scholarly journals A Review article on Semi- Supervised Clustering Framework for High Dimensional Data

2019 ◽  
pp. 102-108
Author(s):  
M. Pavithra ◽  
R. M. S. Parvathi
Keyword(s):  
Expert Knowledge ◽  
Cluster Formation ◽  
Clustering Algorithms ◽  
Ensemble Member ◽  
Unsupervised Clustering ◽  
Outcome Variable ◽  
High Dimensional ◽  
Clustering Methods ◽  
Data Set ◽  
Supervised Clustering

Cluster analysis methods seek to partition a data set into homogeneous subgroups. It is useful in a wide variety of applications, including document processing and modern genetics. Conventional clustering methods are unsupervised, meaning that there is no outcome variable nor is anything known about the relationship between the observations in the data set. In many situations, however, information about the clusters is available in addition to the values of the features [2]. For example, the cluster labels of some observations may be known, or certain observations may be known to belong to the same cluster. In other cases, one may wish to identify clusters that are associated with a particular outcome variable. This review describes several clustering algorithms (known as �semi-supervised clustering� methods) that can be applied in these situations [3]. The majority of these methods are modifications of the popular k-means clustering method, and several of them will be described in detail. A brief description of some other semi-supervised clustering algorithms is also provided. Cluster formation has three types as supervised clustering, unsupervised clustering and semi supervised. This paper reviews traditional and state-of-the-art methods of clustering [1]. Clustering algorithms are based on active learning, with ensemble clustering-means algorithm, data streams with flock, fuzzy clustering for shape annotations, Incremental semi supervised clustering, Weakly supervised clustering, with minimum labeled data, self-organizing based on neural networks. Incremental semi-supervised clustering ensemble framework (ISSCE) which makes utilization of the advantage of the arbitrary subspace method, the limitation spread approach, the proposed incremental ensemble member choice process, and the normalized cut algorithm to perform high dimensional information clustering [4]. Semi-supervised clustering employs limited supervision in the form of labeled instances or pairwise instance constraints to aid unsupervised clustering and often significantly improves the clustering performance. Despite the vast amount of expert knowledge spent on this problem, most existing work is not designed for handling high-dimensional sparse data.

scholarly journals Robust clustering and interpretation of scRNA-seq data using reference component analysis

2021 ◽  
Author(s):  
Florian Schmidt ◽  
Bobby Ranjan ◽  
Quy Xiao Xuan Lin ◽  
Vaidehi Krishnan ◽  
Ignasius Joanito ◽  
...  
Keyword(s):  
Single Cell ◽  
De Novo ◽  
Clustering Algorithms ◽  
Cell Types ◽  
Unsupervised Clustering ◽  
Data Sets ◽  
Clustering Methods ◽  
Robust Clustering ◽  
Supervised Clustering ◽  
Downstream Analysis

MotivationThe transcriptomic diversity of the hundreds of cell types in the human body can be analysed in unprecedented detail using single cell (SC) technologies. Though clustering of cellular transcriptomes is the default technique for defining cell types and subtypes, single cell clustering can be strongly influenced by technical variation. In fact, the prevalent unsupervised clustering algorithms can cluster cells by technical, rather than biological, variation.ResultsCompared to de novo (unsupervised) clustering methods, we demonstrate using multiple benchmarks that supervised clustering, which uses reference transcriptomes as a guide, is robust to batch effects. To leverage the advantages of supervised clustering, we present RCA2, a new, scalable, and broadly applicable version of our RCA algorithm. RCA2 provides a user-friendly framework for supervised clustering and downstream analysis of large scRNA-seq data sets. RCA2 can be seamlessly incorporated into existing algorithmic pipelines. It incorporates various new reference panels for human and mouse, supports generation of custom panels and uses efficient graph-based clustering and sparse data structures to ensure scalability. We demonstrate the applicability of RCA2 on SC data from human bone marrow, healthy PBMCs and PBMCs from COVID-19 patients. Importantly, RCA2 facilitates cell-type-specific QC, which we show is essential for accurate clustering of SC data from heterogeneous tissues. In the era of cohort-scale SC analysis, supervised clustering methods such as RCA2 will facilitate unified analysis of diverse SC datasets.AvailabilityRCA2 is implemented in R and is available at github.com/prabhakarlab/RCAv2

