scholarly journals Semantic Unsupervised Automatic Keyphrases Extraction by Integrating Word Embedding with Clustering Methods

2020 ◽  
Vol 4 (2) ◽  
pp. 30 ◽  
Author(s):  
Isabella Gagliardi ◽  
Maria Teresa Artese
Keyword(s):  
Clustering Algorithms ◽  
Semantic Content ◽  
Word Embedding ◽  
Keyword Extraction ◽  
Clustering Methods ◽  
Novel Method ◽  
The Web

Increasingly, the web produces massive volumes of texts, alone or associated with images, videos, photographs, together with some metadata, indispensable for their finding and retrieval. Keywords/keyphrases that characterize the semantic content of documents should be, automatically or manually, extracted, and/or associated with them. The paper presents a novel method to address the problem of the automatic unsupervised extraction of keywords/phrases from texts, expressed both in English and in Italian. The main feature of this approach is the integration of two methods that have given interesting results: word embedding models, such as Word2Vec or GloVe able to capture the semantics of words and their context, and clustering algorithms, able to identify the essence of the terms and choose the more significant one(s), to represent the contents of a text. In the paper, the datasets used are presented, together with the method implemented and the results obtained. These results will be discussed, commented, and compared with those obtained in previous experimentations, using TextRank, Rapid Automatic Keyword Extraction (RAKE), and TF-IDF.

scholarly journals ClusterEnG: An interactive educational web resource for clustering big data

2017 ◽  
Author(s):  
Mohith Manjunath ◽  
Yi Zhang ◽  
Steve H. Yeo ◽  
Omar Sobh ◽  
Nathan Russell ◽  
...  
Keyword(s):  
Big Data ◽  
State Of The Art ◽  
Clustering Algorithms ◽  
Clustering Methods ◽  
Web Resource ◽  
Interactive Visualizations ◽  
Data Points ◽  
Similarities And Differences ◽  
Intuitive Manner ◽  
The Web

AbstractSummaryClustering is one of the most common techniques used in data analysis to discover hidden structures by grouping together data points that are similar in some measure into clusters. Although there are many programs available for performing clustering, a single web resource that provides both state-of-the-art clustering methods and interactive visualizations is lacking. ClusterEnG (acronym for Clustering Engine for Genomics) provides an interface for clustering big data and interactive visualizations including 3D views, cluster selection and zoom features. ClusterEnG also aims at educating the user about the similarities and differences between various clustering algorithms and provides clustering tutorials that demonstrate potential pitfalls of each algorithm. The web resource will be particularly useful to scientists who are not conversant with computing but want to understand the structure of their data in an intuitive manner.AvailabilityClusterEnG is part of a bigger project called KnowEnG (Knowledge Engine for Genomics) and is available at http://education.knoweng.org/[email protected]

scholarly journals RFCell: A Gene Selection Approach for scRNA-seq Clustering Based on Permutation and Random Forest

2021 ◽  
Vol 12 ◽  
Author(s):  
Yuan Zhao ◽  
Zhao-Yu Fang ◽  
Cui-Xiang Lin ◽  
Chao Deng ◽  
Yun-Pei Xu ◽  
...  
Keyword(s):  
Random Forest ◽  
Single Cell ◽  
Gene Selection ◽  
Clustering Algorithms ◽  
Selection Methods ◽  
Clustering Methods ◽  
Cell Type ◽  
Cell Type Specificity ◽  
Random Forest Classification ◽  
Forest Classification

