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Random Forest Wrapper Code for book chapter "random forest for Bioinformatics"

If you use this code, please cite :

  • Major paper:

@incollection{qi2012random, title={Random forest for bioinformatics}, author={Qi, Yanjun}, booktitle={Ensemble Machine Learning}, pages={307--323}, year={2012}, publisher={Springer} }


  • Related Papers,

Y. Qi, HK. Dhiman, et al, Z. Bar-Joseph, J. Klein-Seetharaman,(2009) "Systematic prediction of human membrane receptor interactions" PROTEOMICS 2009, 9, 5243-5255

I assume that you have the "g77" command in your command list. (most unix machines have this installed.)

If not, for windows, you can install the software: "MinGW". Remember to add the g77 in your windows command list after installations.

It is very easy to run this code:

  1. Just put your parameter in a parameter file for example: testpara.file totally 10 parameters (all related files' names should be also in the input parameter file.)

  2. Then run the perl wrapper perl testpara.file

I assume that your input feature files have been pre-processed ==> which means they contain all real features and the features have no missing values.

In the subdirectory, there exsit the example files configurying in the "testpara.file"

perl wrapper "" is an extra script. Since the RF output contains the voting from all trees about postive leaves or negative leaves.. Thus one summary score could be just the ==> positive vote score - negative vote score

This wrapper would convert the direct output RF file into the summary score file as described.


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