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501
Consistency of spectral clustering
, 2004
"... Consistency is a key property of statistical algorithms, when the data is drawn from some underlying probability distribution. Surprisingly, despite decades of work, little is known about consistency of most clustering algorithms. In this paper we investigate consistency of a popular family of spe ..."
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Cited by 572 (15 self)
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Consistency is a key property of statistical algorithms, when the data is drawn from some underlying probability distribution. Surprisingly, despite decades of work, little is known about consistency of most clustering algorithms. In this paper we investigate consistency of a popular family of spectral clustering algorithms, which cluster the data with the help of eigenvectors of graph Laplacian matrices. We show that one of the two of major classes of spectral clustering (normalized clustering) converges under some very general conditions, while the other (unnormalized), is only consistent under strong additional assumptions, which, as we demonstrate, are not always satisfied in real data. We conclude that our analysis provides strong evidence for the superiority of normalized spectral clustering in practical applications. We believe that methods used in our analysis will provide a basis for future exploration of Laplacianbased methods in a statistical setting.
Data Clustering: 50 Years Beyond KMeans
, 2008
"... Organizing data into sensible groupings is one of the most fundamental modes of understanding and learning. As an example, a common scheme of scientific classification puts organisms into taxonomic ranks: domain, kingdom, phylum, class, etc.). Cluster analysis is the formal study of algorithms and m ..."
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Cited by 294 (7 self)
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Organizing data into sensible groupings is one of the most fundamental modes of understanding and learning. As an example, a common scheme of scientific classification puts organisms into taxonomic ranks: domain, kingdom, phylum, class, etc.). Cluster analysis is the formal study of algorithms and methods for grouping, or clustering, objects according to measured or perceived intrinsic characteristics or similarity. Cluster analysis does not use category labels that tag objects with prior identifiers, i.e., class labels. The absence of category information distinguishes data clustering (unsupervised learning) from classification or discriminant analysis (supervised learning). The aim of clustering is exploratory in nature to find structure in data. Clustering has a long and rich history in a variety of scientific fields. One of the most popular and simple clustering algorithms, Kmeans, was first published in 1955. In spite of the fact that Kmeans was proposed over 50 years ago and thousands of clustering algorithms have been published since then, Kmeans is still widely used. This speaks to the difficulty of designing a general purpose clustering algorithm and the illposed problem of clustering. We provide a brief overview of clustering, summarize well known clustering methods, discuss the major challenges and key issues in designing clustering algorithms, and point out some of the emerging and useful research directions, including semisupervised clustering, ensemble clustering, simultaneous feature selection, and data clustering and large scale data clustering.
Consensus clustering  A resamplingbased method for class discovery and visualization of gene expression microarray data
 MACHINE LEARNING 52 (2003) 91–118 FUNCTIONAL GENOMICS SPECIAL ISSUE
, 2003
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Applications of Resampling Methods to Estimate the Number of Clusters and to Improve the Accuracy of a Clustering Method
, 2001
"... The burgeoning field of genomics, and in particular microarray experiments, have revived interest in both discriminant and cluster analysis, by raising new methodological and computational challenges. The present paper discusses applications of resampling methods to problems in cluster analysis. A r ..."
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Cited by 235 (0 self)
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The burgeoning field of genomics, and in particular microarray experiments, have revived interest in both discriminant and cluster analysis, by raising new methodological and computational challenges. The present paper discusses applications of resampling methods to problems in cluster analysis. A resampling method, known as bagging in discriminant analysis, is applied to increase clustering accuracy and to assess the confidence of cluster assignments for individual observations. A novel predictionbased resampling method is also proposed to estimate the number of clusters, if any, in a dataset. The performance of the proposed and existing methods are compared using simulated data and gene expression data from four recently published cancer microarray studies.
ModelBased Clustering and Data Transformations for Gene Expression Data
, 2001
"... Motivation: Clustering is a useful exploratory technique for the analysis of gene expression data. Many different heuristic clustering algorithms have been proposed in this context. Clustering algorithms based on probability models offer a principled alternative to heuristic algorithms. In particula ..."
