The effect of different hyperparameters in GPR

The following example runs Gaussian Process Regression (GPR) on a simple 1D dataset using squared exponential (i.e., Gaussian or RBF) kernel and different hyperparameters. The resulting classifier solutions are finally visualized in a single figure.

As usual we start by importing all of PyMVPA:

# Lets use LaTeX for proper rendering of greek
from matplotlib import rc
rc('text', usetex=True)

from mvpa2.suite import *

The next lines build two datasets using one of PyMVPA’s data generators.

# Generate dataset for training:
train_size = 40
F = 1
dataset = data_generators.sin_modulated(train_size, F)

# Generate dataset for testing:
test_size = 100
dataset_test = data_generators.sin_modulated(test_size, F, flat=True)

The last configuration step is the definition of four sets of hyperparameters to be used for GPR.

# Hyperparameters. Each row is [sigma_f, length_scale, sigma_noise]
hyperparameters = np.array([[1.0, 0.2, 0.4],
                           [1.0, 0.1, 0.1],
                           [1.0, 1.0, 0.1],
                           [1.0, 0.1, 1.0]])

The plotting of the final figure and the actually GPR runs are performed in a single loop.

rows = 2
columns = 2
pl.figure(figsize=(12, 12))
for i in range(rows*columns):
    pl.subplot(rows, columns, i+1)
    regression = True
    logml = True

    data_train = dataset.samples
    label_train =
    data_test = dataset_test.samples
    label_test =

The next lines configure a squared exponential kernel with the set of hyperparameters for the current subplot and assign the kernel to the GPR instance.

»    sigma_f, length_scale, sigma_noise = hyperparameters[i, :]
     kse = SquaredExponentialKernel(length_scale=length_scale,
     g = GPR(kse, sigma_noise=sigma_noise)
     if not regression:
         g = RegressionAsClassifier(g)
     print g

     if regression:"predicted_variances")

     if logml:"log_marginal_likelihood")

After training GPR the predictions are queried by passing the test dataset samples and accuracy measures are computed.

»    g.train(dataset)
     prediction = g.predict(data_test)

     # print label_test
     # print prediction
     accuracy = None
     if regression:
         accuracy = np.sqrt(((prediction-label_test)**2).sum()/prediction.size)
         print "RMSE:", accuracy
         accuracy = (prediction.astype('l')==label_test.astype('l')).sum() \
                    / float(prediction.size)
         print "accuracy:", accuracy

The remaining code simply plots both training and test datasets, as well as the GPR solutions.

»    if F == 1:
         pl.title(r"$\sigma_f=%0.2f$, $length_s=%0.2f$, $\sigma_n=%0.2f$" \
                 % (sigma_f,length_scale,sigma_noise))
         pl.plot(data_train, label_train, "ro", label="train")
         pl.plot(data_test, prediction, "b-", label="prediction")
         pl.plot(data_test, label_test, "g+", label="test")
         if regression:
             pl.plot(data_test, prediction - np.sqrt(,
                        "b--", label=None)
             pl.plot(data_test, prediction+np.sqrt(,
                        "b--", label=None)
             pl.text(0.5, -0.8, "$RMSE=%.3f$" %(accuracy))
             pl.text(0.5, -0.95, "$LML=%.3f$" %(
             pl.text(0.5, -0.8, "$accuracy=%s" % accuracy)

         pl.legend(loc='lower right')

     print "LML:",

See also

The full source code of this example is included in the PyMVPA source distribution (doc/examples/