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Grant Details

Grant Number: 5R01CA072028-07 Interpret this number
Primary Investigator: Johnstone, Iain
Organization: Stanford University
Project Title: New Statistical Methods for Medical Signals and Images
Fiscal Year: 2002


Abstract

Medical and biological data often come in the form of digitized signals and images; for example, magnetic resonance images, electrocardiogram traces and even the folding paths of proteins. As instrumental data acquisition becomes routine, sequences of such images, signals or paths are collected, often along with other covariate measurements, resulting in datasets where the basic unit of measurement, or response, is a high-dimensional object. The project continues to focus on developing techniques for modelling and understanding such data that explicitly take into account, and indeed exploit inherent spatial or temporal correlation, and when appropriate, relate it to covariate or class label information. To study covariance structure, the project proposes "sparse" forms of principal components and discriminant analysis that may be more sensitive to either local phenomena of not necessarily smooth form or that are more adapted to irregularly observed data. Corresponding quadratically regularized methods in appropriate bases form a natural foil for comparison, and will also be developed in certain applications. For estimation of means, the project will examine sparse empirical Bayes methods for estimating non smooth local phenomena. Much of this work will be carried out in existing and new collaborations with researchers in medical imaging, cardiology and other specialties, working for example on cancer, heart disease and brain mapping.



Publications

Cell type-specific gene expression differences in complex tissues.
Authors: Shen-Orr S.S. , Tibshirani R. , Khatri P. , Bodian D.L. , Staedtler F. , Perry N.M. , Hastie T. , Sarwal M.M. , Davis M.M. , Butte A.J. .
Source: Nature methods, 2010 Apr; 7(4), p. 287-9.
EPub date: 2010-03-07.
PMID: 20208531
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A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis.
Authors: Witten D.M. , Tibshirani R. , Hastie T. .
Source: Biostatistics (Oxford, England), 2009 Jul; 10(3), p. 515-34.
EPub date: 2009-04-17.
PMID: 19377034
Related Citations

MULTIVARIATE ANALYSIS AND JACOBI ENSEMBLES: LARGEST EIGENVALUE, TRACY-WIDOM LIMITS AND RATES OF CONVERGENCE.
Authors: Johnstone I.M. .
Source: Annals of statistics, 2008-12-01; 36(6), p. 2638.
PMID: 20157626
Related Citations

Sparse inverse covariance estimation with the graphical lasso.
Authors: Friedman J. , Hastie T. , Tibshirani R. .
Source: Biostatistics (Oxford, England), 2008 Jul; 9(3), p. 432-41.
EPub date: 2007-12-12.
PMID: 18079126
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Penalized logistic regression for detecting gene interactions.
Authors: Park M.Y. , Hastie T. .
Source: Biostatistics (Oxford, England), 2008 Jan; 9(1), p. 30-50.
EPub date: 2007-04-11.
PMID: 17429103
Related Citations

Averaged gene expressions for regression.
Authors: Park M.Y. , Hastie T. , Tibshirani R. .
Source: Biostatistics (Oxford, England), 2007 Apr; 8(2), p. 212-27.
EPub date: 2006-05-11.
PMID: 16698769
Related Citations

Hybrid hierarchical clustering with applications to microarray data.
Authors: Chipman H. , Tibshirani R. .
Source: Biostatistics (Oxford, England), 2006 Apr; 7(2), p. 286-301.
EPub date: 2005-11-21.
PMID: 16301308
Related Citations

Classification of gene microarrays by penalized logistic regression.
Authors: Zhu J. , Hastie T. .
Source: Biostatistics (Oxford, England), 2004 Jul; 5(3), p. 427-43.
PMID: 15208204
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Diagnosis of multiple cancer types by shrunken centroids of gene expression.
Authors: Tibshirani R. , Hastie T. , Narasimhan B. , Chu G. .
Source: Proceedings of the National Academy of Sciences of the United States of America, 2002-05-14; 99(10), p. 6567-72.
PMID: 12011421
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Missing value estimation methods for DNA microarrays.
Authors: Troyanskaya O. , Cantor M. , Sherlock G. , Brown P. , Hastie T. , Tibshirani R. , Botstein D. , Altman R.B. .
Source: Bioinformatics (Oxford, England), 2001 Jun; 17(6), p. 520-5.
PMID: 11395428
Related Citations

Regression analysis of multiple protein structures.
Authors: Wu T.D. , Schmidler S.C. , Hastie T. , Brutlag D.L. .
Source: Journal of computational biology : a journal of computational molecular cell biology, 1998 Fall; 5(3), p. 585-95.
PMID: 9773352
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Modeling and superposition of multiple protein structures using affine transformations: analysis of the globins.
Authors: Wu T.D. , Schmidler S.C. , Hastie T. , Brutlag D.L. .
Source: Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 1998; , p. 509-20.
PMID: 9697208
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