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259
Dynamic Bayesian Networks: Representation, Inference and Learning
, 2002
"... Modelling sequential data is important in many areas of science and engineering. Hidden Markov models (HMMs) and Kalman filter models (KFMs) are popular for this because they are simple and flexible. For example, HMMs have been used for speech recognition and biosequence analysis, and KFMs have bee ..."
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Cited by 598 (3 self)
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Modelling sequential data is important in many areas of science and engineering. Hidden Markov models (HMMs) and Kalman filter models (KFMs) are popular for this because they are simple and flexible. For example, HMMs have been used for speech recognition and biosequence analysis, and KFMs have been used for problems ranging from tracking planes and missiles to predicting the economy. However, HMMs
and KFMs are limited in their “expressive power”. Dynamic Bayesian Networks (DBNs) generalize HMMs by allowing the state space to be represented in factored form, instead of as a single discrete random variable. DBNs generalize KFMs by allowing arbitrary probability distributions, not just (unimodal) linearGaussian. In this thesis, I will discuss how to represent many different kinds of models as DBNs, how to perform exact and approximate inference in DBNs, and how to learn DBN models from sequential data.
In particular, the main novel technical contributions of this thesis are as follows: a way of representing
Hierarchical HMMs as DBNs, which enables inference to be done in O(T) time instead of O(T 3), where T is the length of the sequence; an exact smoothing algorithm that takes O(log T) space instead of O(T); a simple way of using the junction tree algorithm for online inference in DBNs; new complexity bounds on exact online inference in DBNs; a new deterministic approximate inference algorithm called factored frontier; an analysis of the relationship between the BK algorithm and loopy belief propagation; a way of
applying RaoBlackwellised particle filtering to DBNs in general, and the SLAM (simultaneous localization
and mapping) problem in particular; a way of extending the structural EM algorithm to DBNs; and a variety of different applications of DBNs. However, perhaps the main value of the thesis is its catholic presentation of the field of sequential data modelling.
Clustering Gene Expression Patterns
, 1999
"... Recent advances in biotechnology allow researchers to measure expression levels for thousands of genes simultaneously, across different conditions and over time. Analysis of data produced by such experiments offers potential insight into gene function and regulatory mechanisms. A key step in the ana ..."
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Cited by 362 (10 self)
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Recent advances in biotechnology allow researchers to measure expression levels for thousands of genes simultaneously, across different conditions and over time. Analysis of data produced by such experiments offers potential insight into gene function and regulatory mechanisms. A key step in the analysis of gene expression data is the detection of groups of genes that manifest similar expression patterns. The corresponding algorithmic problem is to cluster multicondition gene expression patterns. In this paper we describe a novel clustering algorithm that was developed for analysis of gene expression data. We define an appropriate stochastic error model on the input, and prove that under the conditions of the model, the algorithm recovers the cluster structure with high probability. The running time of the algorithm on an ngene dataset is O(n 2 (log(n)) c ). We also present a practical heuristic based on the same algorithmic ideas. The heuristic was implemented and its p...
Efficient Clustering of HighDimensional Data Sets with Application to Reference Matching
, 2000
"... Many important problems involve clustering large datasets. Although naive implementations of clustering are computationally expensive, there are established efficient techniques for clustering when the dataset has either (1) a limited number of clusters, (2) a low feature dimensionality, or (3) a sm ..."
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Cited by 275 (13 self)
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Many important problems involve clustering large datasets. Although naive implementations of clustering are computationally expensive, there are established efficient techniques for clustering when the dataset has either (1) a limited number of clusters, (2) a low feature dimensionality, or (3) a small number of data points. However, there has been much less work on methods of efficiently clustering datasets that are large in all three ways at oncefor example, having millions of data points that exist in many thousands of dimensions representing many thousands of clusters. We present a new technique for clustering these large, highdimensional datasets. The key idea involves using a cheap, approximate distance measure to efficiently divide the data into overlapping subsets we call canopies. Then clustering is performed by measuring exact distances only between points that occur in a common canopy. Using canopies, large clustering problems that were formerly impossible become practical. Under r...
InformationTheoretic CoClustering
 In KDD
, 2003
"... Twodimensional contingency or cooccurrence tables arise frequently in important applications such as text, weblog and marketbasket data analysis. A basic problem in contingency table analysis is coclustering: simultaneous clustering of the rows and columns. A novel theoretical formulation views ..."
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Cited by 270 (10 self)
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Twodimensional contingency or cooccurrence tables arise frequently in important applications such as text, weblog and marketbasket data analysis. A basic problem in contingency table analysis is coclustering: simultaneous clustering of the rows and columns. A novel theoretical formulation views the contingency table as an empirical joint probability distribution of two discrete random variables and poses the coclustering problem as an optimization problem in information theory  the optimal coclustering maximizes the mutual information between the clustered random variables subject to constraints on the number of row and column clusters.
