Performing additional validation in LIBSVM matlab

Question

I am working on MATLAB LIBSVM for a while to do prediction. I have a dataset out of which I use 75% for training, 15% for finding best parameters and remaining for testing. The code is given below.

trainX and trainY are the input and output training instances
testValX and testValY are the validation dataset I use
for j = 1:100
    for jj = 1:10
        model(j,jj) = svmtrain(trainY,trainX,...
        ['-s 3 -t 2 -c ' num2str(j) ' -p 0.001 -g ' num2str(jj) '-v 5']);
        [predicted_label, ~, ~]=svmpredict(testValY,...
        testValX,model(j,jj));
        MSE(j,jj) = sum(((predicted_label-testValY).^2)/2);
    end
end
[min_val,min_indi] = min(MSE(:));
best_predicted_model_rbf(i) = model(min_indi);

My question here is whether this is correct. I am creating model matrix with different values of c and g. I use -v option which is a key here. From the predicted models I use validation dataset for prediction and there by compute mean square error. Using this MSE I pick the best c and g. Since I am using -v which returns the cross validated output, is the procedure I follow correct?

Answer 1

First, I think there is a slight problem with the code shown, which is that num2str(jj) '-v 5']); doesn't have a space before the -v. That may cause that flag to not be read. In the other question, you stated that this 'sometimes returns a model', which is what would happen if that flag was not read. If the flag is read, you should only get a number, not a model, when the '-v' flag is used.

Second, it looks like you are doing two different things here, either one of which would be reasonable on its own. Calling svmtrain with '-v' runs cross validation on the training set. That shouldn't return a model, it should just return an mse estimate. You could use these estimates to determine which parameter setting was best, and then train one model with that setting on all of the training data.

Anyway, next you call svmpredict(y,x,model) on a hold-out validation set, testValX, but having called svmtrain with '-v', model should just be a scalar at this point. In order for this call to run correctly, you have to get the model from svmtrain without '-v', so that it is a struct. The rest of what you are doing makes sense for this case, in which you are doing hold-out validation using testValX.