From d84ae52d415abfa92f8f78b2b9954ef4e331edc6 Mon Sep 17 00:00:00 2001 From: James Hensman Date: Tue, 4 Jun 2013 16:21:00 +0100 Subject: [PATCH 1/4] fixed Alan's dependency nightmare. --- GPy/__init__.py | 5 +++-- GPy/core/gp_base.py | 2 +- GPy/models/sparse_GPLVM.py | 2 +- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/GPy/__init__.py b/GPy/__init__.py index fa69dac3..3b656626 100644 --- a/GPy/__init__.py +++ b/GPy/__init__.py @@ -2,16 +2,17 @@ # Licensed under the BSD 3-clause license (see LICENSE.txt) -import kern +import core import models import inference import util import examples -from core import priors import likelihoods import testing from numpy.testing import Tester from nose.tools import nottest +import kern +from core import priors @nottest def tests(): diff --git a/GPy/core/gp_base.py b/GPy/core/gp_base.py index 8df1a5c1..3eb977c6 100644 --- a/GPy/core/gp_base.py +++ b/GPy/core/gp_base.py @@ -4,7 +4,7 @@ from .. import kern from ..util.plot import gpplot, Tango, x_frame1D, x_frame2D import pylab as pb -class GPBase(model): +class GPBase(model.model): """ Gaussian Process model for holding shared behaviour between sprase_GP and GP models diff --git a/GPy/models/sparse_GPLVM.py b/GPy/models/sparse_GPLVM.py index af388f1c..591c49b2 100644 --- a/GPy/models/sparse_GPLVM.py +++ b/GPy/models/sparse_GPLVM.py @@ -8,7 +8,7 @@ import sys, pdb # from .. import kern # from ..core import model # from ..util.linalg import pdinv, PCA -from ..core import GPLVM +from GPLVM import GPLVM from sparse_GP_regression import sparse_GP_regression class sparse_GPLVM(sparse_GP_regression, GPLVM): From 775ec15543dc1105c3b19cb7b92b19b376ba3093 Mon Sep 17 00:00:00 2001 From: Ricardo Date: Tue, 4 Jun 2013 16:23:04 +0100 Subject: [PATCH 2/4] Link functions defined --- GPy/examples/classification.py | 6 +- GPy/likelihoods/EP.py | 1 + GPy/likelihoods/likelihood_functions.py | 155 ++++++++++++++---------- GPy/likelihoods/link_functions.py | 58 +++++++++ 4 files changed, 156 insertions(+), 64 deletions(-) create mode 100644 GPy/likelihoods/link_functions.py diff --git a/GPy/examples/classification.py b/GPy/examples/classification.py index 9168db7c..a96911f4 100644 --- a/GPy/examples/classification.py +++ b/GPy/examples/classification.py @@ -79,12 +79,16 @@ def toy_linear_1d_classification(seed=default_seed): data = GPy.util.datasets.toy_linear_1d_classification(seed=seed) Y = data['Y'][:, 0:1] + Y[Y.flatten() == -1] = 0 # Kernel object kernel = GPy.kern.rbf(1) # Likelihood object - distribution = GPy.likelihoods.likelihood_functions.probit() + link = GPy.likelihoods.link_functions.probit + distribution = GPy.likelihoods.likelihood_functions.binomial(link) + #distribution = GPy.likelihoods.likelihood_functions.binomial() + #distribution = GPy.likelihoods.likelihood_functions.probit() likelihood = GPy.likelihoods.EP(Y, distribution) # Model definition diff --git a/GPy/likelihoods/EP.py b/GPy/likelihoods/EP.py index efca0649..5b538b92 100644 --- a/GPy/likelihoods/EP.py +++ b/GPy/likelihoods/EP.py @@ -20,6 +20,7 @@ class EP(likelihood): self.N, self.D = self.data.shape self.is_heteroscedastic = True self.Nparams = 0 + self._transf_data = self.likelihood_function._preprocess_values(data) #Initial values - Likelihood approximation parameters: #p(y|f) = t(f|tau_tilde,v_tilde) diff --git a/GPy/likelihoods/likelihood_functions.py