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Algorithms for Nonnegative Matrix Factorization
 In NIPS
, 2001
"... Nonnegative matrix factorization (NMF) has previously been shown to be a useful decomposition for multivariate data. Two different multiplicative algorithms for NMF are analyzed. They differ only slightly in the multiplicative factor used in the update rules. One algorithm can be shown to minim ..."
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Cited by 1230 (5 self)
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Nonnegative matrix factorization (NMF) has previously been shown to be a useful decomposition for multivariate data. Two different multiplicative algorithms for NMF are analyzed. They differ only slightly in the multiplicative factor used in the update rules. One algorithm can be shown
Bayes Factors
, 1995
"... In a 1935 paper, and in his book Theory of Probability, Jeffreys developed a methodology for quantifying the evidence in favor of a scientific theory. The centerpiece was a number, now called the Bayes factor, which is the posterior odds of the null hypothesis when the prior probability on the null ..."
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Cited by 1766 (74 self)
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In a 1935 paper, and in his book Theory of Probability, Jeffreys developed a methodology for quantifying the evidence in favor of a scientific theory. The centerpiece was a number, now called the Bayes factor, which is the posterior odds of the null hypothesis when the prior probability on the null
Multiple sequence alignment with the Clustal series of programs
 Nucleic Acids Res
, 2003
"... The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also the ..."
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Cited by 725 (5 self)
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The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also
Determining the Number of Factors in Approximate Factor Models
, 2000
"... In this paper we develop some statistical theory for factor models of large dimensions. The focus is the determination of the number of factors, which is an unresolved issue in the rapidly growing literature on multifactor models. We propose a panel Cp criterion and show that the number of factors c ..."
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Cited by 538 (29 self)
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In this paper we develop some statistical theory for factor models of large dimensions. The focus is the determination of the number of factors, which is an unresolved issue in the rapidly growing literature on multifactor models. We propose a panel Cp criterion and show that the number of factors
Diversity and Multiplexing: A Fundamental Tradeoff in Multiple Antenna Channels
 IEEE Trans. Inform. Theory
, 2002
"... Multiple antennas can be used for increasing the amount of diversity or the number of degrees of freedom in wireless communication systems. In this paper, we propose the point of view that both types of gains can be simultaneously obtained for a given multiple antenna channel, but there is a fund ..."
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Cited by 1143 (20 self)
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Multiple antennas can be used for increasing the amount of diversity or the number of degrees of freedom in wireless communication systems. In this paper, we propose the point of view that both types of gains can be simultaneously obtained for a given multiple antenna channel, but there is a
Factoring wavelet transforms into lifting steps
 J. Fourier Anal. Appl
, 1998
"... ABSTRACT. This paper is essentially tutorial in nature. We show how any discrete wavelet transform or two band subband filtering with finite filters can be decomposed into a finite sequence of simple filtering steps, which we call lifting steps but that are also known as ladder structures. This dec ..."
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Cited by 573 (8 self)
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. This decomposition corresponds to a factorization of the polyphase matrix of the wavelet or subband filters into elementary matrices. That such a factorization is possible is wellknown to algebraists (and expressed by the formula); it is also used in linear systems theory in the electrical engineering community. We
Factor Graphs and the SumProduct Algorithm
 IEEE TRANSACTIONS ON INFORMATION THEORY
, 1998
"... A factor graph is a bipartite graph that expresses how a "global" function of many variables factors into a product of "local" functions. Factor graphs subsume many other graphical models including Bayesian networks, Markov random fields, and Tanner graphs. Following one simple c ..."
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Cited by 1787 (72 self)
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A factor graph is a bipartite graph that expresses how a "global" function of many variables factors into a product of "local" functions. Factor graphs subsume many other graphical models including Bayesian networks, Markov random fields, and Tanner graphs. Following one simple
Algorithms for Quantum Computation: Discrete Logarithms and Factoring
, 1994
"... A computer is generally considered to be a universal computational device; i.e., it is believed able to simulate any physical computational device with a increase in computation time of at most a polynomial factor. It is not clear whether this is still true when quantum mechanics is taken into consi ..."
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Cited by 1103 (7 self)
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A computer is generally considered to be a universal computational device; i.e., it is believed able to simulate any physical computational device with a increase in computation time of at most a polynomial factor. It is not clear whether this is still true when quantum mechanics is taken
2005 MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res
"... The accuracy of multiple sequence alignment program MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement options, HINSi, FINSi and GINSi, in which pairwise alignment information are incorporated into objective function. These new options of MAFFT showed hig ..."
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Cited by 788 (5 self)
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The accuracy of multiple sequence alignment program MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement options, HINSi, FINSi and GINSi, in which pairwise alignment information are incorporated into objective function. These new options of MAFFT showed
Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation
, 2002
"... There are many sources of systematic variation in cDNA microarray experiments which affect the measured gene expression levels (e.g. differences in labeling efficiency between the two fluorescent dyes). The term normalization refers to the process of removing such variation. A constant adjustment is ..."
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Cited by 699 (9 self)
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There are many sources of systematic variation in cDNA microarray experiments which affect the measured gene expression levels (e.g. differences in labeling efficiency between the two fluorescent dyes). The term normalization refers to the process of removing such variation. A constant adjustment is often used to force the distribution of the intensity log ratios to have a median of zero for each slide. However, such global normalization approaches are not adequate in situations where dye biases can depend on spot overall intensity and/or spatial location within the array. This article proposes normalization methods that are based on robust local regression and account for intensity and spatial dependence in dye biases for different types of cDNA microarray experiments. The selection of appropriate controls for normalization is discussed and a novel set of controls (microarray sample pool, MSP) is introduced to aid in intensitydependent normalization. Lastly, to allow for comparisons of expression levels across slides, a robust method based on maximum likelihood estimation is proposed to adjust for scale differences among slides.
Results 1  10
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