In recent years, the application of single cell RNA-seq (scRNA-seq) has become more and more popular in fields such as biology and medical research. Analyzing scRNA-seq data can discover complex cell populations and infer single-cell trajectories in cell development. Clustering is one of the most important methods to analyze scRNA-seq data. In this paper, we focus on improving scRNA-seq clustering through gene selection, which also reduces the dimensionality of scRNA-seq data. Studies have shown that gene selection for scRNA-seq data can improve clustering accuracy. Therefore, it is important to select genes with cell type specificity. Gene selection not only helps to reduce the dimensionality of scRNA-seq data, but also can improve cell type identification in combination with clustering methods. Here, we proposed RFCell, a supervised gene selection method, which is based on permutation and random forest classification. We first use RFCell and three existing gene selection methods to select gene sets on 10 scRNA-seq data sets. Then, three classical clustering algorithms are used to cluster the cells obtained by these gene selection methods. We found that the gene selection performance of RFCell was better than other gene selection methods.

scholarly journals Comparison of dimensionality reduction and clustering methods for SARS-CoV-2 genome

2021 ◽  
Vol 10 (4) ◽  
pp. 2170-2180
Author(s):  
Untari N. Wisesty ◽  
Tati Rajab Mengko
Keyword(s):  
Dimensionality Reduction ◽  
Dimensional Reduction ◽  
Clustering Algorithm ◽  
Sequence Data ◽  
Clustering Algorithms ◽  
Gaussian Mixture Models ◽  
Reduction Process ◽  
Principal Component ◽  
Gaussian Mixture ◽  
Clustering Methods

This paper aims to conduct an analysis of the SARS-CoV-2 genome variation was carried out by comparing the results of genome clustering using several clustering algorithms and distribution of sequence in each cluster. The clustering algorithms used are K-means, Gaussian mixture models, agglomerative hierarchical clustering, mean-shift clustering, and DBSCAN. However, the clustering algorithm has a weakness in grouping data that has very high dimensions such as genome data, so that a dimensional reduction process is needed. In this research, dimensionality reduction was carried out using principal component analysis (PCA) and autoencoder method with three models that produce 2, 10, and 50 features. The main contributions achieved were the dimensional reduction and clustering scheme of SARS-CoV-2 sequence data and the performance analysis of each experiment on each scheme and hyper parameters for each method. Based on the results of experiments conducted, PCA and DBSCAN algorithm achieve the highest silhouette score of 0.8770 with three clusters when using two features. However, dimensionality reduction using autoencoder need more iterations to converge. On the testing process with Indonesian sequence data, more than half of them enter one cluster and the rest are distributed in the other two clusters.

scholarly journals PRIVACY PRESERVING CLUSTERING BASED ON LINEAR APPROXIMATION OF FUNCTION

2013 ◽  
Vol 12 (5) ◽  
pp. 3443-3451
Author(s):  
Rajesh Pasupuleti ◽  
Narsimha Gugulothu
Keyword(s):  
Linear Approximation ◽  
Clustering Algorithms ◽  
Similarity Measures ◽  
Privacy Preserving ◽  
Distance Measures ◽  
Clustering Methods ◽  
Sensitive Data ◽  
Processing Information ◽  
Data Objects ◽  
Approximation Of Function

Clustering analysis initiatives  a new direction in data mining that has major impact in various domains including machine learning, pattern recognition, image processing, information retrieval and bioinformatics. Current clustering techniques address some of the  requirements not adequately and failed in standardizing clustering algorithms to support for all real applications. Many clustering methods mostly depend on user specified parametric methods and initial seeds of clusters are randomly selected by  user.  In this paper, we proposed new clustering method based on linear approximation of function by getting over all idea of behavior knowledge of clustering function, then pick the initial seeds of clusters as the points on linear approximation line and perform clustering operations, unlike grouping data objects into clusters by using distance measures, similarity measures and statistical distributions in traditional clustering methods. We have shown experimental results as clusters based on linear approximation yields good  results in practice with an example of  business data are provided.  It also  explains privacy preserving clusters of sensitive data objects.