b/GPy/likelihoods/likelihood_functions.py index 66c663dc..00100d17 100644 --- a/GPy/likelihoods/likelihood_functions.py +++ b/GPy/likelihoods/likelihood_functions.py @@ -8,19 +8,68 @@ import scipy as sp import pylab as pb from ..util.plot import gpplot from ..util.univariate_Gaussian import std_norm_pdf,std_norm_cdf +import link_functions -class likelihood_function: +class likelihood_function(object): """ Likelihood class for doing Expectation propagation :param Y: observed output (Nx1 numpy.darray) ..Note:: Y values allowed depend on the likelihood_function used """ - def __init__(self,location=0,scale=1): - self.location = location - self.scale = scale + def __init__(self,link): + if link == self._analytical: + self.moments_match = self._moments_match_analytical + else: + assert isinstance(link,link_functions.link_function) + self.link = link + self.moments_match = self._moments_match_numerical -class probit(likelihood_function): + def _preprocess_values(self,Y): + return Y + + def _product(self,gp,obs,mu,sigma): + return stats.norm.pdf(gp,loc=mu,scale=sigma) * self._distribution(gp,obs) + + def _nlog_product(self,gp,obs,mu,sigma): + return -(-.5*(gp-mu)**2/sigma**2 + self._log_distribution(gp,obs)) + + def _locate(self,obs,mu,sigma): + """ + Golden Search to find the mode in the _product function (cavity x exact likelihood) and define a grid around it for numerical integration + """ + golden_A = -1 if obs == 0 else np.array([np.log(obs),mu]).min() #Lower limit + golden_B = np.array([np.log(obs),mu]).max() #Upper limit + return sp.optimize.golden(self._nlog_product, args=(obs,mu,sigma), brack=(golden_A,golden_B)) #Better to work with _nlog_product than with _product + + def _moments_match_numerical(self,obs,tau,v): + """ + Simpson's Rule is used to calculate the moments mumerically, it needs a grid of points as input. + """ + mu = v/tau + sigma = np.sqrt(1./tau) + opt = self._locate(obs,mu,sigma) + width = 3./np.log(max(obs,2)) + A = opt - width #Grid's lower limit + B = opt + width #Grid's Upper limit + K = 10*int(np.log(max(obs,150))) #Number of points in the grid + h = (B-A)/K # length of the intervals + grid_x = np.hstack([np.linspace(opt-width,opt,K/2+1)[1:-1], np.linspace(opt,opt+width,K/2+1)]) # grid of points (X axis) + x = np.hstack([A,B,grid_x[range(1,K,2)],grid_x[range(2,K-1,2)]]) # grid_x rearranged, just to make Simpson's algorithm easier + _aux1 = self._product(A,obs,mu,sigma) + _aux2 = self._product(B,obs,mu,sigma) + _aux3 = 4*self._product(grid_x[range(1,K,2)],obs,mu,sigma) + _aux4 = 2*self._product(grid_x[range(2,K-1,2)],obs,mu,sigma) + zeroth = np.hstack((_aux1,_aux2,_aux3,_aux4)) # grid of points (Y axis) rearranged + first = zeroth*x + second = first*x + Z_hat = sum(zeroth)*h/3 # Zero-th moment + mu_hat = sum(first)*h/(3*Z_hat) # First moment + m2 = sum(second)*h/(3*Z_hat) # Second moment + sigma2_hat = m2 - mu_hat**2 # Second central moment + return float(Z_hat), float(mu_hat), float(sigma2_hat) + +class binomial(likelihood_function): """ Probit likelihood Y is expected to take values in {-1,1} @@ -29,8 +78,33 @@ class probit(likelihood_function): L(x) = \\Phi (Y_i*f_i) $$ """ + def __init__(self,link=None): + self._analytical = link_functions.probit + if not link: + link = self._analytical + super(binomial, self).