Comparison of Discrimination Methods for the Classification of Tumors Using Gene Expression Data
From MaRDI portal
Publication:4468366
DOI10.1198/016214502753479248zbMath1073.62576OpenAlexW1966701961MaRDI QIDQ4468366
Jane Fridlyand, Sandrine Dudoit, Terence P. Speed
Publication date: 10 June 2004
Published in: Journal of the American Statistical Association (Search for Journal in Brave)
Full work available at URL: https://doi.org/10.1198/016214502753479248
Classification and discrimination; cluster analysis (statistical aspects) (62H30) Applications of statistics to biology and medical sciences; meta analysis (62P10) Medical applications (general) (92C50) Biochemistry, molecular biology (92C40)
Related Items
Classification using semiparametric mixtures, A Statistical Framework for Hypothesis Testing in Real Data Comparison Studies, Intelligent predicting reaction performance in multi-dimensional chemical space using quantile regression forest, Forward selection method with regression analysis for optimal gene selection in cancer classification, A resample-replace lasso procedure for combining high-dimensional markers with limit of detection, Selection bias in gene extraction on the basis of microarray gene-expression data, Unnamed Item, Properties of Bagged Nearest Neighbour Classifiers, Bayesian Classification of Tumours by Using Gene Expression Data, A classifier under the strongly spiked eigenvalue model in high-dimension, low-sample-size context, Statistical inference for high-dimension, low-sample-size data, Robust tests of the equality of two high-dimensional covariance matrices, Robust support vector machine for high-dimensional imbalanced data, On the singular gamma, Wishart, and beta matrix‐variate density functions, High-dimensional Canonical Forest, Fast Bayesian variable screenings for binary response regressions with small sample size, An improved modified cholesky decomposition approach for precision matrix estimation, Identification of survival relevant genes with measurement error in gene expression incorporated, Parsimonious Tensor Discriminant Analysis, Inference for sparse linear regression based on the leave-one-covariate-out solution path, Sparse overlapped linear discriminant analysis, Block-diagonal test for high-dimensional covariance matrices, Nested cross-validation with ensemble feature selection and classification model for high-dimensional biological data, Multiclass sparse discriminant analysis incorporating graphical structure among predictors, Unnamed Item, A permutation test approach to the choice of sizekfor the nearest neighbors classifier, Sparse quadratic classification rules via linear dimension reduction, Performance Comparison of Machine Learning Platforms, A link-free sparse group variable selection method for single-index model, Scaling of True and Apparent ROC AUC with Number of Observations and Number of Variables, Classification of Higher-order Data with Separable Covariance and Structured Multiplicative or Additive Mean Models, A comparison of regularization methods applied to the linear discriminant function with high-dimensional microarray data, A New Test on High-Dimensional Mean Vector Without Any Assumption on Population Covariance Matrix, An Improved Method on Wilcoxon Rank Sum Test for Gene Selection from Microarray Experiments, Aggregating classifiers with ordinal response structure, Selection of Binary Variables and Classification by Boosting, A review of modern multiple hypothesis testing, with particular attention to the false discovery proportion, GENE SELECTION USING LOGISTIC REGRESSIONS BASED ON AIC, BIC AND MDL CRITERIA, Hierarchical mixture models for biclustering in microarray data, Sliced Inverse Regression with Regularizations, Identifying Soccer Players on Facebook Through Predictive Analytics, A Method of Finding Predictor Genes for a Particular Disease Using a Clustering Algorithm, Performance of Gene Selection and Classification Methods in a Microarray Setting: A Simulation Study, Rank-Based Classification Using Robust Discriminant Functions, Fully Bayesian logistic regression with hyper-LASSO priors for high-dimensional feature selection, A Robust Maximal F-Ratio Statistic to Detect Clusters Structure, Multicategory composite least squares classifiers, Tests for high-dimensional covariance matrices using the theory ofU-statistics, A nonparametric allocation scheme for classification based on transvariation probabilities, Meta‐learning approach to gene expression data classification, Gene Expression Analysis by Fuzzy and Hybrid Fuzzy Classification, Shrinkage‐based Diagonal Discriminant Analysis and Its Applications in High‐Dimensional Data, A simple model‐based approach to variable selection in classification and clustering, Sparse bayesian kernel multinomial probit regression model for high-dimensional data classification, On rank distribution classifiers for high-dimensional data, A signature enrichment design with Bayesian adaptive randomization, Modified linear discriminant analysis using block covariance matrix in high-dimensional data, High-Dimensional Data Classification, Bayesian variable selection with sparse and correlation priors for high-dimensional data analysis, Sparse sufficient dimension reduction using optimal scoring, Clustering and classification based on the L\(_{1}\) data depth, Finding predictive gene groups from microarray data, Modeling Microarray Data Using a Threshold Mixture Model, Stability of feature selection in classification