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237
Consensus clustering -- A resampling-based method for class discovery and visualization of gene expression microarray data
- MACHINE LEARNING, FUNCTIONAL GENOMICS SPECIAL ISSUE
, 2003
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Integrating topics and syntax
- In Advances in Neural Information Processing Systems 17
, 2005
"... Statistical approaches to language learning typically focus on either short-range syntactic dependencies or long-range semantic dependencies between words. We present a generative model that uses both kinds of dependencies, and can be used to simultaneously find syntactic classes and semantic topics ..."
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Cited by 89 (12 self)
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Statistical approaches to language learning typically focus on either short-range syntactic dependencies or long-range semantic dependencies between words. We present a generative model that uses both kinds of dependencies, and can be used to simultaneously find syntactic classes and semantic topics despite having no representation of syntax or semantics beyond statistical dependency. This model is competitive on tasks like part-of-speech tagging and document classification with models that exclusively use short- and long-range dependencies respectively. 1
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 ..."
Abstract
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Cited by 88 (8 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.
Learning systems of concepts with an infinite relational model
- In Proceedings of the 21st National Conference on Artificial Intelligence
, 2006
"... Relationships between concepts account for a large proportion of semantic knowledge. We present a nonparametric Bayesian model that discovers systems of related concepts. Given data involving several sets of entities, our model discovers the kinds of entities in each set and the relations between ki ..."
Abstract
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Cited by 86 (14 self)
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Relationships between concepts account for a large proportion of semantic knowledge. We present a nonparametric Bayesian model that discovers systems of related concepts. Given data involving several sets of entities, our model discovers the kinds of entities in each set and the relations between kinds that are possible or likely. We apply our approach to four problems: clustering objects and features, learning ontologies, discovering kinship systems, and discovering structure in political data. Philosophers, psychologists and computer scientists have proposed that semantic knowledge is best understood as a system of relations. Two questions immediately arise: how can these systems be represented, and how are these representations acquired? Researchers who start with the
Learning the k in k-means
- In Proc. 17th NIPS
, 2003
"... When clustering a dataset, the right number k of clusters to use is often not obvious, and choosing k automatically is a hard algorithmic problem. In this paper we present an improved algorithm for learning k while clustering. The G-means algorithm is based on a statistical test for the hypothesis t ..."
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Cited by 64 (5 self)
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When clustering a dataset, the right number k of clusters to use is often not obvious, and choosing k automatically is a hard algorithmic problem. In this paper we present an improved algorithm for learning k while clustering. The G-means algorithm is based on a statistical test for the hypothesis that a subset of data follows a Gaussian distribution. G-means runs k-means with increasing k in a hierarchical fashion until the test accepts the hypothesis that the data assigned to each k-means center are Gaussian. Two key advantages are that the hypothesis test does not limit the covariance of the data and does not compute a full covariance matrix. Additionally, G-means only requires one intuitive parameter, the standard statistical significance level α. We present results from experiments showing that the algorithm works well, and better than a recent method based on the BIC penalty for model complexity. In these experiments, we show that the BIC is ineffective as a scoring function, since it does
Comparing clusterings: an axiomatic view
- In ICML ’05: Proceedings of the 22nd international conference on Machine learning
, 2005
"... This paper views clusterings as elements of a lattice. Distances between clusterings are analyzed in their relationship to the lattice. From this vantage point, we first give an axiomatic characterization of some criteria for comparing clusterings, including the variation of information and the unad ..."
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Cited by 51 (3 self)
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This paper views clusterings as elements of a lattice. Distances between clusterings are analyzed in their relationship to the lattice. From this vantage point, we first give an axiomatic characterization of some criteria for comparing clusterings, including the variation of information and the unadjusted Rand index. Then we study other distances between partitions w.r.t these axioms and prove an impossibility result: there is no “sensible” criterion for comparing clusterings that is simultaneously (1) aligned with the lattice of partitions, (2) convexely additive, and (3) bounded. 1.
Comparing Clusterings
, 2002
"... This paper proposes an information theoretic criterion for comparing two clusterings of the same data set. The criterion, called variation of information measures the amount of information that is lost or gained in changing from clustering C to dustering C '. The criterion makes no assumptions about ..."
