Algorithms for clustering data
Algorithms for clustering data
Self-organization and associative memory: 3rd edition
Self-organization and associative memory: 3rd edition
Automatic subspace clustering of high dimensional data for data mining applications
SIGMOD '98 Proceedings of the 1998 ACM SIGMOD international conference on Management of data
IPCAT '97 Proceedings of the second international workshop on Information processing in cell and tissues
OPTICS: ordering points to identify the clustering structure
SIGMOD '99 Proceedings of the 1999 ACM SIGMOD international conference on Management of data
ACM Computing Surveys (CSUR)
A clustering algorithm based on graph connectivity
Information Processing Letters
Class discovery in gene expression data
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Clustering by pattern similarity in large data sets
Proceedings of the 2002 ACM SIGMOD international conference on Management of data
Analysis of gene expression profiles: class discovery and leaf ordering
Proceedings of the sixth annual international conference on Computational biology
An iterative strategy for pattern discovery in high-dimensional data sets
Proceedings of the eleventh international conference on Information and knowledge management
On Clustering Validation Techniques
Journal of Intelligent Information Systems
Biclustering of Expression Data
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
Center CLICK: A Clustering Algorithm with Applications to Gene Expression Analysis
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
Interrelated Two-way Clustering: An Unsupervised Approach for Gene Expression Data Analysis
BIBE '01 Proceedings of the 2nd IEEE International Symposium on Bioinformatics and Bioengineering
DHC: A Density-Based Hierarchical Clustering Method for Time Series Gene Expression Data
BIBE '03 Proceedings of the 3rd IEEE Symposium on BioInformatics and BioEngineering
d-Clusters: Capturing Subspace Correlation in a Large Data Set
ICDE '02 Proceedings of the 18th International Conference on Data Engineering
Interactive exploration of coherent patterns in time-series gene expression data
Proceedings of the ninth ACM SIGKDD international conference on Knowledge discovery and data mining
Mining phenotypes and informative genes from gene expression data
Proceedings of the ninth ACM SIGKDD international conference on Knowledge discovery and data mining
Resampling Method for Unsupervised Estimation of Cluster Validity
Neural Computation
Attribute Clustering for Grouping, Selection, and Classification of Gene Expression Data
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Multi-Metric and Multi-Substructure Biclustering Analysis for Gene Expression Data
CSB '05 Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference
ICA Based Supervised Gene Classification of Microarray Data in Yeast Functional Genome
HPCASIA '05 Proceedings of the Eighth International Conference on High-Performance Computing in Asia-Pacific Region
Gene Cluster Algorithm Based on Most Similarity Tree
HPCASIA '05 Proceedings of the Eighth International Conference on High-Performance Computing in Asia-Pacific Region
Pattern Recognition Letters
Additional limitations of the clustering validation method figure of merit
ACM-SE 45 Proceedings of the 45th annual southeast regional conference
Dynamic agglomerative clustering of gene expression profiles
Pattern Recognition Letters
A fast and effective method to find correlations among attributes in databases
Data Mining and Knowledge Discovery
Identifying and discriminating between web and peer-to-peer traffic in the network core
Proceedings of the 16th international conference on World Wide Web
A clustering procedure for exploratory mining of vector time series
Pattern Recognition
Possibilistic approach for biclustering microarray data
Computers in Biology and Medicine
MMR: An algorithm for clustering categorical data using Rough Set Theory
Data & Knowledge Engineering
Development of Two-Stage SVM-RFE Gene Selection Strategy for Microarray Expression Data Analysis
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A novel approach to revealing positive and negative co-regulated genes
Journal of Computer Science and Technology
High Confidence Rule Mining for Microarray Analysis
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A genetic approach for efficient outlier detection in projected space
Pattern Recognition
Novel Algorithm for Coexpression Detection in Time-Varying Microarray Data Sets
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A heuristic algorithm for clustering rooted ordered trees
Intelligent Data Analysis
Mining images using clustering and data compressing techniques
International Journal of Information and Communication Technology
Focused local cluster formation for multidimensional microarray data
AEE'08 Proceedings of the 7th WSEAS International Conference on Application of Electrical Engineering