A New semi-supervised clustering for incomplete data

2021 ◽  
pp. 1-13
Author(s):  
Sonia Goel ◽  
Meena Tushir
Keyword(s):  
Incomplete Data ◽  
Missing Values ◽  
Clustering Algorithms ◽  
Complete Data ◽  
Unlabeled Data ◽  
Misclassification Rate ◽  
Data Sets ◽  
Clustering Methods ◽  
Data Set ◽  
Supervised Clustering

Semi-supervised clustering technique partitions the unlabeled data based on prior knowledge of labeled data. Most of the semi-supervised clustering algorithms exist only for the clustering of complete data, i.e., the data sets with no missing features. In this paper, an effort has been made to check the effectiveness of semi-supervised clustering when applied to incomplete data sets. The novelty of this approach is that it considers the missing features along with available knowledge (labels) of the data set. The linear interpolation imputation technique initially imputes the missing features of the data set, thus completing the data set. A semi-supervised clustering is now employed on this complete data set, and missing features are regularly updated within the clustering process. In the proposed work, the labeled percentage range used is 30, 40, 50, and 60% of the total data. Data is further altered by arbitrarily eliminating certain features of its components, which makes the data incomplete with partial labeling. The proposed algorithm utilizes both labeled and unlabeled data, along with certain missing values in the data. The proposed algorithm is evaluated using three performance indices, namely the misclassification rate, random index metric, and error rate. Despite the additional missing features, the proposed algorithm has been successfully implemented on real data sets and showed better/competing results than well-known standard semi-supervised clustering methods.

scholarly journals GRAPH BASED CLUSTERING WITH CONSTRAINTS AND ACTIVE LEARNING

2021 ◽  
Vol 37 (1) ◽  
pp. 71-89
Author(s):  
Vu-Tuan Dang ◽  
Viet-Vu Vu ◽  
Hong-Quan Do ◽  
Thi Kieu Oanh Le
Keyword(s):  
Active Learning ◽  
Clustering Algorithm ◽  
Side Information ◽  
Clustering Algorithms ◽  
Real Data ◽  
Data Sets ◽  
Data Set ◽  
Supervised Clustering ◽  
Class Labels ◽  
Graph Based Clustering

During the past few years, semi-supervised clustering has emerged as a new interesting direction in machine learning research. In a semi-supervised clustering algorithm, the clustering results can be significantly improved by using side information, which is available or collected from users. There are two main kinds of side information that can be learned in semi-supervised clustering algorithms: the class labels - called seeds or the pairwise constraints. The first semi-supervised clustering was introduced in 2000, and since that, many algorithms have been presented in literature. However, it is not easy to use both types of side information in the same algorithm. To address the problem, this paper proposes a semi-supervised graph based clustering algorithm that tries to use seeds and constraints in the clustering process, called MCSSGC. Moreover, we introduces a simple but efficient active learning method to collect the constraints that can boost the performance of MCSSGC, named KMMFFQS. In order to verify effectiveness of the proposed algorithm, we conducted a series of experiments not only on real data sets from UCI, but also on a document data set applied in an Information Extraction of Vietnamese documents. These obtained results show that the proposed algorithm can significantly improve the clustering process compared to some recent algorithms.

scholarly journals VDPC: Variational Density Peak Clustering Algorithm

2021 ◽  
Author(s):  
Yizhang Wang ◽  
Di Wang ◽  
You Zhou ◽  
Chai Quek ◽  
Xiaofeng Zhang
Keyword(s):  
Clustering Algorithm ◽  
Cluster Formation ◽  
Clustering Algorithms ◽  
Data Distribution ◽  
Distribution Patterns ◽  
Clustering Methods ◽  
Density Peak ◽  
Global Parameter ◽  
Density Peak Clustering ◽  
Parameter Values

<div>Clustering is an important unsupervised knowledge acquisition method, which divides the unlabeled data into different groups \cite{atilgan2021efficient,d2021automatic}. Different clustering algorithms make different assumptions on the cluster formation, thus, most clustering algorithms are able to well handle at least one particular type of data distribution but may not well handle the other types of distributions. For example, K-means identifies convex clusters well \cite{bai2017fast}, and DBSCAN is able to find clusters with similar densities \cite{DBSCAN}. </div><div>Therefore, most clustering methods may not work well on data distribution patterns that are different from the assumptions being made and on a mixture of different distribution patterns. Taking DBSCAN as an example, it is sensitive to the loosely connected points between dense natural clusters as illustrated in Figure~\ref{figconnect}. The density of the connected points shown in Figure~\ref{figconnect} is different from the natural clusters on both ends, however, DBSCAN with fixed global parameter values may wrongly assign these connected points and consider all the data points in Figure~\ref{figconnect} as one big cluster.</div>

scholarly journals M-Denclue for Effective Data Clustering in High Dimensional Non-Linear Data

