Literature DB >> 20890391

Bayesian Learning in Sparse Graphical Factor Models via Variational Mean-Field Annealing.

Ryo Yoshida1, Mike West.   

Abstract

We describe a class of sparse latent factor models, called graphical factor models (GFMs), and relevant sparse learning algorithms for posterior mode estimation. Linear, Gaussian GFMs have sparse, orthogonal factor loadings matrices, that, in addition to sparsity of the implied covariance matrices, also induce conditional independence structures via zeros in the implied precision matrices. We describe the models and their use for robust estimation of sparse latent factor structure and data/signal reconstruction. We develop computational algorithms for model exploration and posterior mode search, addressing the hard combinatorial optimization involved in the search over a huge space of potential sparse configurations. A mean-field variational technique coupled with annealing is developed to successively generate "artificial" posterior distributions that, at the limiting temperature in the annealing schedule, define required posterior modes in the GFM parameter space. Several detailed empirical studies and comparisons to related approaches are discussed, including analyses of handwritten digit image and cancer gene expression data.

Entities:  

Year:  2010        PMID: 20890391      PMCID: PMC2947451     

Source DB:  PubMed          Journal:  J Mach Learn Res        ISSN: 1532-4435            Impact factor:   3.654


  12 in total

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Authors:  N Ueda; R Nakano
Journal:  Neural Netw       Date:  1998-03

2.  Integrated modeling of clinical and gene expression information for personalized prediction of disease outcomes.

Authors:  Jennifer Pittman; Erich Huang; Holly Dressman; Cheng-Fang Horng; Skye H Cheng; Mei-Hua Tsou; Chii-Ming Chen; Andrea Bild; Edwin S Iversen; Andrew T Huang; Joseph R Nevins; Mike West
Journal:  Proc Natl Acad Sci U S A       Date:  2004-05-19       Impact factor: 11.205

3.  ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles.

Authors:  Ryo Yoshida; Tomoyuki Higuchi; Seiya Imoto; Satoru Miyano
Journal:  Bioinformatics       Date:  2006-04-10       Impact factor: 6.937

4.  A mixed factors model for dimension reduction and extraction of a group structure in gene expression data.

Authors:  Ryo Yoshida; Tomoyuki Higuchi; Seiya Imoto
Journal:  Proc IEEE Comput Syst Bioinform Conf       Date:  2004

5.  Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models.

Authors:  Osamu Hirose; Ryo Yoshida; Seiya Imoto; Rui Yamaguchi; Tomoyuki Higuchi; D Stephen Charnock-Jones; Cristin Print; Satoru Miyano
Journal:  Bioinformatics       Date:  2008-02-21       Impact factor: 6.937

6.  Predicting the clinical status of human breast cancer by using gene expression profiles.

Authors:  M West; C Blanchette; H Dressman; E Huang; S Ishida; R Spang; H Zuzan; J A Olson; J R Marks; J R Nevins
Journal:  Proc Natl Acad Sci U S A       Date:  2001-09-18       Impact factor: 11.205

7.  High-Dimensional Sparse Factor Modeling: Applications in Gene Expression Genomics.

Authors:  Carlos M Carvalho; Jeffrey Chang; Joseph E Lucas; Joseph R Nevins; Quanli Wang; Mike West
Journal:  J Am Stat Assoc       Date:  2008-12-01       Impact factor: 5.033

8.  Gene expression predictors of breast cancer outcomes.

Authors:  Erich Huang; Skye H Cheng; Holly Dressman; Jennifer Pittman; Mei Hua Tsou; Cheng Fang Horng; Andrea Bild; Edwin S Iversen; Ming Liao; Chii Ming Chen; Mike West; Joseph R Nevins; Andrew T Huang
Journal:  Lancet       Date:  2003-05-10       Impact factor: 79.321

9.  Evolutionary recombination hotspot around GSDML-GSDM locus is closely linked to the oncogenomic recombination hotspot around the PPP1R1B-ERBB2-GRB7 amplicon.

Authors:  Masuko Katoh; Masaru Katoh
Journal:  Int J Oncol       Date:  2004-04       Impact factor: 5.650

10.  A genomic strategy to elucidate modules of oncogenic pathway signaling networks.

Authors:  Jeffrey T Chang; Carlos Carvalho; Seiichi Mori; Andrea H Bild; Michael L Gatza; Quanli Wang; Joseph E Lucas; Anil Potti; Phillip G Febbo; Mike West; Joseph R Nevins
Journal:  Mol Cell       Date:  2009-04-10       Impact factor: 17.970

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  5 in total

1.  Identifying regulational alterations in gene regulatory networks by state space representation of vector autoregressive models and variational annealing.

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Journal:  BMC Genomics       Date:  2012-01-17       Impact factor: 3.969

2.  GPU-powered Shotgun Stochastic Search for Dirichlet process mixtures of Gaussian Graphical Models.

Authors:  Chiranjit Mukherjee; Abel Rodriguez
Journal:  J Comput Graph Stat       Date:  2016-08-05       Impact factor: 2.302

3.  BAYESIAN JOINT MODELING OF CHEMICAL STRUCTURE AND DOSE RESPONSE CURVES.

Authors:  Kelly R Moran; David Dunson; Matthew W Wheeler; Amy H Herring
Journal:  Ann Appl Stat       Date:  2021-09-23       Impact factor: 1.959

4.  Complex Disease Individual Molecular Characterization Using Infinite Sparse Graphical Independent Component Analysis.

Authors:  Sarah-Laure Rincourt; Stefan Michiels; Damien Drubay
Journal:  Cancer Inform       Date:  2022-07-15

5.  Mathematical and statistical modeling in cancer systems biology.

Authors:  Rachael Hageman Blair; David L Trichler; Daniel P Gaille
Journal:  Front Physiol       Date:  2012-06-28       Impact factor: 4.566

  5 in total

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