issues for high-dimensional correlated data, Asymptotic inference for high-dimensional data, Optimal properties of centroid-based classifiers for very high-dimensional data, Non-parametric shrinkage mean estimation for quadratic loss functions with unknown covariance matrices, Cancer classification using ensemble of neural networks with multiple significant gene subsets, A sparse negative binomial classifier with covariate adjustment for RNA-seq data, Weighted Lasso estimates for sparse logistic regression: non-asymptotic properties with measurement errors, Markov blanket-embedded genetic algorithm for gene selection, Tilting Methods for Assessing the Influence of Components in a Classifier, Independence index sufficient variable screening for categorical responses, A DC Programming Approach for Sparse Linear Discriminant Analysis, Geometric Classifier for Multiclass, High-Dimensional Data, A weight function method for selection of proteins to predict an outcome using protein expression data, Separable linear discriminant analysis, Predicting partial customer churn using Markov for discrimination for modeling first purchase sequences, A simultaneous testing of the mean vector and the covariance matrix among two populations for high-dimensional data, Estimation of multivariate 3rd moment for high-dimensional data and its application for testing multivariate normality, Tumor classification using phylogenetic methods on expression data, Systematic benchmarking of microarray data feature extraction and classification, Detecting differentially expressed genes by relative entropy, Variable selection in linear mixed effects models, Fast approximate inference for variable selection in Dirichlet process mixtures, with an application to pan-cancer proteomics, Variational discriminant analysis with variable selection, Variable selection for multicategory SVM via adaptive sup-norm regularization, Penalized model-based clustering, Variable selection for binary classification in large dimensions: comparisons and application to microarray data, Comparing the linear and quadratic discriminant analysis of diabetes disease classification based on data multicollinearity, Regularized \(k\)-means clustering of high-dimensional data and its asymptotic consistency, PPtree: projection pursuit classification tree, Penalized model-based clustering with unconstrained covariance matrices, Effective dimensionality reduction using kernel locality preserving partial least squares discriminant analysis, Variable Selection in Penalized Model‐Based Clustering Via Regularization on Grouped Parameters, Statistical analysis of C‐DNA microarray data for sample clustering and gene identification, Monotone false discovery rate, Marginal asymptotics for the ``large \(p\), small \(n\) paradigm: with applications to microarray data, A method for constructing a confidence bound for the actual error rate of a prediction rule in high dimensions, Variable selection and dependency networks for genomewide data, Robust depth-based tools for the analysis of gene expression data, Penalized Independence Rule for Testing High-Dimensional Hypotheses, CLASSIFICATION OF HIGH-DIMENSIONAL MICROARRAY DATA WITH A TWO-STEP PROCEDURE VIA A WILCOXON CRITERION AND MULTILAYER PERCEPTRON, Evolutionary Tolerance-Based Gene Selection in Gene Expression Data, Development and validation of biomarker classifiers for treatment selection, Several biplot methods applied to gene expression data, A test for the mean vector with fewer observations than the dimension, A method for selecting the relevant dimensions for high-dimensional classification in singular vector spaces, Estimations for some functions of covariance matrix in high dimension under non-normality and its applications, Distance-based classifier by data transformation for high-dimension, strongly spiked eigenvalue models, Biomarker discovery: classification using pooled samples, Partial least squares classification for high dimensional data using the PCOUT algorithm, Some theory for Fisher's linear discriminant function, `naive Bayes', and some alternatives when there are many more variables than observations, Graphical tools for model-based mixture discriminant analysis, Applications of Bayesian gene selection and classification with mixtures of generalized singular \(g\)-priors, Comparison of different EHG feature selection methods for the detection of preterm labor, Reducing multiclass cancer classification to binary by output coding and SVM, Classifying G-protein coupled receptors with bagging classification tree, A probabilistic relaxation labeling framework for reducing the noise effect in geometric biclustering of gene expression data, A distribution-based Lasso for a general single-index model, Boosting for high-dimensional linear models, Multi-class clustering and prediction in the analysis of microarray data, A nonparametric test for block-diagonal covariance structure in high dimension and small samples, Two-group classification with high-dimensional correlated data: a factor model approach, Bandwidth choice for nonparametric classification, Blockwise projection matrix versus blockwise data on undersampled problems: analysis, comparison and applications, Sphericity and identity test for high-dimensional covariance matrix using random matrix theory, RFCRYS: sequence-based protein crystallization propensity prediction by means of random forest, On the dimension effect of regularized linear discriminant analysis, A new