KAUSTNMF – Non-negative Matrix Factorization by Maximizing Correntropy for Cancer Clustering

KAUSTNMF

:: DESCRIPTION

KAUSTNMF is a maximum correntropy criterion-based non-negative matrix factorization package.

::DEVELOPER

Structural and Functional Bioinformatics Group, King Abdullah University of Science and Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • MatLab

:: DOWNLOAD

 KAUSTNMF 

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Mar 24;14:107. doi: 10.1186/1471-2105-14-107.
Non-negative matrix factorization by maximizing correntropy for cancer clustering.
Wang JJ1, Wang X, Gao X.

NMF-mGPU 1.0 – Non-negative Matrix Factorization on multi-GPU Systems

NMF-mGPU 1.0

:: DESCRIPTION

NMF-mGPU implements the Non-negative Matrix Factorization (NMF) algorithm by making use of Graphics Processing Units (GPUs).

::DEVELOPER

Biocomputing Unit – CNB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • CUDA Toolkit and CUDA Driver:

:: DOWNLOAD

 NMF-mGPU

:: MORE INFORMATION

Citation:

NMF-mGPU: non-negative matrix factorization on multi-GPU systems.
Mejía-Roa E, Tabas-Madrid D, Setoain J, García C, Tirado F, Pascual-Montano A.
BMC Bioinformatics. 2015 Feb 13;16:43. doi: 10.1186/s12859-015-0485-4.

GraDe – Knowledge-based Matrix Factorization resolves the Cellular Responses to IL-6 Stimulation

GraDe

:: DESCRIPTION

GraDe (graph-decorrelation) provides a novel framework for the decomposition of large-scale ‘omics’ data. Including prior knowledge into the separation task leads to a much more structured and detailed separation of the time-dependent responses upon IL-6 stimulation compared to standard methods.

::DEVELOPER

Institute of Computational Biology, German Research Center for Environmental Health (GmbH)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • MatLab

:: DOWNLOAD

GraDe

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Nov 30;11:585. doi: 10.1186/1471-2105-11-585.
Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation.
Kowarsch A, Blöchl F, Bohl S, Saile M, Gretz N, Klingmüller U, Theis FJ.

NMF – Metagenes and Molecular Pattern discovery using Matrix Factorization

NMF

:: DESCRIPTION

NMF (Non-negative Matrix Factorization), an algorithm based on decomposition-by-parts, recovers meaningful information without supervision. Coupled with a novel model selection mechanism, and efficiently implemented in Matlab, NMF is a powerful method for identification of context-dependent patterns in complex biological systems.

::DEVELOPER

Broad Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux / MacOsX
  • MatLab

:: DOWNLOAD

 NMF

:: MORE INFORMATION

Citation

Jean-Philippe Brunet, Pablo Tamayo, Todd Golub, Jill Mesirov
Metagenes and molecular pattern discovery using matrix factorization
Proc. Natl. Acad. Sci. USA 2004 101: 4164-4169