diff --git a/GPy/examples/classification.py b/GPy/examples/classification.py index bff8dcd1..648ddb5a 100644 --- a/GPy/examples/classification.py +++ b/GPy/examples/classification.py @@ -26,32 +26,40 @@ def crescent_data(seed=default_seed): # FIXME m = GPy.models.GPClassification(data['X'], Y) m.ensure_default_constraints() - m.update_likelihood_approximation() - m.optimize() + #m.update_likelihood_approximation() + #m.optimize() + m.pseudo_EM() print(m) m.plot() return m -def oil(): +def oil(num_inducing=50): """ Run a Gaussian process classification on the oil data. The demonstration calls the basic GP classification model and uses EP to approximate the likelihood. """ data = GPy.util.datasets.oil() - Y = data['Y'][:, 0:1] + X = data['X'][:600,:] + X_test = data['X'][600:,:] + Y = data['Y'][:600, 0:1] Y[Y.flatten()==-1] = 0 + Y_test = data['Y'][600:, 0:1] # Create GP model - m = GPy.models.GPClassification(data['X'], Y) + m = GPy.models.SparseGPClassification(X, Y,num_inducing=num_inducing) # Contrain all parameters to be positive m.constrain_positive('') m.tie_params('.*len') + m['.*len'] = 10. m.update_likelihood_approximation() # Optimize m.optimize() - print(m) + + #Test + probs = m.predict(X_test)[0] + GPy.util.classification.conf_matrix(probs,Y_test) return m def toy_linear_1d_classification(seed=default_seed): @@ -70,20 +78,20 @@ def toy_linear_1d_classification(seed=default_seed): m.ensure_default_constraints() # Optimize - m.update_likelihood_approximation() + #m.update_likelihood_approximation() # Parameters optimization: - m.optimize() + #m.optimize() + m.pseudo_EM() # Plot - pb.subplot(211) - m.plot_f() - pb.subplot(212) - m.plot() + fig, axes = pb.subplots(2,1) + m.plot_f(ax=axes[0]) + m.plot(ax=axes[1]) print(m) return m -def sparse_toy_linear_1d_classification(seed=default_seed): +def sparse_toy_linear_1d_classification(num_inducing=10,seed=default_seed): """ Sparse 1D classification example :param seed : seed value for data generation (default is 4). @@ -95,25 +103,25 @@ def sparse_toy_linear_1d_classification(seed=default_seed): Y[Y.flatten() == -1] = 0 # Model definition - m = GPy.models.SparseGPClassification(data['X'], Y) - m['.*len']= 2. + m = GPy.models.SparseGPClassification(data['X'], Y,num_inducing=num_inducing) + m['.*len']= 4. m.ensure_default_constraints() # Optimize - m.update_likelihood_approximation() + #m.update_likelihood_approximation() # Parameters optimization: - m.optimize() + #m.optimize() + m.pseudo_EM() # Plot - pb.subplot(211) - m.plot_f() - pb.subplot(212) - m.plot() + fig, axes = pb.subplots(2,1) + m.plot_f(ax=axes[0]) + m.plot(ax=axes[1]) print(m) return m -def sparse_crescent_data(inducing=10, seed=default_seed): +def sparse_crescent_data(num_inducing=10, seed=default_seed): """ Run a Gaussian process classification with DTC approxiamtion on the crescent data. The demonstration calls the basic GP classification model and uses EP to approximate the likelihood. @@ -128,16 +136,17 @@ def sparse_crescent_data(inducing=10, seed=default_seed): Y = data['Y'] Y[Y.flatten()==-1]=0 - m = GPy.models.SparseGPClassification(data['X'], Y) + m = GPy.models.SparseGPClassification(data['X'], Y,num_inducing=num_inducing) m.ensure_default_constraints() m['.*len'] = 10. - m.update_likelihood_approximation() - m.optimize() + #m.update_likelihood_approximation() + #m.optimize() + m.pseudo_EM() print(m) m.plot() return m -def FITC_crescent_data(inducing=10, seed=default_seed): +def FITC_crescent_data(num_inducing=10, seed=default_seed): """ Run a Gaussian process classification with FITC approximation on the crescent data. The demonstration uses EP to approximate the likelihood. @@ -145,7 +154,7 @@ def FITC_crescent_data(inducing=10, seed=default_seed): :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 + :type num_inducing: int """ data = GPy.util.datasets.crescent_data(seed=seed) @@ -157,12 +166,12 @@ def FITC_crescent_data(inducing=10, seed=default_seed): Y = data['Y'] Y[Y.flatten()==-1]=0 - m = GPy.models.FITCClassification(data['X'], Y) + m = GPy.models.FITCClassification(data['X'], Y,num_inducing=num_inducing) m.ensure_default_constraints() m['.*len'] = 3. - m.update_likelihood_approximation() - m.optimize() + #m.update_likelihood_approximation() + #m.optimize() + m.pseudo_EM() print(m) m.plot() return m -