geometric biclustering algorithm based on the Hough transform for analysis of large-scale microarray data, Classification tree algorithm for grouped variables, Kick-one-out-based variable selection method for Euclidean distance-based classifier in high-dimensional settings, A truncation algorithm for minimizing the Frobenius-Schatten norm to find a sparse matrix, The horseshoe-like regularization for feature subset selection, Affine-transformation invariant clustering models, Ensemble quantile classifier, Optimal feature selection for sparse linear discriminant analysis and its applications in gene expression data, Bias-Corrected Diagonal Discriminant Rules for High-Dimensional Classification, Characterizing the Relationship Between HIV-1 Genotype and Phenotype: Prediction-Based Classification, Combining Several Screening Tests: Optimality of the Risk Score, Comparison of Support Vector Machines to Other Classifiers Using Gene Expression Data, Robust penalized logistic regression with truncated loss functions, Bayesian variable selection in clustering high-dimensional data via a mixture of finite mixtures, Multiclass Probability Estimation With Support Vector Machines, Diagonal Discriminant Analysis With Feature Selection for High-Dimensional Data, Geometric classifiers for high-dimensional noisy data, Tuning parameter calibration for \(\ell_1\)-regularized logistic regression, Two-Stage Procedures for High-Dimensional Data, Estimating prediction error in microarray classification: Modifications of the 0.632+ bootstrap when ${\bf n} < {\bf p}$, Proximal gradient method for huberized support vector machine, Design Considerations for Efficient and Effective Microarray Studies, Penalized Discriminant Methods for the Classification of Tumors from Gene Expression Data, The Asymptotic Approximation of EPMC for Linear Discriminant Rules Using a Moore-Penrose Inverse Matrix in High Dimension, Parametric and Nonparametric FDR Estimation Revisited, A Multivariate Two-Sample Mean Test for Small Sample Size and Missing Data, Random projections as regularizers: learning a linear discriminant from fewer observations than dimensions, Using visual statistical inference to better understand random class separations in high dimension, low sample size data, Bayesian variable selection in multinomial probit model for classifying high-dimensional data, Improved second order estimation in the singular multivariate normal model, Variable selection for Fisher linear discriminant analysis using the modified sequential backward selection algorithm for the microarray data, Feature selection with SVD entropy: some modification and extension, Sequential double cross-validation for assessment of added predictive ability in high-dimensional omic applications, On selecting interacting features from high-dimensional data, Stein's method in high dimensional classification and applications, Nonparametric Stein-type shrinkage covariance matrix estimators in high-dimensional settings, Comprehensive comparative analysis and identification of RNA-binding protein domains: multi-class classification and feature selection, A moment-distance hybrid method for estimating a mixture of two symmetric densities, Pattern classification in DNA microarray data of multiple tumor types, Asymtotics of Dantzig selector for a general single-index model, Minimum distance classification rules for high dimensional data, Sparse Bayesian multinomial probit regression model with correlation prior for high-dimensional data classification, High dimensional covariance matrix estimation by penalizing the matrix-logarithm transformed likelihood, The use of random-effect models for high-dimensional variable selection problems, Robust groupwise least angle regression, A \(U\)-classifier for high-dimensional data under non-normality, Improved discriminate analysis for high-dimensional data and its application to face recognition, Sparse HDLSS discrimination with constrained data piling, Improved methods for the imputation of missing data by nearest neighbor methods, A multivariate empirical Bayes statistic for replicated microarray time course data, Discrimination and scoring using small sets of genes for two-sample microarray data, Comparisons of classification methods for viral genomes and protein families using alignment-free vectorization, Regularization in statistics, PCA consistency for the power spiked model in high-dimensional settings, Grid topologies for the self-organizing map, Robust classification using \(\ell _{2,1}\)-norm based regression model, Regularized orthogonal linear discriminant analysis, Penalized spline support vector classifiers computational issues, Penalized multimodal mixture logit model, Algorithmic paradigms for stability-based cluster validity and model selection statistical methods, with applications to microarray data analysis, Shrinkage-based diagonal Hotelling's tests for high-dimensional small sample size data, A Bayesian hybrid huberized support vector machine and its applications in high-dimensional medical data, Improved Stein-type shrinkage estimators for the high-dimensional multivariate normal covariance matrix, Multiple Subject Barycentric Discriminant Analysis (MUSUBADA): how to assign scans to categories without using spatial normalization, Coordinate ascent for penalized semiparametric regression on high-dimensional panel count data, The EM algorithm and the rise of computational biology, Non-convex penalized estimation in high-dimensional models