2019 ◽  
Vol 9 (1) ◽  
pp. 2925-2927
Keyword(s):  
Clustering Algorithms ◽  
High Dimensional Data ◽  
Research Work ◽  
Curse Of Dimensionality ◽  
Distance Measures ◽  
High Dimensional ◽  
Clustering Methods ◽  
Non Linear ◽  
Low Dimensional ◽  
Automatic Grouping

Clustering is a data mining task devoted to the automatic grouping of data based on mutual similarity. Clustering in high-dimensional spaces is a recurrent problem in many domains. It affects time complexity, space complexity, scalability and accuracy of clustering methods. Highdimensional non-linear datausually live in different low dimensional subspaces hidden in the original space. As high‐dimensional objects appear almost alike, new approaches for clustering are required. This research has focused on developing Mathematical models, techniques and clustering algorithms specifically for high‐dimensional data. The innocent growth in the fields of communication and technology, there is tremendous growth in high dimensional data spaces. As the variant of dimensions on high dimensional non-linear data increases, many clustering techniques begin to suffer from the curse of dimensionality, de-grading the quality of the results. In high dimensional non-linear data, the data becomes very sparse and distance measures become increasingly meaningless. The principal challenge for clustering high dimensional data is to overcome the “curse of dimensionality”. This research work concentrates on devising an enhanced algorithm for clustering high dimensional non-linear data.

Soft Subspace Clustering for High-Dimensional Data

2011 ◽  
pp. 1810-1814
Author(s):  
Liping Jing ◽  
Michael K. Ng ◽  
Joshua Zhexue Huang
Keyword(s):  
High Dimensional Data ◽  
Subspace Clustering ◽  
High Dimensional ◽  
Special Treatment ◽  
Clustering Methods ◽  
Real World Data ◽  
Text Data ◽  
Data Set ◽  
Dna Microarray Data ◽  
Text Document

High dimensional data is a phenomenon in real-world data mining applications. Text data is a typical example. In text mining, a text document is viewed as a vector of terms whose dimension is equal to the total number of unique terms in a data set, which is usually in thousands. High dimensional data occurs in business as well. In retails, for example, to effectively manage supplier relationship, suppliers are often categorized according to their business behaviors (Zhang, Huang, Qian, Xu, & Jing, 2006). The supplier’s behavior data is high dimensional, which contains thousands of attributes to describe the supplier’s behaviors, including product items, ordered amounts, order frequencies, product quality and so forth. One more example is DNA microarray data. Clustering high-dimensional data requires special treatment (Swanson, 1990; Jain, Murty, & Flynn, 1999; Cai, He, & Han, 2005; Kontaki, Papadopoulos & Manolopoulos., 2007), although various methods for clustering are available (Jain & Dubes, 1988). One type of clustering methods for high dimensional data is referred to as subspace clustering, aiming at finding clusters from subspaces instead of the entire data space. In a subspace clustering, each cluster is a set of objects identified by a subset of dimensions and different clusters are represented in different subsets of dimensions. Soft subspace clustering considers that different dimensions make different contributions to the identification of objects in a cluster. It represents the importance of a dimension as a weight that can be treated as the degree of the dimension in contribution to the cluster. Soft subspace clustering can find the cluster memberships of objects and identify the subspace of each cluster in the same clustering process.

scholarly journals A Novel Complex Networks Clustering Algorithm Based on the Core Influence of Nodes

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Chao Tong ◽  
Jianwei Niu ◽  
Bin Dai ◽  
Zhongyu Xie
Keyword(s):  
Complex Networks ◽  
Clustering Algorithm ◽  
Cluster Formation ◽  
Clustering Algorithms ◽  
Cluster Structure ◽  
Network Clustering ◽  
Clustering Methods ◽  
Positive Role ◽  
The Core ◽  
Final Cluster

In complex networks, cluster structure, identified by the heterogeneity of nodes, has become a common and important topological property. Network clustering methods are thus significant for the study of complex networks. Currently, many typical clustering algorithms have some weakness like inaccuracy and slow convergence. In this paper, we propose a clustering algorithm by calculating the core influence of nodes. The clustering process is a simulation of the process of cluster formation in sociology. The algorithm detects the nodes with core influence through their betweenness centrality, and builds the cluster’s core structure by discriminant functions. Next, the algorithm gets the final cluster structure after clustering the rest of the nodes in the network by optimizing method. Experiments on different datasets show that the clustering accuracy of this algorithm is superior to the classical clustering algorithm (Fast-Newman algorithm). It clusters faster and plays a positive role in revealing the real cluster structure of complex networks precisely.

