Ultranet: Efficient solver for the sparse inverse covariance selection problem in gene network modeling

Bioinformatics

Volumn 29, Issue 4, 2013, Pages 511-512

  Järvstråt, Linnea ^a   Johansson, Mikael ^b   Gullberg, Urban ^a   Nilsson, Björn ^a,c  

^a LUND UNIVERSITY HOSPITAL   (Sweden)

^b ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^c BROAD INSTITUTE OF MIT AND HARVARD   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ARTICLE; BIOLOGICAL MODEL; COMPUTER PROGRAM; GENE REGULATORY NETWORK; GENOMICS; HUMAN; NORMAL DISTRIBUTION;

GENE REGULATORY NETWORKS; GENOMICS; HUMANS; MODELS, GENETIC; NORMAL DISTRIBUTION; SOFTWARE; TRANSCRIPTOME;

MLCS; MLOWN;

EID: 84874322384     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts717     Document Type: Article

References (9)

1. Duchi, J.C. et al. (2008) Projected subgradient methods for learning sparse Gaussians. In: Proceedings of the Conference Uncertainty in Artificial Intelligence. Helsinki.
2. Friedman, J. et al. (2008) Sparse inverse covariance estimation with the graphical lasso. Biostatistics, 9, 432-441.
3. Haferlach, T. et al. (2010) Clinical utility of microarray-based gene expression profiling in the diagnosis and classification of leukemia. J. Clin. Oncol., 28, 2529-2537.
4. Lu, Z. (2009) Smooth optimization approach for sparse covariance selection. SIAM J. Optim., 19, 1807-1827.
5. Markowetz, F. and Spang, R. (2007) Inferring cellular networks-a review. BMC Bioinformatics, 8 (Suppl. 6), S5.
6. Scheinberg, K. et al. (2010) Sparse inverse covariance selection via alternating linearization methods. In: Proceedings of Neural Information Processing Systems. Vancouver.
7. Schäfer, J. and Strimmer, K. (2005a) An empirical bayes approach to inferring largescale gene association networks. Bioinformatics, 21, 754-64.
8. Schäfer, J. and Strimmer, K. (2005b) A shrinkage approach to large-scale covariance matrix estimation and implications for genomics. Stat. Appl. Genet. Mol. Biol., 4, Article 32.
9. Yuan, X. (2009) Alternating direction methods for sparse covariance selection. Optimization Online, http://www.optimization-online.org/DB-FILE/2009/ 09/2390.pdf (17 January 2013, date last accessed).