A Novel EPA-KNN Gene Classification Algorithm
ISNN '07 Proceedings of the 4th international symposium on Neural Networks: Part II--Advances in Neural Networks
Clustering Microarray Data with Space Filling Curves
WILF '07 Proceedings of the 7th international workshop on Fuzzy Logic and Applications: Applications of Fuzzy Sets Theory
Robust Clustering by Aggregation and Intersection Methods
KES '08 Proceedings of the 12th international conference on Knowledge-Based Intelligent Information and Engineering Systems, Part III
KES '08 Proceedings of the 12th international conference on Knowledge-Based Intelligent Information and Engineering Systems, Part III
Coclustering of Human Cancer Microarrays Using Minimum Sum-Squared Residue Coclustering
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
ACM Transactions on Knowledge Discovery from Data (TKDD)
Expert Systems with Applications: An International Journal
On comparing two sequences of numbers and its applications to clustering analysis
Information Sciences: an International Journal
A new approach for clustering gene expression time series data
International Journal of Bioinformatics Research and Applications
Two FCA-Based Methods for Mining Gene Expression Data
ICFCA '09 Proceedings of the 7th International Conference on Formal Concept Analysis
Interactive Visualization Tools for Meta-Clustering
Proceedings of the 2009 conference on New Directions in Neural Networks: 18th Italian Workshop on Neural Networks: WIRN 2008
An Evolutionary Hierarchical Clustering Method with a Visual Validation Tool
IWANN '09 Proceedings of the 10th International Work-Conference on Artificial Neural Networks: Part I: Bio-Inspired Systems: Computational and Ambient Intelligence
An Evolutionary Approach for Sample-Based Clustering on Microarray Data
IWANN '09 Proceedings of the 10th International Work-Conference on Artificial Neural Networks: Part II: Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living
Clustering of gene expression data based on shape similarity
EURASIP Journal on Bioinformatics and Systems Biology - Special issue on applications of signal procesing techniques to bioinformatics, genomics, and proteomics
Partition clustering of high dimensional low sample size data based on p-values
Computational Statistics & Data Analysis
Exploring ant-based algorithms for gene expression data analysis
Artificial Intelligence in Medicine
Improving k-NN for Human Cancer Classification Using the Gene Expression Profiles
IDA '09 Proceedings of the 8th International Symposium on Intelligent Data Analysis: Advances in Intelligent Data Analysis VIII
Discovering pattern-based subspace clusters by pattern tree
Knowledge-Based Systems
A stability-based algorithm to validate hierarchical clusters of genes
International Journal of Knowledge Engineering and Soft Data Paradigms
Concordance indices for comparing fuzzy, possibilistic, rough and grey partitions
International Journal of Knowledge Engineering and Soft Data Paradigms
A survey of evolutionary algorithms for clustering
IEEE Transactions on Systems, Man, and Cybernetics, Part C: Applications and Reviews
Data mining of vector–item patterns using neighborhood histograms
Knowledge and Information Systems
A novel ensemble machine learning for robust microarray data classification
Computers in Biology and Medicine
Kernel Alignment k-NN for Human Cancer Classification Using the Gene Expression Profiles
ICANN '09 Proceedings of the 19th International Conference on Artificial Neural Networks: Part II
Improved Visual Clustering through Unsupervised Dimensionality Reduction
RSFDGrC '09 Proceedings of the 12th International Conference on Rough Sets, Fuzzy Sets, Data Mining and Granular Computing
Investigation of a new GRASP-based clustering algorithm applied to biological data
Computers and Operations Research
Ranking through integration of protein-similarity for identification of cell-cyclic genes
International Journal of Bioinformatics Research and Applications
A method of tumor classification based on wavelet packet transforms and neighborhood rough set
Computers in Biology and Medicine
Boosting support vector machines using multiple dissimilarities
KES'07/WIRN'07 Proceedings of the 11th international conference, KES 2007 and XVII Italian workshop on neural networks conference on Knowledge-based intelligent information and engineering systems: Part I
Generalized external indexes for comparing data partitions with overlapping categories
Pattern Recognition Letters
On the combination of dissimilarities for gene expression data analysis
ICANN'07 Proceedings of the 17th international conference on Artificial neural networks
Ensemble of dissimilarity based classifiers for cancerous samples classification
PRIB'07 Proceedings of the 2nd IAPR international conference on Pattern recognition in bioinformatics
FPF-SB: a scalable algorithm for microarray gene expression data clustering
