R help - Jan 2011 - help! complete the reviewer's suggest: carry out GA+GP (gaussian process)!

Hello, all experts,

My major is computer-aied drug design ( main QSAR).

Now, my paper need be reviesed, and one reviewer ask me do genetic algorithm
coupled with gaussian process method (GA+GP).

my data:
training set: 191*106
    test set: 73*106

here, I need use GA+GP to do variable selection when building the model. 

In R, there are not GA package like in matlab
GA-toolbox(http://www.sheffield.ac.uk/acse/research/ecrg/gat.html) .

now, I just can use the matlab GA-tool box, however, I can not use
GP-toolbox in matlab. so I search the internet, find R package
"genalg" can
do GA. and an example given is to do wavelength selection by GA+PLS, so I
think i certainly do the GA+GP. unfortunately, in this genalg package, i do
not know how to extract the selected variables, it seems likes there is not
such function. So I want to all friends help me to solve the reviewer's
suggestion: do GA+GP and extract the optimal variables and get the some
statistical parameters (i.e., cross-validation R2, pred R2 etc).

now, I can do GA+svm to do variable selection and build the models and get
some statistical paramets depicted above.

GA: matlab GA toolbox
(http://www.sheffield.ac.uk/acse/research/ecrg/gat.html)
svm: libsvm (http://www.csie.ntu.edu.tw/~cjlin/libsvm/)

now I want to know, how to get the predicted values :

In libsvm for example:
cmd = ['-v ',num2str(v),' -c',num2str(cgp(nind,1)),  '-g
',num2str(cgp(nind,2)),' -p ',num2str(cgp(nind,3)),' -s 3'];
model = svmtrain(train_y,train_data_best,cmd);
train_pred = svmpredict(train_y,train_data_best,model); % get the predicted
values for the training set

I can get the train_pred, likewise I can get the test_pred (tes_pred
svmpredict(test_y,test_data_best,model);)

If I have the obsved train_y,test_y and the predicted train_pred and
test_pred, some statistical parameter can be calculated. 

But For GP, how can i get the predicted values?

(from GP website:  http://www.gaussianprocess.org/gpml/code/matlab/doc/)

prediction: [ymu ys2 fmu fs2   ] = gp(hyp, inf, mean, cov, lik, x, y, xs); 

here, the "ymu" are the predicted values that similar to
"test_pred" in
libsvm?  

I hope all friends  can give me a hand, sincere there are little days i
should upload my revised manuscript, but until now this quest can not be
soved.

thanks for your help.

kevin




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I do not know about what you are asking. But your thread was helpful for me
to workout some libsvm codes. Thank you for your help. Maybe we can interact
for more productive work.

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