A Nonparametric Clustering Algorithm with a Quantile-Based Likelihood Estimator

2014 ◽  
Vol 26 (9) ◽  
pp. 2074-2101 ◽  
Author(s):  
Hideitsu Hino ◽  
Noboru Murata
Keyword(s):  
Clustering Algorithm ◽  
Clustering Algorithms ◽  
Conditional Entropy ◽  
Tuning Parameter ◽  
Clustering Methods ◽  
Sampling Weights ◽  
Data Set ◽  
Information Theoretic ◽  
Nonparametric Clustering ◽  
Conditional Information

Clustering is a representative of unsupervised learning and one of the important approaches in exploratory data analysis. By its very nature, clustering without strong assumption on data distribution is desirable. Information-theoretic clustering is a class of clustering methods that optimize information-theoretic quantities such as entropy and mutual information. These quantities can be estimated in a nonparametric manner, and information-theoretic clustering algorithms are capable of capturing various intrinsic data structures. It is also possible to estimate information-theoretic quantities using a data set with sampling weight for each datum. Assuming the data set is sampled from a certain cluster and assigning different sampling weights depending on the clusters, the cluster-conditional information-theoretic quantities are estimated. In this letter, a simple iterative clustering algorithm is proposed based on a nonparametric estimator of the log likelihood for weighted data sets. The clustering algorithm is also derived from the principle of conditional entropy minimization with maximum entropy regularization. The proposed algorithm does not contain a tuning parameter. The algorithm is experimentally shown to be comparable to or outperform conventional nonparametric clustering methods.

scholarly journals Unsupervised clustering analysis reveals global population structure of SARS-CoV-2

2020 ◽  
Author(s):  
Yawei Li ◽  
Qingyun Liu ◽  
Zexian Zeng ◽  
Yuan Luo
Keyword(s):  
Population Structure ◽  
Health Management ◽  
Clustering Algorithms ◽  
Unsupervised Clustering ◽  
Human Migration ◽  
Clustering Methods ◽  
Sequencing Data ◽  
Population Structures ◽  
Genomic Clusters ◽  
Global Population

AbstractIdentifying the population structure of the newly emerged coronavirus SARS-CoV-2 has significant potential to inform public health management and diagnosis. As SARS-CoV-2 sequencing data is accruing rapidly, grouping them into clusters is important for organizing the landscape of the population structure of the virus. Since we have little prior information about the newly emerged coronavirus, we applied unsupervised clustering algorithms to group 16,873 SARS-CoV-2 strains, which automatically minimize intra-cluster distances and maximize inter-cluster distances. Six distinct genomic clusters were identified, with mutation profiles as input features. The varied proportions of the six clusters within different continents revealed specific geographical distributions. Comprehensive analysis indicated that genetic factors and human migration played an important role in shaping the specific geographical distribution of population structure. This study provides a concrete framework for the use of clustering methods in phylogenetic analysis to study the global population structure of SARS-CoV-2. In addition, clustering methods can be used for future studies of variant population structures in specific regions of these fast-growing viruses.

Urban green economic development indicators based on spatial clustering algorithm and blockchain

2020 ◽  
pp. 1-12
Author(s):  
Xiaoguang Gao
Keyword(s):  
Development Strategy ◽  
Clustering Algorithm ◽  
Spatial Clustering ◽  
Clustering Algorithms ◽  
High Dimensional Data ◽  
Large Data ◽  
Experimental Comparison ◽  
High Dimensional ◽  
Density Peak ◽  
Data Set

The unbalanced development strategy makes the regional development unbalanced. Therefore, in the development process, resources must be effectively utilized according to the level and characteristics of each region. Considering the resource and environmental constraints, this paper measures and analyzes China’s green economic efficiency and green total factor productivity. Moreover, by expounding the characteristics of high-dimensional data, this paper points out the problems of traditional clustering algorithms in high-dimensional data clustering. This paper proposes a density peak clustering algorithm based on sampling and residual squares, which is suitable for high-dimensional large data sets. The algorithm finds abnormal points and boundary points by identifying halo points, and finally determines clusters. In addition, from the experimental comparison on the data set, it can be seen that the improved algorithm is better than the DPC algorithm in both time complexity and clustering results. Finally, this article analyzes data based on actual cases. The research results show that the method proposed in this paper is effective.

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