ICDHM'07 Proceedings of the 1st international conference on Digital human modeling
Gene clustering by using query-based self-organizing maps
Expert Systems with Applications: An International Journal
A boltzmann theory based dynamic agglomerative hierarchical clustering
CIRA'09 Proceedings of the 8th IEEE international conference on Computational intelligence in robotics and automation
Application notes: data mining in cancer research
IEEE Computational Intelligence Magazine
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Projection based clustering of gene expression data
CIBB'09 Proceedings of the 6th international conference on Computational intelligence methods for bioinformatics and biostatistics
Comparing fuzzy, probabilistic, and possibilistic partitions
IEEE Transactions on Fuzzy Systems
Techniques for finding similarity knowledge in OLAP reports
Expert Systems with Applications: An International Journal
Bi-k-bi clustering: mining large scale gene expression data using two-level biclustering
International Journal of Data Mining and Bioinformatics
International Journal of Approximate Reasoning
WF-MSB: A weighted fuzzy-based biclustering method for gene expression data
International Journal of Data Mining and Bioinformatics
Mining gene expression data with pattern structures in formal concept analysis
Information Sciences: an International Journal
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A general stochastic clustering method for automatic cluster discovery
Pattern Recognition
Biclustering numerical data in formal concept analysis
ICFCA'11 Proceedings of the 9th international conference on Formal concept analysis
A systematic comparison of genome scale clustering algorithms
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
BARTMAP: A viable structure for biclustering
Neural Networks
PAKDD'11 Proceedings of the 15th Pacific-Asia conference on Advances in knowledge discovery and data mining - Volume Part I
Approximate kernel k-means: solution to large scale kernel clustering
Proceedings of the 17th ACM SIGKDD international conference on Knowledge discovery and data mining
Mutual information criteria for feature selection
SIMBAD'11 Proceedings of the First international conference on Similarity-based pattern recognition
Spectral clustering: A semi-supervised approach
Neurocomputing
International Journal of Information Technology and Management
On combining fractal dimension with GA for feature subset selecting
MICAI'06 Proceedings of the 5th Mexican international conference on Artificial Intelligence
Subspace clustering of microarray data based on domain transformation
VDMB'06 Proceedings of the First international conference on Data Mining and Bioinformatics
Effectivity of internal validation techniques for gene clustering
ISBMDA'06 Proceedings of the 7th international conference on Biological and Medical Data Analysis
A distributed, parallel system for large-scale structure recognition in gene expression data
HPCC'06 Proceedings of the Second international conference on High Performance Computing and Communications
The practical method of fractal dimensionality reduction based on z-ordering technique
ADMA'06 Proceedings of the Second international conference on Advanced Data Mining and Applications
Co-expression gene discovery from microarray for integrative systems biology
ADMA'06 Proceedings of the Second international conference on Advanced Data Mining and Applications
Spectral clustering with discriminant cuts
Knowledge-Based Systems
Gene selection by cooperative competition clustering
ICIC'06 Proceedings of the 2006 international conference on Computational Intelligence and Bioinformatics - Volume Part III
Evaluation of the contents of partitions obtained with clustering gene expression data
BSB'05 Proceedings of the 2005 Brazilian conference on Advances in Bioinformatics and Computational Biology
Relevant gene selection using normalized cut clustering with maximal compression similarity measure
PAKDD'10 Proceedings of the 14th Pacific-Asia conference on Advances in Knowledge Discovery and Data Mining - Volume Part II
Virtual gene: a gene selection algorithm for sample classification on microarray datasets
ICCS'05 Proceedings of the 5th international conference on Computational Science - Volume Part II
Virtual gene: using correlations between genes to select informative genes on microarray datasets
Transactions on Computational Systems Biology II
International Journal of Bioinformatics Research and Applications
Boost feature subset selection: a new gene selection algorithm for microarray dataset
ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part II
Dynamic bayesian network modeling of cyanobacterial biological processes via gene clustering
ICONIP'11 Proceedings of the 18th international conference on Neural Information Processing - Volume Part I
An approach to find embedded clusters using density based techniques
