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432
Model-Based Clustering, Discriminant Analysis, and Density Estimation
- JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
, 2000
"... Cluster analysis is the automated search for groups of related observations in a data set. Most clustering done in practice is based largely on heuristic but intuitively reasonable procedures and most clustering methods available in commercial software are also of this type. However, there is little ..."
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Cited by 557 (28 self)
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Cluster analysis is the automated search for groups of related observations in a data set. Most clustering done in practice is based largely on heuristic but intuitively reasonable procedures and most clustering methods available in commercial software are also of this type. However, there is little systematic guidance associated with these methods for solving important practical questions that arise in cluster analysis, such as \How many clusters are there?", "Which clustering method should be used?" and \How should outliers be handled?". We outline a general methodology for model-based clustering that provides a principled statistical approach to these issues. We also show that this can be useful for other problems in multivariate analysis, such as discriminant analysis and multivariate density estimation. We give examples from medical diagnosis, mineeld detection, cluster recovery from noisy data, and spatial density estimation. Finally, we mention limitations of the methodology, a...
Survey of clustering data mining techniques
, 2002
"... Accrue Software, Inc. Clustering is a division of data into groups of similar objects. Representing the data by fewer clusters necessarily loses certain fine details, but achieves simplification. It models data by its clusters. Data modeling puts clustering in a historical perspective rooted in math ..."
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Cited by 400 (0 self)
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Accrue Software, Inc. Clustering is a division of data into groups of similar objects. Representing the data by fewer clusters necessarily loses certain fine details, but achieves simplification. It models data by its clusters. Data modeling puts clustering in a historical perspective rooted in mathematics, statistics, and numerical analysis. From a machine learning perspective clusters correspond to hidden patterns, the search for clusters is unsupervised learning, and the resulting system represents a data concept. From a practical perspective clustering plays an outstanding role in data mining applications such as scientific data exploration, information retrieval and text mining, spatial database applications, Web analysis, CRM, marketing, medical diagnostics, computational biology, and many others. Clustering is the subject of active research in several fields such as statistics, pattern recognition, and machine learning. This survey focuses on clustering in data mining. Data mining adds to clustering the complications of very large datasets with very many attributes of different types. This imposes unique
Interactive Control of Avatars Animated with Human Motion Data
, 2002
"... Real-time control of three-dimensional avatars is an important problem in the context of computer games and virtual environments. Avatar animation and control is difficult, however, because a large repertoire of avatar behaviors must be made available, and the user must be able to select from this s ..."
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Cited by 369 (37 self)
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Real-time control of three-dimensional avatars is an important problem in the context of computer games and virtual environments. Avatar animation and control is difficult, however, because a large repertoire of avatar behaviors must be made available, and the user must be able to select from this set of behaviors, possibly with a low-dimensional input device. One appealing approach to obtaining a rich set of avatar behaviors is to collect an extended, unlabeled sequence of motion data appropriate to the application. In this paper, we show that such a motion database can be preprocessed for flexibility in behavior and efficient search and exploited for real-time avatar control. Flexibility is created by identifying plausible transitions between motion segments, and efficient search through the resulting graph structure is obtained through clustering. Three interface techniques are demonstrated for controlling avatar motion using this data structure: the user selects from a set of available choices, sketches a path through an environment, or acts out a desired motion in front of a video camera. We demonstrate the flexibility of the approach through four different applications and compare the avatar motion to directly recorded human motion.
Robust Data Clustering
, 2003
"... We address the problem of robust clustering by combining data partitions (forming a clustering ensemble) produced by multiple clusterings. We formulate robust clustering under an information-theoretical framework; mutual information is the underlying concept used in the definition of quantitative me ..."
Abstract
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Cited by 276 (8 self)
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We address the problem of robust clustering by combining data partitions (forming a clustering ensemble) produced by multiple clusterings. We formulate robust clustering under an information-theoretical framework; mutual information is the underlying concept used in the definition of quantitative measures of agreement or consistency between data partitions. Robustness is assessed by variance of the cluster membership, based on bootstrapping. We propose and analyze a voting mechanism on pairwise associations of patterns for combining data partitions. We show that the proposed technique attempts to optimize the mutual information based criteria, although the optimality is not ensured in all situations. This evidence accumulation method is demonstrated by combining the well-known Kmeans algorithm to produce clustering ensembles. Experimental results show the ability of the technique to identify clusters with arbitrary shapes and sizes.
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 233 (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 prediction-based 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.
Model-Based 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 196 (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, model-based 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 142 (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.
Random projection for high dimensional data clustering: A cluster ensemble approach
- In: Proceedings of the 20th International Conference on Machine Learning (ICML
"... We investigate how random projection can best be used for clustering high dimensional data. Random projection has been shown to have promising theoretical properties. In practice, however, we find that it results in highly unstable clustering performance. Our solution is to use random projection in ..."
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Cited by 138 (4 self)
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We investigate how random projection can best be used for clustering high dimensional data. Random projection has been shown to have promising theoretical properties. In practice, however, we find that it results in highly unstable clustering performance. Our solution is to use random projection in a cluster ensemble approach. Empirical results show that the proposed approach achieves better and more robust clustering performance compared to not only single runs of random projection/clustering but also clustering with PCA, a traditional data reduction method for high dimensional data. To gain insights into the performance improvement obtained by our ensemble method, we analyze and identify the influence of the quality and the diversity of the individual clustering solutions on the final ensemble performance. 1.
Clustering of time-course gene expression data using a mixed-effects model with splines
- 04, 2002, Rowe Program in Human Genetics, UC Davis School of Medicine
, 2002
"... Motivation: Time-course gene expression data are often measured to study dynamic biological systems and gene regulatory networks. To account for time dependency of the gene expression measurements over time and the noisy nature of the microarray data, the mixed-effects model using B-splines was intr ..."
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Cited by 134 (4 self)
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Motivation: Time-course gene expression data are often measured to study dynamic biological systems and gene regulatory networks. To account for time dependency of the gene expression measurements over time and the noisy nature of the microarray data, the mixed-effects model using B-splines was introduced. This paper further explores such mixed-effects model in analyzing the time-course gene expression data and in performing clustering of genes in a mixture model framework. Results: After fitting the mixture model in the framework of the mixed-effects model using an EM algorithm, we obtained the smooth mean gene expression curve for each cluster. For each gene, we obtained the best linear unbiased smooth estimate of its gene expression trajectory over time, combining data from that gene and other genes in the same cluster. Simulated data indicate that the methods can effectively cluster noisy curves into clusters differing in either the shapes of the curves or the times to the peaks of the curves. We further demonstrate the proposed method by clustering the yeast genes based on their cell cycle gene expression data and the human genes based on the temporal transcriptional response of fibroblasts to serum. Clear periodic patterns and varying times to peaks are observed for different clusters of the cell-cycle regulated genes. Results of the analysis of the human fibroblasts data show seven distinct transcriptional response profiles with biological relevance. Availability: Matlab programs are available on request from the authors.
