input: training (gene expression) data with ordinal labels 1,2,3,...
(binary classification is a special case of ordinal regression with labels 1 and 2 only)
output: select relevant features (selected genes as biomarkers).

1. Installation
	a. download http://www.gatsby.ucl.ac.uk/~chuwei/code/gpgenes.tar to your root
	b. tar -xvf gpgenes.tar
	c. cd ./gpgenes
	d. ./setup.sh

2. Data Format
        a) a space delimited plain text file with a new-line character 
         at the end of each line
        b) each line contains one sample.
        c) On each line, the last element is the target, integers from 1
         to rank R; other elements are of the input vector.
        d) the samples are sorted in ascending order by their ranks. 
        e) training data saved in a text file, say "mytask_train.1".
        f) the data for test with/without targets saved in "mytask_test.1".
        g) the test targets are saved in "mytask_targets.1" if available.
        h) "mytask" could be any string followed by "_train" and "_test".
        i) see the example files under the folder:
          mytask_train.1, mytask_test.1 and mytask_targets.1.   

3. Input and Output
        a) prepare your data files in the format of
                "mytask_train.1"
                "mytask_test.1"
                "mytask_targets.1" (optional)
        b) run the program
                ./gpgenes.sh mytask_train.0
	c) output files
                1) "mytask_train.0.topfeat" to save the indice of the selected features.
                2) "reduce_mytask_train.0" to save the reduced training data set with the selected features.
                3) "reduce_mytask_test.0" to save the reduced test data set with the selected features.

Reference:
W. Chu, Z. Ghahramani, F. Falciani and D. L. Wild (2005),
Biomarker discovery in microarray gene expression data with
Gaussian processes. submitted to Bioinformatics
http://www.gatsby.ucl.ac.uk/~chuwei/paper/ismbgp.pdf

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This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

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