Abstract
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Cited by 43 (2 self)
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This paper proposes an information theoretic criterion for comparing two clusterings of the same data set. The criterion, called variation of information measures the amount of information that is lost or gained in changing from clustering C to dustering C '. The criterion makes no assumptions about how the dusterings were generated and applies to both soft and hard dusterings.The basic properties of VI are presented and discussed from the point of view of comparing c!usterings. In particular, the VI is positive, symmetric and transitive and thus, surprisingly enough, is a true metric on the space of c1usterings.
Computing communities in large networks using random walks
- J. of Graph Alg. and App. bf
, 2004
"... Dense subgraphs of sparse graphs (communities), which appear in most real-world complex networks, play an important role in many contexts. Computing them however is generally expensive. We propose here a measure of similarities between vertices based on random walks which has several important advan ..."
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Cited by 43 (1 self)
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Dense subgraphs of sparse graphs (communities), which appear in most real-world complex networks, play an important role in many contexts. Computing them however is generally expensive. We propose here a measure of similarities between vertices based on random walks which has several important advantages: it captures well the community structure in a network, it can be computed efficiently, and it can be used in an agglomerative algorithm to compute efficiently the community structure of a network. We propose such an algorithm, called Walktrap, which runs in time O(mn 2) and space O(n 2) in the worst case, and in time O(n 2 log n) and space O(n 2) in most real-world cases (n and m are respectively the number of vertices and edges in the input graph). Extensive comparison tests show that our algorithm surpasses previously proposed ones concerning the quality of the obtained community structures and that it stands among the best ones concerning the running time.
Toward Objective Evaluation of Image Segmentation Algorithms
, 2007
"... Unsupervised image segmentation is an important component in many image understanding algorithms and practical vision systems. However, evaluation of segmentation algorithms thus far has been largely subjective, leaving a system designer to judge the effectiveness of a technique based only on intui ..."
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Cited by 40 (2 self)
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Unsupervised image segmentation is an important component in many image understanding algorithms and practical vision systems. However, evaluation of segmentation algorithms thus far has been largely subjective, leaving a system designer to judge the effectiveness of a technique based only on intuition and results in the form of a few example segmented images. This is largely due to image segmentation being an ill-defined problem—there is no unique ground-truth segmentation of an image against which the output of an algorithm may be compared. This paper demonstrates how a recently proposed measure of similarity, the Normalized Probabilistic Rand (NPR) index, can be used to perform a quantitative comparison between image segmentation algorithms using a hand-labeled set of ground-truth segmentations. We show that the measure allows principled comparisons between segmentations created by different algorithms, as well as segmentations on different images. We outline a procedure for algorithm evaluation through an example evaluation of some familiar algorithms—the mean-shift-based algorithm, an efficient graph-based segmentation algorithm, a hybrid algorithm that combines the strengths of both methods, and expectation maximization. Results are presented on the 300 images in the publicly available Berkeley Segmentation Data Set.
Evolutionary Spectral Clustering by Incorporating Temporal Smoothness
, 2007
"... Evolutionary clustering is an emerging research area essential to important applications such as clustering dynamic Web and blog contents and clustering data streams. In evolutionary clustering, a good clustering result should fit the current data well, while simultaneously not deviate too dramatica ..."
Abstract
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Cited by 38 (6 self)
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Evolutionary clustering is an emerging research area essential to important applications such as clustering dynamic Web and blog contents and clustering data streams. In evolutionary clustering, a good clustering result should fit the current data well, while simultaneously not deviate too dramatically from the recent history. To fulfill this dual purpose, a measure of temporal smoothness is integrated in the overall measure of clustering quality. In this paper, we propose two frameworks that incorporate temporal smoothness in evolutionary spectral clustering. For both frameworks, we start with intuitions gained from the well-known k-means clustering problem, and then propose and solve corresponding cost functions for the evolutionary spectral clustering problems. Our solutions to the evolutionary spectral clustering problems provide more stable and consistent clustering results that are less sensitive to short-term noises while at the same time are adaptive to long-term cluster drifts. Furthermore, we demonstrate that our methods provide the optimal solutions to the relaxed versions of the corresponding evolutionary k-means clustering problems. Performance experiments over a number of real and synthetic data sets illustrate our evolutionary spectral clustering methods provide more robust clustering results that are not sensitive to noise and can adapt to data drifts.