__init__(link) - def moments_match(self,data_i,tau_i,v_i): + def _distribution(self,gp,obs): + pass + + def _log_distribution(self,gp,obs): + pass + + def _preprocess_values(self,Y): + """ + Check if the values of the observations correspond to the values + assumed by the likelihood function. + + ..Note:: Binary classification algorithm works better with classes {-1,1} + """ + Y_prep = Y.copy() + Y1 = Y[Y.flatten()==1].size + Y2 = Y[Y.flatten()==0].size + assert Y1 + Y2 == Y.size, 'Binomial likelihood is meant to be used only with outputs in {0,1}.' + Y_prep[Y.flatten() == 0] = -1 + return Y_prep + + def _moments_match_analytical(self,data_i,tau_i,v_i): """ Moments match of the marginal approximation in EP algorithm @@ -38,8 +112,6 @@ class probit(likelihood_function): :param tau_i: precision of the cavity distribution (float) :param v_i: mean/variance of the cavity distribution (float) """ - #if data_i == 0: data_i = -1 #NOTE Binary classification algorithm works better with classes {-1,1}, 1D-plotting works better with classes {0,1}. - # TODO: some version of assert z = data_i*v_i/np.sqrt(tau_i**2 + tau_i) Z_hat = std_norm_cdf(z) phi = std_norm_pdf(z) @@ -50,6 +122,8 @@ class probit(likelihood_function): def predictive_values(self,mu,var): """ Compute mean, variance and conficence interval (percentiles 5 and 95) of the prediction + :param mu: mean of the latent variable + :param var: variance of the latent variable """ mu = mu.flatten() var = var.flatten() @@ -69,68 +143,23 @@ class Poisson(likelihood_function): L(x) = \exp(\lambda) * \lambda**Y_i / Y_i! $$ """ - def moments_match(self,data_i,tau_i,v_i): - """ - Moments match of the marginal approximation in EP algorithm + def __init__(self,link=None): + self._analytical = None + if not link: + link = link_functions.log() + super(Poisson, self).__init__(link) - :param i: number of observation (int) - :param tau_i: precision of the cavity distribution (float) - :param v_i: mean/variance of the cavity distribution (float) - """ - mu = v_i/tau_i - sigma = np.sqrt(1./tau_i) - def poisson_norm(f): - """ - Product of the likelihood and the cavity distribution - """ - pdf_norm_f = stats.norm.pdf(f,loc=mu,scale=sigma) - rate = np.exp( (f*self.scale)+self.location) - poisson = stats.poisson.pmf(float(data_i),rate) - return pdf_norm_f*poisson + def _distribution(self,gp,obs): + return stats.poisson.pmf(obs,self.link.inv_transf(gp)) - def log_pnm(f): - """ - Log of poisson_norm - """ - return -(-.5*(f-mu)**2/sigma**2 - np.exp( (f*self.scale)+self.location) + ( (f*self.scale)+self.location)*data_i) - - """ - Golden Search and Simpson's Rule - -------------------------------- - Simpson's Rule is used to calculate the moments mumerically, it needs a grid of points as input. - Golden Search is used to find the mode in the poisson_norm distribution and define around it the grid for Simpson's Rule - """ - #TODO golden search & simpson's rule can be defined in the general likelihood class, rather than in each specific case. - - #Golden search - golden_A = -1 if data_i == 0 else np.array([np.log(data_i),mu]).min() #Lower limit - golden_B = np.array([np.log(data_i),mu]).max() #Upper limit - golden_A = (golden_A - self.location)/self.scale - golden_B = (golden_B - self.location)/self.scale - opt = sp.optimize.golden(log_pnm,brack=(golden_A,golden_B)) #Better to work with log_pnm than with poisson_norm - - # Simpson's approximation - width = 3./np.log(max(data_i,2)) - A = opt - width #Lower limit - B = opt + width #Upper limit - K = 10*int(np.log(max(data_i,150))) #Number of points in the grid, we DON'T want K to be the same number for every case - h = (B-A)/K # length of the intervals - grid_x = np.hstack([np.linspace(opt-width,opt,K/2+1)[1:-1], np.linspace(opt,opt+width,K/2+1)]) # grid of points (X axis) - x = np.hstack([A,B,grid_x[range(1,K,2)],grid_x[range(2,K-1,2)]]) # grid_x rearranged, just to make Simpson's algorithm easier - zeroth = np.hstack([poisson_norm(A),poisson_norm(B),[4*poisson_norm(f) for f in grid_x[range(1,K,2)]],[2*poisson_norm(f) for f in grid_x[range(2,K-1,2)]]]) # grid of points (Y axis) rearranged like x - first = zeroth*x - second = first*x - Z_hat = sum(zeroth)*h/3 # Zero-th moment - mu_hat = sum(first)*h/(3*Z_hat) # First moment - m2 = sum(second)*h/(3*Z_hat) # Second moment - sigma2_hat = m2 - mu_hat**2 # Second central moment - return float(Z_hat), float(mu_hat), float(sigma2_hat) + def _log_distribution(self,gp,obs): + return - self.link.inv_transf(gp) + obs * self.link.log_inv_transf(gp) def predictive_values(self,mu,var): """ Compute mean, and conficence interval (percentiles 5 and 95) of the prediction """ - mean = np.exp(mu*self.scale + self.location) + mean = self.link.transf(mu)#np.exp(mu*self.scale + self.location) tmp = stats.poisson.ppf(np.array([.025,.975]),mean) p_025 = tmp[:,0] p_975 = tmp[:,1] diff --git a/GPy/likelihoods/link_functions.py b/GPy/likelihoods/link_functions.py new file mode 100644 index 00000000..28beac71 --- /dev/null +++ b/GPy/likelihoods/link_functions.py @@ -0,0 +1,58 @@ +# Copyright (c) 2012, 2013 Ricardo Andrade +# Licensed under the BSD 3-clause license (see LICENSE.txt) + + +import numpy as np +from scipy import stats +import scipy as sp +import pylab as pb +from ..util.plot import gpplot +from ..util.univariate_Gaussian import std_norm_pdf,std_norm_cdf + +class link_function(object): + """ + Link function class for doing non-Gaussian likelihoods approximation + + :param Y: observed output (Nx1 numpy.darray) + ..Note:: Y values allowed depend on the likelihood_function used + """ + def __init__(self): + pass + + + +class identity(link_function): + def transf(self,mu): + return mu + + def inv_transf(self,f): + return f + + def log_inv_transf(self,f): + return np.log(f) + +class log(link_function): + + def transf(self,mu): + return np.log(mu) + + def inv_transf(self,f): + return np.exp(f) + + def log_inv_transf(self,f): + return f + +class log_ex_1(link_function): + def transf(self,mu): + return np.log(np.exp(mu) - 1) + + def inv_transf(self,f): + return np.log(np.exp(f)+1) + + def log_inv_tranf(self,f): + return np.log(np.log(np.exp(f)+1)) + +class probit(link_function): + pass + + From 362389781b87a067c6cd2350b95f09f689c06d98 Mon Sep 17 00:00:00 2001 From: James Hensman Date: Tue, 4 Jun 2013 16:28:20 +0100 Subject: [PATCH 3/4] fixing some examples --- GPy/core/gp_base.py | 3 +++ GPy/models/GP_regression.py | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/GPy/core/gp_base.py b/GPy/core/gp_base.py index 3eb977c6..29234c4d 100644 --- a/GPy/core/gp_base.py +++ b/GPy/core/gp_base.py @@ -24,6 +24,9 @@ class GPBase(model.model): self._Xmean = X.mean(0)[None, :] self._Xstd = X.std(0)[None, :] self.X = (X.copy() - self._Xmean) / self._Xstd + else: + self._Xmean = np.zeros((1,self.Q)) + self._Xstd = np.ones((1,self.Q)) super(GPBase, self).