Short Text Clustering Algorithms for Weibo Topic Detection

2014 ◽  
Vol 971-973 ◽  
pp. 1747-1751 ◽  
Author(s):  
Lei Zhang ◽  
Hai Qiang Chen ◽  
Wei Jie Li ◽  
Yan Zhao Liu ◽  
Run Pu Wu
Keyword(s):  
Text Analysis ◽  
Semantic Information ◽  
Clustering Algorithms ◽  
Text Clustering ◽  
Massive Data ◽  
Topic Detection ◽  
Clustering Methods ◽  
Short Text ◽  
Short Text Clustering ◽  
Application Requirements

Text clustering is a popular research topic in the field of text mining, and now there are a lot of text clustering methods catering to different application requirements. Currently, Weibo data acquisition is through the API provided by big microblogging platforms. In this essay, we will discuss the algorithm of extracting popular topics posted by Weibo users by text clustering after massive data collection. Due to the fact that traditional text analysis may not be applicable to short texts used in Weibo, text clustering shall be carried out through combining multiple posts into long texts, based on their features (forwards, comments and followers, etc.). Either frequency-based or density-based short text clustering can deliver in most cases. The former is applicable to find hot topics from large Weibo short texts, and the latter is applicable to find abnormal contents. Both the two methods use semantic information to improve the accuracy of clustering. Besides, they improve the performance of clustering through the parallelism.

EdClust: A heuristic sequence clustering method with higher sensitivity

2021 ◽  
Author(s):  
Ming Cao ◽  
Qinke Peng ◽  
Ze-Gang Wei ◽  
Fei Liu ◽  
Yi-Fan Hou
Keyword(s):  
Large Scale ◽  
Sequence Data ◽  
Clustering Algorithms ◽  
Clustering Methods ◽  
Sequencing Data ◽  
Clustering Method ◽  
Cluster Number ◽  
Sequence Clustering ◽  
Downstream Analysis ◽  
Heuristic Clustering

The development of high-throughput technologies has produced increasing amounts of sequence data and an increasing need for efficient clustering algorithms that can process massive volumes of sequencing data for downstream analysis. Heuristic clustering methods are widely applied for sequence clustering because of their low computational complexity. Although numerous heuristic clustering methods have been developed, they suffer from two limitations: overestimation of inferred clusters and low clustering sensitivity. To address these issues, we present a new sequence clustering method (edClust) based on Edlib, a C/C[Formula: see text] library for fast, exact semi-global sequence alignment to group similar sequences. The new method edClust was tested on three large-scale sequence databases, and we compared edClust to several classic heuristic clustering methods, such as UCLUST, CD-HIT, and VSEARCH. Evaluations based on the metrics of cluster number and seed sensitivity (SS) demonstrate that edClust can produce fewer clusters than other methods and that its SS is higher than that of other methods. The source codes of edClust are available from https://github.com/zhang134/EdClust.git under the GNU GPL license.

Data Clustering Algorithms Using Rough Sets

2013 ◽  
pp. 297-327 ◽  
Author(s):  
B.K. Tripathy ◽  
Adhir Ghosh
Keyword(s):  
Comparative Study ◽  
Rough Set ◽  
Fuzzy Clustering ◽  
Fuzzy Set ◽  
Rough Sets ◽  
Data Clustering ◽  
Clustering Algorithms ◽  
Clustering Methods ◽  
Future Studies ◽  
Multiple Clusters

Developing Data Clustering algorithms have been pursued by researchers since the introduction of k-means algorithm (Macqueen 1967; Lloyd 1982). These algorithms were subsequently modified to handle categorical data. In order to handle the situations where objects can have memberships in multiple clusters, fuzzy clustering and rough clustering methods were introduced (Lingras et al 2003, 2004a). There are many extensions of these initial algorithms (Lingras et al 2004b; Lingras 2007; Mitra 2004; Peters 2006, 2007). The MMR algorithm (Parmar et al 2007), its extensions (Tripathy et al 2009, 2011a, 2011b) and the MADE algorithm (Herawan et al 2010) use rough set techniques for clustering. In this chapter, the authors focus on rough set based clustering algorithms and provide a comparative study of all the fuzzy set based and rough set based clustering algorithms in terms of their efficiency. They also present problems for future studies in the direction of the topics covered.