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Cited by 200 (9 self)
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Motivation: Clustering is a useful exploratory technique for the analysis of gene expression data. Many different heuristic clustering algorithms have been proposed in this context. Clustering algorithms based on probability models offer a principled alternative to heuristic algorithms. In particular, modelbased clustering assumes that the data is generated by a finite mixture of underlying probability distributions such as multivariate normal distributions. The issues of selecting a 'good' clustering method and determining the 'correct' number of clusters are reduced to model selection problems in the probability framework. Gaussian mixture models have been shown to be a powerful tool for clustering in many applications.
Cluster Analysis for Gene Expression Data: A Survey
 IEEE Transactions on Knowledge and Data Engineering
, 2004
"... Abstract—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 f ..."
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Cited by 149 (5 self)
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Abstract—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. Index Terms—Microarray technology, gene expression data, clustering.
From patterns to pathways: gene expression data analysis comes of age.
 Nature Genetics
, 2002
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Graph mining: laws, generators, and algorithms
 ACM COMPUT SURV (CSUR
, 2006
"... How does the Web look? How could we tell an abnormal social network from a normal one? These and similar questions are important in many fields where the data can intuitively be cast as a graph; examples range from computer networks to sociology to biology and many more. Indeed, any M: N relation in ..."
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Cited by 132 (7 self)
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How does the Web look? How could we tell an abnormal social network from a normal one? These and similar questions are important in many fields where the data can intuitively be cast as a graph; examples range from computer networks to sociology to biology and many more. Indeed, any M: N relation in database terminology can be represented as a graph. A lot of these questions boil down to the following: “How can we generate synthetic but realistic graphs? ” To answer this, we must first understand what patterns are common in realworld graphs and can thus be considered a mark of normality/realism. This survey give an overview of the incredible variety of work that has been done on these problems. One of our main contributions is the integration of points of view from physics, mathematics, sociology, and computer science. Further, we briefly describe recent advances on some related and interesting graph problems.
Determining the number of clusters/segments in hierarchical clustering/segmentation algorithms
, 2003
"... Many clustering and segmentation algorithms both suffer from the limitation that the number of clusters/segments are specified by a human user. It is often impractical to expect a human with sufficient domain knowledge to be available to select the number of clusters/segments to return. In this pape ..."
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Cited by 101 (2 self)
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Many clustering and segmentation algorithms both suffer from the limitation that the number of clusters/segments are specified by a human user. It is often impractical to expect a human with sufficient domain knowledge to be available to select the number of clusters/segments to return. In this paper, we investigate techniques to determine the number of clusters or segments to return from hierarchical clustering and segmentation algorithms. We propose an efficient algorithm, the L method, that finds the “knee ” in a ‘ # of clusters vs. clustering evaluation metric ’ graph. Using the knee is wellknown, but is not a particularly wellunderstood method to determine the number of clusters. We explore the feasibility of this method, and attempt to determine in which situations it will and will not work. We also compare the L method to existing methods based on the accuracy of the number of clusters that are determined and efficiency. Our results show favorable performance for these criteria compared to the existing methods that were evaluated.
CLICK and EXPANDER: a system for clustering and visualizing gene expression data
 Bioinformatics
, 2003
"... Motivation: Microarrays have become a central tool in biological research. Their applications range from functional annotation to tissue classification and genetic network inference. A key step in the analysis of gene expression data is the identification of groups of genes that manifest similar exp ..."
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Cited by 99 (6 self)
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Motivation: Microarrays have become a central tool in biological research. Their applications range from functional annotation to tissue classification and genetic network inference. A key step in the analysis of gene expression data is the identification of groups of genes that manifest similar expression patterns. This translates to the algorithmic problem of clustering genes based on their expression patterns. Results: We present a novel clustering algorithm, called CLICK, and its applications to gene expression analysis. The algorithm utilizes graphtheoretic and statistical techniques to identify tight groups (kernels) of highly similar elements, which are likely to belong to the same true cluster. Several heuristic procedures are then used to expand the kernels into the full clusters. We report on the application of CLICK to a variety of gene expression data sets. In all those applications it outperformed extant algorithms according to several common figures of merit. We also point out that CLICK can be successfully used for the identification of common regulatory motifs in the upstream regions of coregulated genes. Furthermore, we demonstrate how CLICK can be used to accurately classify tissue samples into disease types, based on their expression profiles. Finally, we present a new javabased graphical tool, called EXPANDER, for gene expression analysis and visualization, which incorporates CLICK and several other popular clustering algorithms.