__init__() diff --git a/GPy/models/GP_regression.py b/GPy/models/GP_regression.py index 2979456b..e5acb4f7 100644 --- a/GPy/models/GP_regression.py +++ b/GPy/models/GP_regression.py @@ -31,5 +31,5 @@ class GP_regression(GP): likelihood = likelihoods.Gaussian(Y,normalize=normalize_Y) - super(GP_regression, self).__init__(self, X, likelihood, kernel, normalize_X=normalize_X) + super(GP_regression, self).__init__(X, likelihood, kernel, normalize_X=normalize_X) self._set_params(self._get_params()) From 78aedd84af66d5ed6909e5f58bd4200903e307a3 Mon Sep 17 00:00:00 2001 From: Ricardo Date: Tue, 4 Jun 2013 16:32:12 +0100 Subject: [PATCH 4/4] Examples changed to use new link_functions --- GPy/examples/classification.py | 24 +++++++++++++++--------- 1 file changed, 15 insertions(+), 9 deletions(-) diff --git a/GPy/examples/classification.py b/GPy/examples/classification.py index a96911f4..f3adebaa 100644 --- a/GPy/examples/classification.py +++ b/GPy/examples/classification.py @@ -21,13 +21,15 @@ def crescent_data(seed=default_seed): # FIXME """ data = GPy.util.datasets.crescent_data(seed=seed) + Y = data['Y'] + Y[Y.flatten()==-1] = 0 # Kernel object kernel = GPy.kern.rbf(data['X'].shape[1]) # Likelihood object - distribution = GPy.likelihoods.likelihood_functions.probit() - likelihood = GPy.likelihoods.EP(data['Y'], distribution) + distribution = GPy.likelihoods.likelihood_functions.binomial() + likelihood = GPy.likelihoods.EP(Y, distribution) m = GPy.models.GP(data['X'], likelihood, kernel) @@ -49,12 +51,15 @@ def oil(): 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] + Y[Y.flatten()==-1] = 0 + # Kernel object kernel = GPy.kern.rbf(12) # Likelihood object - distribution = GPy.likelihoods.likelihood_functions.probit() - likelihood = GPy.likelihoods.EP(data['Y'][:, 0:1], distribution) + distribution = GPy.likelihoods.likelihood_functions.binomial() + likelihood = GPy.likelihoods.EP(Y, distribution) # Create GP model m = GPy.models.GP(data['X'], likelihood=likelihood, kernel=kernel) @@ -87,8 +92,6 @@ def toy_linear_1d_classification(seed=default_seed): # Likelihood object link = GPy.likelihoods.link_functions.probit distribution = GPy.likelihoods.likelihood_functions.binomial(link) - #distribution = GPy.likelihoods.likelihood_functions.binomial() - #distribution = GPy.likelihoods.likelihood_functions.probit() likelihood = GPy.likelihoods.EP(Y, distribution) # Model definition @@ -119,12 +122,13 @@ def sparse_toy_linear_1d_classification(seed=default_seed): data = GPy.util.datasets.toy_linear_1d_classification(seed=seed) Y = data['Y'][:, 0:1] + Y[Y.flatten() == -1] = 0 # Kernel object kernel = GPy.kern.rbf(1) + GPy.kern.white(1) # Likelihood object - distribution = GPy.likelihoods.likelihood_functions.probit() + distribution = GPy.likelihoods.likelihood_functions.binomial() likelihood = GPy.likelihoods.EP(Y, distribution) Z = np.random.uniform(data['X'].min(), data['X'].max(), (10, 1)) @@ -160,13 +164,15 @@ def sparse_crescent_data(inducing=10, seed=default_seed): """ data = GPy.util.datasets.crescent_data(seed=seed) + Y = data['Y'] + Y[Y.flatten()==-1]=0 # 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) + distribution = GPy.likelihoods.likelihood_functions.binomial() + likelihood = GPy.likelihoods.EP(Y, distribution) sample = np.random.randint(0, data['X'].shape[0], inducing) Z = data['X'][sample, :]