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4,278
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 bio-sequence analysis, and KFMs have bee ..."
Abstract
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Cited by 770 (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 bio-sequence analysis, and KFMs have
A Bayesian Framework for the Analysis of Microarray Expression Data: Regularized t-Test and Statistical Inferences of Gene Changes
- Bioinformatics
, 2001
"... Motivation: DNA microarrays are now capable of providing genome-wide patterns of gene expression across many different conditions. The first level of analysis of these patterns requires determining whether observed differences in expression are significant or not. Current methods are unsatisfactory ..."
Abstract
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Cited by 491 (6 self)
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due to the lack of a systematic framework that can accommodate noise, variability, and low replication often typical of microarray data. Results: We develop a Bayesian probabilistic framework for microarray data analysis. At the simplest level, we model log-expression values by independent normal
Loopy belief propagation for approximate inference: An empirical study. In:
- Proceedings of Uncertainty in AI,
, 1999
"... Abstract Recently, researchers have demonstrated that "loopy belief propagation" -the use of Pearl's polytree algorithm in a Bayesian network with loops -can perform well in the context of error-correcting codes. The most dramatic instance of this is the near Shannon-limit performanc ..."
Abstract
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Cited by 676 (15 self)
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. For each experimental run, we first gen erated random CPTs. We then sampled from the joint distribution defined by the network and clamped the observed nodes (all nodes in the bottom layer) to their sampled value. Given a structure and observations, we then ran three inference algorithms -junction tree
Verbal reports as data
- Psychological Review
, 1980
"... The central proposal of this article is that verbal reports are data. Accounting for verbal reports, as for other kinds of data, requires explication of the mech-anisms by which the reports are generated, and the ways in which they are sensitive to experimental factors (instructions, tasks, etc.). W ..."
Abstract
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Cited by 513 (3 self)
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The central proposal of this article is that verbal reports are data. Accounting for verbal reports, as for other kinds of data, requires explication of the mech-anisms by which the reports are generated, and the ways in which they are sensitive to experimental factors (instructions, tasks, etc
Application of Phylogenetic Networks in Evolutionary Studies
- SUBMITTED TO MBE 2005
, 2005
"... The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evoluti ..."
Abstract
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Cited by 887 (15 self)
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evolution proceeds in a tree-like manner, analysis of the data may not be best served by using methods that enforce a tree structure, but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step. Thus, phylogenetic networks should be employed when
A new approach to the maximum flow problem
- JOURNAL OF THE ACM
, 1988
"... All previously known efficient maximum-flow algorithms work by finding augmenting paths, either one path at a time (as in the original Ford and Fulkerson algorithm) or all shortest-length augmenting paths at once (using the layered network approach of Dinic). An alternative method based on the pre ..."
Abstract
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Cited by 672 (33 self)
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to be shortest paths. The algorithm and its analysis are simple and intuitive, yet the algorithm runs as fast as any other known method on dense. graphs, achieving an O(n³) time bound on an n-vertex graph. By incorporating the dynamic tree data structure of Sleator and Tarjan, we obtain a version
Inferring Web Communities from Link Topology
, 1998
"... The World Wide Web grows through a decentralized, almost anarchic process, and this has resulted in a large hyperlinked corpus without the kind of logical organization that can be built into more traditionally-created hypermedia. To extract meaningful structure under such circumstances, we develop a ..."
Abstract
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Cited by 415 (4 self)
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a notion of hyperlinked communities on the www through an analysis of the link topology. Byinvoking a simple, mathematically clean method for de ning and exposing the structure of these communities, we are able to derive anumber of themes: The communities can be viewed as containing a core
Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments
- STATISTICA SINICA
, 2002
"... DNA microarrays are a new and promising biotechnology whichallows the monitoring of expression levels in cells for thousands of genes simultaneously. The present paper describes statistical methods for the identification of differentially expressed genes in replicated cDNA microarray experiments. A ..."
Abstract
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Cited by 438 (12 self)
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into account the dependence structure between the gene expression levels. No specific parametric form is assumed for the distribution of the test statistics and a permutation procedure is used to estimate adjusted p-values. Several data displays are suggested for the visual identification of differentially
Self-tuning spectral clustering
- Advances in Neural Information Processing Systems 17
, 2004
"... We study a number of open issues in spectral clustering: (i) Selecting the appropriate scale of analysis, (ii) Handling multi-scale data, (iii) Clustering with irregular background clutter, and, (iv) Finding automatically the number of groups. We first propose that a ‘local ’ scale should be used to ..."
Abstract
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Cited by 362 (2 self)
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to compute the affinity between each pair of points. This local scaling leads to better clustering especially when the data includes multiple scales and when the clusters are placed within a cluttered background. We further suggest exploiting the structure of the eigenvectors to infer automatically
Mining anomalies using traffic feature distributions
- In ACM SIGCOMM
, 2005
"... The increasing practicality of large-scale flow capture makes it possible to conceive of traffic analysis methods that detect and identify a large and diverse set of anomalies. However the challenge of effectively analyzing this massive data source for anomaly diagnosis is as yet unmet. We argue tha ..."
Abstract
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Cited by 322 (8 self)
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that the distributions of packet features (IP addresses and ports) observed in flow traces reveals both the presence and the structure of a wide range of anomalies. Using entropy as a summarization tool, we show that the analysis of feature distributions leads to significant advances on two fronts: (1) it enables highly
Results 1 - 10
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4,278