Survey of clustering algorithms
 IEEE TRANSACTIONS ON NEURAL NETWORKS
, 2005
"... Data analysis plays an indispensable role for understanding various phenomena. Cluster analysis, primitive exploration with little or no prior knowledge, consists of research developed across a wide variety of communities. The diversity, on one hand, equips us with many tools. On the other hand, the ..."
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Cited by 270 (3 self)
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Data analysis plays an indispensable role for understanding various phenomena. Cluster analysis, primitive exploration with little or no prior knowledge, consists of research developed across a wide variety of communities. The diversity, on one hand, equips us with many tools. On the other hand, the profusion of options causes confusion. We survey clustering algorithms for data sets appearing in statistics, computer science, and machine learning, and illustrate their applications in some benchmark data sets, the traveling salesman problem, and bioinformatics, a new field attracting intensive efforts. Several tightly related topics, proximity measure, and cluster validation, are also discussed.
Recognizing Imprecisely Localized, Partially Occluded and Expression Variant Faces from a Single Sample per Class
, 2002
"... The classical way of attempting to solve the face (or object) recognition problem is by using large and representative datasets. In many applications though, only one sample per class is available to the system. In this contribution, we describe a probabilistic approach that is able to compensate fo ..."
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Cited by 166 (8 self)
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The classical way of attempting to solve the face (or object) recognition problem is by using large and representative datasets. In many applications though, only one sample per class is available to the system. In this contribution, we describe a probabilistic approach that is able to compensate for imprecisely localized, partially occluded and expression variant faces even when only one single training sample per class is available to the system. To solve the localization problem, we find the subspace (within the feature space, e.g. eigenspace) that represents this error for each of the training images. To resolve the occlusion problem, each face is divided into k local regions which are analyzed in isolation. In contrast with other approaches, where a simple voting space is used, we present a probabilistic method that analyzes how "good" a local match is. To make the recognition system less sensitive to the differences between the facial expression displayed on the training and the testing images, we weight the results obtained on each local area on the bases of how much of this local area is affected by the expression displayed on the current test image.
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 92 (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.
Just relax: Convex programming methods for subset selection and sparse approximation
, 2004
"... Abstract. Subset selection and sparse approximation problems request a good approximation of an input signal using a linear combination of elementary signals, yet they stipulate that the approximation may only involve a few of the elementary signals. This class of problems arises throughout electric ..."
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Cited by 92 (4 self)
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Abstract. Subset selection and sparse approximation problems request a good approximation of an input signal using a linear combination of elementary signals, yet they stipulate that the approximation may only involve a few of the elementary signals. This class of problems arises throughout electrical engineering, applied mathematics and statistics, but small theoretical progress has been made over the last fifty years. Subset selection and sparse approximation both admit natural convex relaxations, but the literature contains few results on the behavior of these relaxations for general input signals. This report demonstrates that the solution of the convex program frequently coincides with the solution of the original approximation problem. The proofs depend essentially on geometric properties of the ensemble of elementary signals. The results are powerful because sparse approximation problems are combinatorial, while convex programs can be solved in polynomial time with standard software. Comparable new results for a greedy algorithm, Orthogonal Matching Pursuit, are also stated. This report should have a major practical impact because the theory applies immediately to many realworld signal processing problems. 1.
Multivariate information bottleneck
, 2001
"... The Information bottleneck method is an unsupervised nonparametric data organization technique. Given a joint distribution¢¤£¦¥¨§�©� � , this method constructs a new variable � that extracts partitions, or clusters, over the values of ¥ that are informative about ©. The information bottleneck has a ..."
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Cited by 85 (14 self)
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The Information bottleneck method is an unsupervised nonparametric data organization technique. Given a joint distribution¢¤£¦¥¨§�©� � , this method constructs a new variable � that extracts partitions, or clusters, over the values of ¥ that are informative about ©. The information bottleneck has already been applied to document classification, gene expression, neural code, and spectral analysis. In this paper, we introduce a general principled framework for multivariate extensions of the information bottleneck method. This allows us to consider multiple systems of data partitions that are interrelated. Our approach utilizes Bayesian networks for specifying the systems of clusters and what information each captures. We show that this construction provides insight about bottleneck variations and enables us to characterize solutions of these variations. We also present a general framework for iterative algorithms for constructing solutions, and apply it to several examples. 1
Spatiallydistributed coverage optimization and control with limitedrange interactions
 ESAIM Control, Optimisation Calculus Variations
, 2005
"... Abstract. This paper presents coordination algorithms for groups of mobile agents performing deployment and coverage tasks. As an important modeling constraint, we assume that each mobile agent has a limited sensing/communication radius. Based on the geometry of Voronoi partitions and proximity grap ..."
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Cited by 78 (34 self)
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Abstract. This paper presents coordination algorithms for groups of mobile agents performing deployment and coverage tasks. As an important modeling constraint, we assume that each mobile agent has a limited sensing/communication radius. Based on the geometry of Voronoi partitions and proximity graphs, we analyze a class of aggregate objective functions and propose coverage algorithms in continuous and discrete time. These algorithms have convergence guarantees and are spatially distributed with respect to appropriate proximity graphs. Numerical simulations illustrate the results.