Head of group or Cluster Head (CH) is an eminent method to develop the endurance of WSN that aggregates the WSN with higher energy. CH for intra-cluster and inter-cluster communication becomes dependent. For complete, in WSN, the Energy level of CH extends its life of cluster. While evolving cluster algorithms, the complicated job is to identify the energy utilization amount of heterogeneous WSNs. Based on Chaotic Firefly Algorithm CH (CFACH) selection, the formulated work is named “Novel Distributed Entropy Energy-Efficient Clustering Algorithm”, in short, DEEEC for HWSNs. The formulated DEEEC Algorithm, which is a CH, has two main stages. In the first stage, the identification of temporary CHs along with its entropy value is found using the correlative measure of residual and original energy. Along with this, in the clustering algorithm, the rotating epoch and its entropy value must be predicted automatically by its sensor nodes. In the second stage, if any member in the cluster having larger residual energy, shall modify the temporary CHs in the direction of the deciding set. The target of the nodes with large energy has the probability to be CHs which is determined by the above two stages meant for CH selection. The MATLAB is required to simulate the DEEEC Algorithm. The simulated results of the formulated DEEEC Algorithm produce good results with respect to the energy and increased lifetime when it is correlated with the current traditional clustering protocols being used in the Heterogeneous WSNs.

Handling WSD using Hierarchical Clustering Algorithm with sentences

2018 ◽  
pp. 83-88
Author(s):  
Mohana Priya K ◽  
Pooja Ragavi S ◽  
Krishna Priya G
Keyword(s):  
Hierarchical Clustering ◽  
Similarity Measure ◽  
Clustering Algorithm ◽  
Clustering Algorithms ◽  
Cosine Similarity Measure ◽  
Hierarchical Clustering Algorithm ◽  
Multiple Levels ◽  
Pos Tagger ◽  
Sentence Clustering ◽  
The Right

Clustering is the process of grouping objects into subsets that have meaning in the context of a particular problem. It does not rely on predefined classes. It is referred to as an unsupervised learning method because no information is provided about the "right answer" for any of the objects. Many clustering algorithms have been proposed and are used based on different applications. Sentence clustering is one of best clustering technique. Hierarchical Clustering Algorithm is applied for multiple levels for accuracy. For tagging purpose POS tagger, porter stemmer is used. WordNet dictionary is utilized for determining the similarity by invoking the Jiang Conrath and Cosine similarity measure. Grouping is performed with respect to the highest similarity measure value with a mean threshold. This paper incorporates many parameters for finding similarity between words. In order to identify the disambiguated words, the sense identification is performed for the adjectives and comparison is performed. semcor and machine learning datasets are employed. On comparing with previous results for WSD, our work has improvised a lot which gives a percentage of 91.2%

K-MEANS CLUSTERING ALGORITHM BASED CLASSIFICATION OF SOIL FERTILITY IN NORTH WEST NIGERIA

2020 ◽  
Vol 4 (2) ◽  
pp. 780-787
Author(s):  
Ibrahim Hassan Hayatu ◽  
Abdullahi Mohammed ◽  
Barroon Ahmad Isma’eel ◽  
Sahabi Yusuf Ali
Keyword(s):  
Soil Fertility ◽  
Crop Yield ◽  
Clustering Algorithm ◽  
Soil Samples ◽  
North West ◽  
R Programming ◽  
Available Information ◽  
Northwest Region ◽  
The Relationship

Soil fertility determines a plant's development process that guarantees food sufficiency and the security of lives and properties through bumper harvests. The fertility of soil varies according to regions, thereby determining the type of crops to be planted. However, there is no repository or any source of information about the fertility of the soil in any region in Nigeria especially the Northwest of the country. The only available information is soil samples with their attributes which gives little or no information to the average farmer. This has affected crop yield in all the regions, more particularly the Northwest region, thus resulting in lower food production.  Therefore, this study is aimed at classifying soil data based on their fertility in the Northwest region of Nigeria using R programming. Data were obtained from the department of soil science from Ahmadu Bello University, Zaria. The data contain 400 soil samples containing 13 attributes. The relationship between soil attributes was observed based on the data. K-means clustering algorithm was employed in analyzing soil fertility clusters. Four clusters were identified with cluster 1 having the highest fertility, followed by 2 and the fertility decreases with an increasing number of clusters. The identification of the most fertile clusters will guide farmers on where best to concentrate on when planting their crops in order to improve productivity and crop yield.

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