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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
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COVARIANCE ASSISTED SCREENING AND ESTIMATION.

By Tracy Ke1, Jiashun Jin1, Jianqing Fan1

  • 1Princeton University and Carnegie Mellon University.

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|December 27, 2014
PubMed
Summary
This summary is machine-generated.

This study introduces Covariance Assisted Screening and Estimation (CASE) for variable selection in challenging linear models. CASE effectively identifies rare and weak signals by transforming non-sparse matrices into sparse ones, achieving optimal convergence rates.

Keywords:
Asymptotic minimaxityGraph of Least Favorables (GOLF)Graph of Strong Dependence (GOSD)Hamming distanceRare and Weak signal modelmultivariate screeningphase diagramsparsityvariable selection

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Area of Science:

  • Statistics
  • Machine Learning
  • Time Series Analysis

Background:

  • Linear models (Y = Xβ + z) with Gaussian noise are common.
  • Variable selection aims to identify non-zero coefficients in β.
  • Challenges arise with non-sparse Gram matrices (X'X) and rare, weak signals.

Purpose of the Study:

  • To develop a novel procedure for variable selection in challenging linear models.
  • To address situations where the Gram matrix is non-sparse but sparsifiable.
  • To achieve optimal convergence rates for variable selection under rare and weak signal conditions.

Main Methods:

  • Introduced Covariance Assisted Screening and Estimation (CASE) procedure.
  • CASE employs linear filtering to transform the regression setting, yielding a sparse Gram matrix.
  • Utilizes a graph-based approach for multivariate screening and a 'patching' technique to handle information leakage.

Main Results:

  • CASE successfully decomposes the problem into smaller subproblems by leveraging signal sparsity and graph structure.
  • The 'patching' technique effectively overcomes information leakage issues.
  • CASE achieves the optimal rate of convergence for variable selection in a broad class of non-sparse but sparsifiable Gram matrices.

Conclusions:

  • CASE provides an effective solution for variable selection in complex statistical models.
  • The method demonstrates strong performance in challenging scenarios with rare and weak signals.
  • Successfully applied to long-memory time series and change-point models, showcasing practical utility.