Ranking Vector Machine
supplementary materials of: "Lowe, R., Mussa, H. Y., Mitchell, J. B., & Glen, R. C. (2011). Classifying molecules using a sparse probabilistic kernel binary classifier. Journal of chemical information and modeling, 51(7), 1539-1544."
SI: https://pubs.acs.org/doi/full/10.1021/ci200128w
zip: https://pubs.acs.org/doi/suppl/10.1021/ci200128w/suppl_file/ci200128w_si_001.zip
- RVM SOURCE
- DESCRIPTOR CALCULATION
- MDDR DATA
- RVM SOURCE
Currently there is only support for Mac OS X as we are using the Accelerate Framework for the BLAS libraries.
To Compile, type make. This will compile a binary for your system named RVM
You can then run the program as
./RVM
Arguments:
-k STRING Must be [Gaus,Cauch,Binary] This defines which kernel to use
-b DOUBLE This defines the hyperparameter for that kernel
-t STRING Directory of training file. The file must be tab separated and have the last column as the class label 1 or 0
-v STRING Directory of Validation file
-s STRING Directory of Test file
-i INT Iteration limit for algorithm
-o STRING Directory of output file
-r STRING Not used
-y Output probabilities
- DESCRIPTOR CALCULATION
The descriptors used were MOLPRINT 2D descriptors. These can be calculated using the free available software from http://molprint.com/
- MDDR DATA
The MDDR data is licensed so can not be included in the supporting information. We can supply the MDDR Codes used and these are attached in a separate file MDDR_IDS