Evaluation of Clustering Methods for Adaptive Learning Systems

2015 ◽  
pp. 237-260 ◽  
Author(s):  
Wilhelmiina Hämäläinen ◽  
Ville Kumpulainen ◽  
Maxim Mozgovoy
Keyword(s):  
Data Mining ◽  
Adaptive Learning ◽  
Clustering Algorithms ◽  
Educational Data Mining ◽  
Optimal Choice ◽  
Learning Systems ◽  
Learning Tools ◽  
Clustering Methods ◽  
Central Task ◽  
Adaptive Learning Systems

Clustering student data is a central task in the educational data mining and design of intelligent learning tools. The problem is that there are thousands of clustering algorithms but no general guidelines about which method to choose. The optimal choice is of course problem- and data-dependent and can seldom be found without trying several methods. Still, the purposes of clustering students and the typical features of educational data make certain clustering methods more suitable or attractive. In this chapter, the authors evaluate the main clustering methods from this perspective. Based on the analysis, the authors suggest the most promising clustering methods for different situations.

SeqPAM

2008 ◽  
pp. 17-38 ◽  
Author(s):  
Pradeep Kumar Kumar ◽  
Raju S. Bapi ◽  
P. Radha Krishna
Keyword(s):  
Similarity Measure ◽  
Clustering Algorithm ◽  
Clustering Algorithms ◽  
Similarity Measures ◽  
Sequential Data ◽  
Cluster Validation ◽  
Web Personalization ◽  
Similarity Preserving ◽  
Validation Technique ◽  
The Web

With the growth in the number of web users and necessity for making information available on the web, the problem of web personalization has become very critical and popular. Developers are trying to customize a web site to the needs of specific users with the help of knowledge acquired from user navigational behavior. Since user page visits are intrinsically sequential in nature, efficient clustering algorithms for sequential data are needed. In this paper, we introduce a similarity preserving function called sequence and set similarity measure S3M that captures both the order of occurrence of page visits as well as the content of pages. We conducted pilot experiments comparing the results of PAM, a standard clustering algorithm, with two similarity measures: Cosine and S3M. The goodness of the clusters resulting from both the measures was computed using a cluster validation technique based on average levensthein distance. Results on pilot dataset established the effectiveness of S3M for sequential data. Based on these results, we proposed a new clustering algorithm, SeqPAM for clustering sequential data. We tested the new algorithm on two datasets namely, cti and msnbc datasets. We provided recommendations for web personalization based on the clusters obtained from SeqPAM for msnbc dataset.

scholarly journals Majority Voting Based Multi-Task Clustering of Air Quality Monitoring Network in Turkey

2019 ◽  
Vol 9 (8) ◽  
pp. 1610
Author(s):  
Goksu Tuysuzoglu ◽  
Derya Birant ◽  
Aysegul Pala
Keyword(s):  
Air Pollution ◽  
Air Quality ◽  
Clustering Algorithms ◽  
Experimental Studies ◽  
Monitoring Network ◽  
Environmental Parameters ◽  
Global Scale ◽  
Majority Voting ◽  
Clustering Methods ◽  
Task Clustering

Air pollution, which is the result of the urbanization brought by modern life, has a dramatic impact on the global scale as well as local and regional scales. Since air pollution has important effects on human health and other living things, the issue of air quality is of great importance all over the world. Accordingly, many studies based on classification, clustering and association rule mining applications for air pollution have been proposed in the field of data mining and machine learning to extract hidden knowledge from environmental parameters. One approach is to model a region in a way that cities having similar characteristics are determined and placed into the same clusters. Instead of using traditional clustering algorithms, a novel algorithm, named Majority Voting based Multi-Task Clustering (MV-MTC), is proposed and utilized to consider multiple air pollutants jointly. Experimental studies showed that the proposed method is superior to five well-known clustering algorithms: K-Means, Expectation Maximization, Canopy, Farthest First and Hierarchical clustering methods.

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