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 -- View this message in context: http://r.789695.n4.nabble.com/help-complete-the-reviewer-s-suggest-carry-out-GA-GP-gaussian-process-tp3229097p3229097.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.