https://github.com/unixjunkie/rvm
Ranking Vector Machine
https://github.com/unixjunkie/rvm
classification cpp-program rvm
Last synced: 10 months ago
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Ranking Vector Machine
- Host: GitHub
- URL: https://github.com/unixjunkie/rvm
- Owner: UnixJunkie
- Created: 2019-06-10T05:04:27.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2019-06-10T05:15:58.000Z (over 6 years ago)
- Last Synced: 2025-01-31T09:31:18.419Z (11 months ago)
- Topics: classification, cpp-program, rvm
- Language: C++
- Homepage: https://pubs.acs.org/doi/full/10.1021/ci200128w
- Size: 18.6 KB
- Stars: 1
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# RVM
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
***************************************************************************
1) RVM SOURCE
2) DESCRIPTOR CALCULATION
3) MDDR DATA
***************************************************************************
1) 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
***************************************************************************
2) DESCRIPTOR CALCULATION
The descriptors used were MOLPRINT 2D descriptors. These can be calculated using the free available software from http://molprint.com/
***************************************************************************
3) 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