cwKBMF: Kernelized Bayesian Matrix Factorization with Component-Wise Multiple Kernel Learning

The source code below implements the kernelized Bayesian matrix factorization with component-wise MKL. The zip-package contains both, the code for learning the model and running on a toy dataset.

Source Code

Download: cwkbmf.zip (Matlab Implementation, Version 0.1, 05 April 2016)
License: Licensed under the FreeBSD open source license.

This is experimental software provided as is; we welcome any comments and corrections but cannot give any guarantees about the code. If you have any comments or bug reports, please direct them to Muhammad Ammad-ud-din.

Data sets

If you use any of the data sets, please cite the original sources (listed below in the CITATION INFO), in addition to the Ammad-ud-din et al. (2016).

1: GDSC (Matlab and R formats, more details in readMe.pdf)
2: CTRP_CCLE (Matlab and R formats, more details in readMe.pdf).

CITATION INFO

• Muhammad Ammad-ud-din, Suleiman A.Khan, Disha Malani, Astrid Murumägi, Olli Kallioniemi, Tero Aittokallio and Samuel Kaski. Drug response prediction by inferring pathway-response associations with Kernelized Bayesian Matrix Factorization. Bioinformatics, 32(17):i455--i463, 2016
• Mathew J Garnett, Elena J Edelman, Sonja J Heidorn, Chris D Greenman, Anahita Dastur, King Wai Lau, Patricia Greninger, I Richard Thompson, Xi Luo, Jorge Soares, et al. Systematic identication of genomic markers of drug sensitivity in cancer cells. Nature, 483(7391):570--575, 2012
• Wanjuan Yang, Jorge Soares, Patricia Greninger, Elena J Edelman, Howard Lightfoot, Simon Forbes, Nidhi Bindal, Dave Beare, James A Smith, I Richard Thompson, et al. Genomics of drug sensitivity in cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells. Nucleic Acids Res., 41(D1):D955--D961, 2013.
• J. Barretina, G. Caponigro, N. Stransky, K. Venkatesan, A. A. Margolin, S. Kim, C. J. Wilson, J. Lehar, G. V. Kryukov, D. Sonkin, et al. The cancer cell line encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature, vol. 483, no. 7391, pp. 603--607, 2012.
• A. Basu, N. E. Bodycombe, J. H. Cheah, E. V. Price, K. Liu, G. I. Schaefer, R. Y. Ebright, M. L. Stewart, D. Ito, S. Wang and others, An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules. Cell, vol. 154, no. 5, pp. 1151--1161, 2013..
• A. Liberzon, A. Subramanian, R. Pinchback, H. Thorvaldsdottir, P. Tamayo, and J. P. Mesirov. Molecular signatures database MSigDB 3.0. Bioinformatics, vol. 27, no. 12, pp. 1739--1740, 2011.