diff --git a/GPy/examples/fitc_class_01.py b/GPy/examples/fitc_class_01.py deleted file mode 100644 index 38c9da63..00000000 --- a/GPy/examples/fitc_class_01.py +++ /dev/null @@ -1,53 +0,0 @@ -import pylab as pb -import numpy as np -import GPy -pb.ion() -pb.close('all') - -""" -Simple 1D classification example -:param seed : seed value for data generation (default is 4). -:type seed: int -""" -seed=10000 - -#data = GPy.util.datasets.toy_linear_1d_classification(seed=seed) -#X = data['X'] -#Y = data['Y'][:, 0:1] -#Y[Y == -1] = 0 - - - -X = np.vstack((np.random.uniform(0,10,(10,1)),np.random.uniform(7,17,(10,1)),np.random.uniform(15,25,(10,1)))) -Y = np.vstack((np.zeros((10,1)),np.ones((10,1)),np.zeros((10,1)))) - -# Kernel object -kernel = GPy.kern.rbf(1) + GPy.kern.white(1) - -# Likelihood object -distribution = GPy.likelihoods.likelihood_functions.probit() -likelihood = GPy.likelihoods.EP(Y,distribution) - -Z = np.random.uniform(X.min(),X.max(),(10,1)) -#Z = np.array([0,20])[:,None] -print Z - -# Model definition -m = GPy.models.generalized_FITC(X,likelihood=likelihood,kernel=kernel,Z=Z,normalize_X=False) -m.set('len',2.) - -m.ensure_default_constraints() -# Optimize -#m.constrain_fixed('iip') -m.update_likelihood_approximation() -print m.checkgrad(verbose=1) -# Parameters optimization: -#m.optimize() -m.pseudo_EM() #FIXME - -# Plot -pb.subplot(211) -m.plot_f() -pb.subplot(212) -m.plot() -print(m) diff --git a/GPy/examples/fitc_class_02.py b/GPy/examples/fitc_class_02.py deleted file mode 100644 index 71e10081..00000000 --- a/GPy/examples/fitc_class_02.py +++ /dev/null @@ -1,67 +0,0 @@ -import pylab as pb -import numpy as np -import GPy -pb.close('all') - -seed=10000 -"""Run a Gaussian process classification on the crescent data. The demonstration calls the basic GP classification model and uses EP to approximate the likelihood. - -:param model_type: type of model to fit ['Full', 'FITC', 'DTC']. -:param seed : seed value for data generation. -:type seed: int -:param inducing : number of inducing variables (only used for 'FITC' or 'DTC'). -:type inducing: int -""" - -data = GPy.util.datasets.crescent_data(seed=seed) - -# Kernel object -kernel = GPy.kern.rbf(data['X'].shape[1]) + GPy.kern.white(data['X'].shape[1]) - -# Likelihood object -distribution = GPy.likelihoods.likelihood_functions.probit() -likelihood = GPy.likelihoods.EP(data['Y'],distribution) - -sample = np.random.randint(0,data['X'].shape[0],10) -Z = data['X'][sample,:] -# create sparse GP EP model -m = GPy.models.generalized_FITC(data['X'],likelihood=likelihood,kernel=kernel,Z=Z) -m.ensure_default_constraints() -m.set('len',10.) - -#m.update_likelihood_approximation() - -# optimize -#m.optimize() -m.pseudo_EM() -print(m) - -# plot -m.plot() -fitc = m - -pb.figure() -# Kernel object -kernel = GPy.kern.rbf(data['X'].shape[1]) + GPy.kern.white(data['X'].shape[1]) - -# Likelihood object -distribution = GPy.likelihoods.likelihood_functions.probit() -likelihood = GPy.likelihoods.EP(data['Y'],distribution) - -#sample = np.random.randint(0,data['X'].shape[0],10) -#Z = data['X'][sample,:] -# create sparse GP EP model -m = GPy.models.sparse_GP(data['X'],likelihood=likelihood,kernel=kernel,Z=Z) -m.ensure_default_constraints() -m.set('len',10.) - -#m.update_likelihood_approximation() - -# optimize -#m.optimize() -m.pseudo_EM() -print(m) - -# plot -m.plot() -variational = m diff --git a/GPy/examples/fitc_regr_01.py b/GPy/examples/fitc_regr_01.py deleted file mode 100644 index 815e31a7..00000000 --- a/GPy/examples/fitc_regr_01.py +++ /dev/null @@ -1,53 +0,0 @@ -import pylab as pb -import numpy as np -import GPy -pb.ion() -pb.close('all') - -N = 400 -M = 10 -# sample inputs and outputs -X = np.random.uniform(-3.,3.,(N,1)) -Y = np.sin(X)+np.random.randn(N,1)*0.05 - -"""Run a 1D example of a sparse GP regression.""" -""" -rbf = GPy.kern.rbf(1) -noise = GPy.kern.white(1) -kernel = rbf + noise -Z = np.random.uniform(-3,3,(M,1)) -likelihood = GPy.likelihoods.Gaussian(Y) -m = GPy.models.sparse_GP(X, likelihood, kernel, Z) -m.scale_factor=10000 -m.constrain_positive('(variance|lengthscale|precision)') -m.checkgrad(verbose=1) -m.optimize('tnc', messages = 1) -pb.figure() -m.plot() - -variational = m -""" - -# construct kernel -rbf = GPy.kern.rbf(1) -noise = GPy.kern.white(1) -kernel = rbf + noise -#Z = np.random.uniform(-3,3,(M,1)) -Z = variational.Z -likelihood = GPy.likelihoods.Gaussian(Y) -# create simple GP model -m = GPy.models.generalized_FITC(X, likelihood, kernel, Z=Z) -m.constrain_positive('(variance|lengthscale|precision)') -#m.constrain_fixed('iip') -m.checkgrad(verbose=1) -m.optimize('tnc', messages = 1) -#pb.figure() -#m.plot() -""" -Xnew = X.copy().flatten() -Xnew.sort() -Xnew = Xnew[:,None] -mean,var,low,up = m.predict(Xnew) -GPy.util.plot.gpplot(Xnew,mean,low,up) -fitc = m -"""