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277
Regularization paths for generalized linear models via coordinate descent
, 2009
"... We develop fast algorithms for estimation of generalized linear models with convex penalties. The models include linear regression, twoclass logistic regression, and multinomial regression problems while the penalties include ℓ1 (the lasso), ℓ2 (ridge regression) and mixtures of the two (the elastic ..."
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Cited by 375 (9 self)
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We develop fast algorithms for estimation of generalized linear models with convex penalties. The models include linear regression, twoclass logistic regression, and multinomial regression problems while the penalties include ℓ1 (the lasso), ℓ2 (ridge regression) and mixtures of the two (the elastic net). The algorithms use cyclical coordinate descent, computed along a regularization path. The methods can handle large problems and can also deal efficiently with sparse features. In comparative timings we find that the new algorithms are considerably faster than competing methods.
Sparse Principal Component Analysis
 Journal of Computational and Graphical Statistics
, 2004
"... Principal component analysis (PCA) is widely used in data processing and dimensionality reduction. However, PCA su#ers from the fact that each principal component is a linear combination of all the original variables, thus it is often di#cult to interpret the results. We introduce a new method ca ..."
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Cited by 206 (5 self)
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Principal component analysis (PCA) is widely used in data processing and dimensionality reduction. However, PCA su#ers from the fact that each principal component is a linear combination of all the original variables, thus it is often di#cult to interpret the results. We introduce a new method called sparse principal component analysis (SPCA) using the lasso (elastic net) to produce modified principal components with sparse loadings. We show that PCA can be formulated as a regressiontype optimization problem, then sparse loadings are obtained by imposing the lasso (elastic net) constraint on the regression coe#cients. E#cient algorithms are proposed to realize SPCA for both regular multivariate data and gene expression arrays. We also give a new formula to compute the total variance of modified principal components. As illustrations, SPCA is applied to real and simulated data, and the results are encouraging.
Consensus clustering  A resamplingbased method for class discovery and visualization of gene expression microarray data
 MACHINE LEARNING 52 (2003) 91–118 FUNCTIONAL GENOMICS SPECIAL ISSUE
, 2003
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The Entire Regularization Path for the Support Vector Machine
, 2004
"... In this paper we argue that the choice of the SVM cost parameter can be critical. We then derive an algorithm that can fit the entire path of SVM solutions for every value of the cost parameter, with essentially the same computational cost as fitting one SVM model. ..."
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Cited by 177 (9 self)
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In this paper we argue that the choice of the SVM cost parameter can be critical. We then derive an algorithm that can fit the entire path of SVM solutions for every value of the cost parameter, with essentially the same computational cost as fitting one SVM model.
The mathematics of learning: Dealing with data
 Notices of the American Mathematical Society
, 2003
"... Draft for the Notices of the AMS Learning is key to developing systems tailored to a broad range of data analysis and information extraction tasks. We outline the mathematical foundations of learning theory and describe a key algorithm of it. 1 ..."
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Cited by 145 (16 self)
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Draft for the Notices of the AMS Learning is key to developing systems tailored to a broad range of data analysis and information extraction tasks. We outline the mathematical foundations of learning theory and describe a key algorithm of it. 1
A comparative study of feature selection and multiclass classification methods for tissue classification based on gene expression
 Bioinformatics
, 2004
"... This paper studies the problem of building multiclass classifiers for tissue classification based on gene expression. The recent development of microarray technologies has enabled biologists to quantify gene expression of tens of thousands of genes in a single experiment. Biologists have begun colle ..."
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Cited by 119 (5 self)
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This paper studies the problem of building multiclass classifiers for tissue classification based on gene expression. The recent development of microarray technologies has enabled biologists to quantify gene expression of tens of thousands of genes in a single experiment. Biologists have begun collecting gene expression for a large number of samples. One of the urgent issues in the use of microarray data is to develop methods for characterizing samples based on their gene expression. The most basic step in the research direction is binary sample classification, which has been studied extensively over the past few years. This paper investigates the next step—multiclass classification of samples based on gene expression. The characteristics of expression data (e.g., large number of genes with small sample size)
Everything Old Is New Again: A Fresh Look at Historical Approaches
 in Machine Learning. PhD thesis, MIT
, 2002
"... 2 Everything Old Is New Again: A Fresh Look at Historical ..."
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Cited by 100 (7 self)
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2 Everything Old Is New Again: A Fresh Look at Historical
Class prediction by nearest shrunken centroids, with applicaitons to dna microarrays
 Stat Sci
, 2003
"... Abstract. We propose a new method for class prediction in DNA microarray studies based on an enhancement of the nearest prototype classifier. Our technique uses “shrunken ” centroids as prototypes for each class to identify the subsets of the genes that best characterize each class. The method is ge ..."
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Cited by 79 (15 self)
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Abstract. We propose a new method for class prediction in DNA microarray studies based on an enhancement of the nearest prototype classifier. Our technique uses “shrunken ” centroids as prototypes for each class to identify the subsets of the genes that best characterize each class. The method is general and can be applied to other highdimensional classification problems. The method is illustrated on data from two gene expression studies: lymphoma and cancer cell lines. Key words and phrases: Sample classification, gene expression arrays. 1.
Prediction by supervised principal components
 Journal of the American Statistical Association
, 2006
"... In regression problems where the number of predictors greatly exceeds the number of observations, conventional regression techniques may produce unsatisfactory results. We describe a technique called supervised principal components that can be applied to this type of problem. Supervised principal co ..."
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Cited by 79 (9 self)
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In regression problems where the number of predictors greatly exceeds the number of observations, conventional regression techniques may produce unsatisfactory results. We describe a technique called supervised principal components that can be applied to this type of problem. Supervised principal components is similar to conventional principal components analysis except that it uses a subset of the predictors selected based on their association with the outcome. Supervised principal components can be applied to regression and generalized regression problems, such as survival analysis. It compares favorably to other techniques for this type of problem, and can also account for the effects of other covariates and help identify which predictor variables are most important. We also provide asymptotic consistency results to help support our empirical findings. These methods could become important tools for DNA microarray data, where they may be used to more accurately diagnose and treat cancer. KEY WORDS: Gene expression; Microarray; Regression; Survival analysis. 1.
Class prediction and discovery using gene microarray and proteomics mass spectroscopy data: curses, caveats, cautions
 Bioinformatics
, 2003
"... Motivation: Two practical realities constrain the analysis of microarray data, mass spectra from proteomics, and biomedical infrared or magnetic resonance spectra. One is the ‘curse of dimensionality’: the number of features characterizing these data is in the thousands or tens of thousands. The oth ..."
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Cited by 66 (3 self)
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Motivation: Two practical realities constrain the analysis of microarray data, mass spectra from proteomics, and biomedical infrared or magnetic resonance spectra. One is the ‘curse of dimensionality’: the number of features characterizing these data is in the thousands or tens of thousands. The other is the ‘curse of dataset sparsity’: the number of samples is limited. The consequences of these two curses are farreaching when such data are used to classify the presence or absence of disease. Results: Using very simple classifiers, we show for several publicly available microarray and proteomics datasets how these curses influence classification outcomes. In particular, even if the sample per feature ratio is increased to the recommended 5–10 by feature extraction/reduction methods, dataset sparsity can render any classification result statistically suspect. In addition, several ‘optimal’ feature sets are typically identifiable for sparse datasets, all producing perfect classification results, both for the training and independent validation sets. This nonuniqueness leads to interpretational difficulties and casts doubt on the biological relevance of any of these ‘optimal’ feature sets. We suggest an approach to assess the relative quality of apparently equally good classifiers.