ICDCIT'05 Proceedings of the Second international conference on Distributed Computing and Internet Technology
Integrating wavelets with clustering and indexing for effective content-based image retrieval
Knowledge-Based Systems
Clustering high dimensional data
Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery
Finding gene coherent patterns using PATSUB+
Proceedings of the International Conference on Advances in Computing, Communications and Informatics
Multi-level description of leaf index based on analysis of canopy structure
ICSI'12 Proceedings of the Third international conference on Advances in Swarm Intelligence - Volume Part II
Hypergraph based information-theoretic feature selection
Pattern Recognition Letters
A visual analytics framework for cluster analysis of DNA microarray data
Expert Systems with Applications: An International Journal
A generalized automatic clustering algorithm in a multiobjective framework
Applied Soft Computing
Comparing partitions by means of fuzzy data mining tools
SUM'12 Proceedings of the 6th international conference on Scalable Uncertainty Management
A survey on enhanced subspace clustering
Data Mining and Knowledge Discovery
MicroClAn: Microarray clustering analysis
Journal of Parallel and Distributed Computing
An evolutionary computational model applied to cluster analysis of DNA microarray data
Expert Systems with Applications: An International Journal
Comparing relational and non-relational algorithms for clustering propositional data
Proceedings of the 28th Annual ACM Symposium on Applied Computing
Analysis of mixed C-means clustering approach for brain tumour gene expression data
International Journal of Data Analysis Techniques and Strategies
Rough-Fuzzy Clustering for Grouping Functionally Similar Genes from Microarray Data
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
MAR: Maximum Attribute Relative of soft set for clustering attribute selection
Knowledge-Based Systems
A new measure for gene expression biclustering based on non-parametric correlation
Computer Methods and Programs in Biomedicine
Gene expression data clustering using a multiobjective symmetry based clustering technique
Computers in Biology and Medicine
An automatic method to determine the number of clusters using decision-theoretic rough set
International Journal of Approximate Reasoning
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Instability and cluster stability variance for real clusterings
Information Sciences: an International Journal
Fuzzy clustering with biological knowledge for gene selection
Applied Soft Computing
Hierarchical Social Network Analysis Using a Multi-Agent System: A School System Case
International Journal of Agent Technologies and Systems
Review: Knowledge discovery in medicine: Current issue and future trend
Expert Systems with Applications: An International Journal
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DNA microarray technology has now made it possible to simultaneously monitor the expression levels of thousands of genes during important biological processes and across collections of related samples. Elucidating the patterns hidden in gene expression data offers a tremendous opportunity for an enhanced understanding of functional genomics. However, the large number of genes and the complexity of biological networks greatly increases the challenges of comprehending and interpreting the resulting mass of data, which often consists of millions of measurements. A first step toward addressing this challenge is the use of clustering techniques, which is essential in the data mining process to reveal natural structures and identify interesting patterns in the underlying data. Cluster analysis seeks to partition a given data set into groups based on specified features so that the data points within a group are more similar to each other than the points in different groups. A very rich literature on cluster analysis has developed over the past three decades. Many conventional clustering algorithms have been adapted or directly applied to gene expression data, and also new algorithms have recently been proposed specifically aiming at gene expression data. These clustering algorithms have been proven useful for identifying biologically relevant groups of genes and samples. In this paper, we first briefly introduce the concepts of microarray technology and discuss the basic elements of clustering on gene expression data. In particular, we divide cluster analysis for gene expression data into three categories. Then, we present specific challenges pertinent to each clustering category and introduce several representative approaches. We also discuss the problem of cluster validation in three aspects and review various methods to assess the quality and reliability of clustering results. Finally, we conclude this paper and suggest the promising trends in this field.