with single-index structure, Testing the structure of the covariance matrix with fewer observations than the dimension, A model selection criterion for discriminant analysis of high-dimensional data with fewer observations, A unified algorithm for mixed \(l_{2,p}\)-minimizations and its application in feature selection, Methods for pattern selection, class-specific feature selection and classification for automated learning, Complexity-reduced implementations of complete and null-space-based linear discriminant analysis, Integrated use of statistical-based approaches and computational intelligence techniques for tumors classification using microarray, Statistical challenges in functional genomics. (With comments and a rejoinder)., Optimization-based model fitting for latent class and latent profile analyses, Regression adjustment for treatment effect with multicollinearity in high dimensions, Consistency of large dimensional sample covariance matrix under weak dependence, Rank discriminants for predicting phenotypes from RNA expression, Independent feature screening for ultrahigh-dimensional models with interactions, New perspectives on multilocus ancestry informativeness, Going beyond oracle property: selection consistency and uniqueness of local solution of the generalized linear model, Profile forward regression screening for ultra-high dimensional semiparametric varying coefficient partially linear models, Estimation of the precision matrix of a singular Wishart distribution and its application in high-dimensional data, On partial least squares dimension reduction for microarray-based classification: a simulation study, Stable classification with applications to microarray data, An extensive comparison of recent classification tools applied to microarray data, Bundling classifiers by bagging trees, Identification of interaction patterns and classification with applications to microarray data, Simultaneous cancer classification and gene selection with Bayesian nearest neighbor method: an integrated approach, Survival prediction using gene expression data: a review and comparison, Modified linear discriminant analysis approaches for classification of high-dimensional microarray data, A robust unified approach to analyzing methylation and gene expression data, Selecting marker genes for cancer classification using supervised weighted kernel clustering and the support vector machine, Simple Bayesian binary framework for discovering significant genes and classifying cancer diagnosis, A flexible approximate likelihood ratio test for detecting differential expression in microarray data, Bayesian binary kernel probit model for microarray based cancer classification and gene selection, Pattern recognition via projection-based \(k\)NN rules, A new and fast implementation for null space based linear discriminant analysis, Visualization of ``high \(p\) small \(n\) data, Bayesian semi-supervised learning with support vector machine, Knowledge discovery by accuracy maximization, Multicategory vertex discriminant analysis for high-dimensional data, Sparse Bayesian hierarchical modeling of high-dimensional clustering problems, Asymptotic properties of the EPMC for modified linear discriminant analysis when sample size and dimension are both large, Customer base analysis: partial defection of behaviourally loyal clients in a non-contractual FMCG retail setting, Alternating direction method of multipliers for penalized zero-variance discriminant analysis, Bayesian Weibull tree models for survival analysis of clinico-genomic data, Nonlinear logistic discrimination via regularized radial basis functions for classifying high-dimensional data, High-dimensional classification using features annealed independence rules, Sparse optimal scoring for multiclass cancer diagnosis and biomarker detection using microarray data, Optimal classification for time-course gene expression data using functional data analysis, Projection Pursuit Based on Gaussian Mixtures and Evolutionary Algorithms, A modified local quadratic approximation algorithm for penalized optimization problems, A test for the equality of covariance matrices when the dimension is large relative to the sample sizes, A new test for sphericity of the covariance matrix for high dimensional data, A distance-based, misclassification rate adjusted classifier for multiclass, high-dimensional data, Missing value imputation for gene expression data by tailored nearest neighbors, Multiclass sparse logistic regression for classification of multiple cancer types using gene expression data, Local likelihood regression in generalized linear single-index models with applications to microarray data, Classification by ensembles from random partitions of high-dimensional data, Class prediction and gene selection for DNA microarrays using regularized sliced inverse regression, High-dimensional pseudo-logistic regression and classification with applications to gene expression data, Discrimination of locally stationary time series using wavelets, Outlier identification in high dimensions, Estimation of the conditional risk in classification: the swapping method, Classification and clustering of sequencing data using a Poisson model, Variable selection and pattern recognition with gene expression data generated by the microarray technology, Dimension reduction strategies for analyzing global gene expression data with a response, Classification of cyclical time series using complex demodulation
Uses Software
