Removing unnecessary stuff...

GPy/likelihoods/noise_models/binomial_noise.py

@@ -1,6 +1,7 @@
 # Copyright (c) 2012, 2013 Ricardo Andrade
 # Licensed under the BSD 3-clause license (see LICENSE.txt)
 
+
 import numpy as np
 from scipy import stats,special
 import scipy as sp
@@ -116,18 +117,3 @@ class Binomial(NoiseDistribution):
 
     def _d2variance_dgp2(self,gp):
         return self.gp_link.d2transf_df2(gp)*(1. - 2.*self.gp_link.transf(gp)) - 2*self.gp_link.dtransf_df(gp)**2
-
-    """
-    def predictive_values(self,mu,var): #TODO remove
-        mu = mu.flatten()
-        var = var.flatten()
-        #mean = stats.norm.cdf(mu/np.sqrt(1+var))
-        mean = self._predictive_mean_analytical(mu,np.sqrt(var))
-        norm_025 = [stats.norm.ppf(.025,m,v) for m,v in zip(mu,var)]
-        norm_975 = [stats.norm.ppf(.975,m,v) for m,v in zip(mu,var)]
-        #p_025 = stats.norm.cdf(norm_025/np.sqrt(1+var))
-        #p_975 = stats.norm.cdf(norm_975/np.sqrt(1+var))
-        p_025 = self._predictive_mean_analytical(norm_025,np.sqrt(var))
-        p_975 = self._predictive_mean_analytical(norm_975,np.sqrt(var))
-        return mean[:,None], np.nan*var, p_025[:,None], p_975[:,None] # TODO: var
-    """

GPy/likelihoods/noise_models/exponential_noise.py

@@ -11,7 +11,7 @@ from noise_distributions import NoiseDistribution
 
 class Exponential(NoiseDistribution):
     """
-    Gamma likelihood
+    Expoential likelihood
     Y is expected to take values in {0,1,2,...}
     -----
     $$

GPy/likelihoods/noise_models/gaussian_noise.py

@@ -57,12 +57,12 @@ class Gaussian(NoiseDistribution):
         new_sigma2 = self.predictive_variance(mu,sigma)
         return new_sigma2*(mu/sigma**2 + self.gp_link.transf(mu)/self.variance)
 
-    def _predictive_variance_analytical(self,mu,sigma,*args): #TODO *args?
+    def _predictive_variance_analytical(self,mu,sigma):
         return 1./(1./self.variance + 1./sigma**2)
 
     def _mass(self,gp,obs):
         #return std_norm_pdf( (self.gp_link.transf(gp)-obs)/np.sqrt(self.variance) )
-        return stats.norm.pdf(obs,self.gp_link.transf(gp),np.sqrt(self.variance)) #FIXME
+        return stats.norm.pdf(obs,self.gp_link.transf(gp),np.sqrt(self.variance))
 
     def _nlog_mass(self,gp,obs):
         return .5*((self.gp_link.transf(gp)-obs)**2/self.variance + np.log(2.*np.pi*self.variance))

GPy/likelihoods/noise_models/gp_transformations.py

@@ -10,7 +10,6 @@ from GPy.util.univariate_Gaussian import std_norm_pdf,std_norm_cdf,inv_std_norm_
 
 class GPTransformation(object):
     """
-
     Link function class for doing non-Gaussian likelihoods approximation
 
     :param Y: observed output (Nx1 numpy.darray)
@@ -21,6 +20,24 @@ class GPTransformation(object):
     def __init__(self):
         pass
 
+    def transf(self,f):
+        """
+        Gaussian process tranformation function, latent space -> output space
+        """
+        pass
+
+    def dtransf_df(self,f):
+        """
+        derivative of transf(f) w.r.t. f
+        """
+        pass
+
+    def d2transf_df2(self,f):
+        """
+        second derivative of transf(f) w.r.t. f
+        """
+        pass
+
 class Identity(GPTransformation):
     """
     .. math::
@@ -28,9 +45,6 @@ class Identity(GPTransformation):
         g(f) = f
 
     """
-    #def transf(self,mu):
-    #    return mu
-
     def transf(self,f):
         return f
 
@@ -48,9 +62,6 @@ class Probit(GPTransformation):
         g(f) = \\Phi^{-1} (mu)
 
     """
-    #def transf(self,mu):
-    #    return inv_std_norm_cdf(mu)
-
     def transf(self,f):
         return std_norm_cdf(f)
 
@@ -63,12 +74,10 @@ class Probit(GPTransformation):
 class Log(GPTransformation):
     """
     .. math::
+
         g(f) = \\log(\\mu)
 
     """
-    #def transf(self,mu):
-    #    return np.log(mu)
-
     def transf(self,f):
         return np.exp(f)
 
@@ -81,19 +90,11 @@ class Log(GPTransformation):
 class Log_ex_1(GPTransformation):
     """
     .. math::
+
         g(f) = \\log(\\exp(\\mu) - 1)
 
     """
-    #def transf(self,mu):
-    #    """
-    #    function: output space -> latent space
-    #    """
-    #    return np.log(np.exp(mu) - 1)
-
     def transf(self,f):
-        """
-        function: latent space -> output space
-        """
         return np.log(1.+np.exp(f))
 
     def dtransf_df(self,f):

GPy/likelihoods/noise_models/noise_distributions.py

@@ -20,7 +20,7 @@ class NoiseDistribution(object):
     .. note:: Y values allowed depend on the LikelihoodFunction used
     """
     def __init__(self,gp_link,analytical_mean=False,analytical_variance=False):
-        #assert isinstance(gp_link,gp_transformations.GPTransformation), "gp_link is not a valid GPTransformation."#FIXME
+        assert isinstance(gp_link,gp_transformations.GPTransformation), "gp_link is not a valid GPTransformation."
         self.gp_link = gp_link
         self.analytical_mean = analytical_mean
         self.analytical_variance = analytical_variance
@@ -51,7 +51,8 @@ class NoiseDistribution(object):
         """
         In case it is needed, this function assess the output values or makes any pertinent transformation on them.
 
-        :param Y: observed output (Nx1 numpy.darray)
+        :param Y: observed output
+        :type Y: Nx1 numpy.darray
 
         """
         return Y

GPy/likelihoods/noise_models/poisson_noise.py

@@ -12,29 +12,22 @@ from noise_distributions import NoiseDistribution
 class Poisson(NoiseDistribution):
     """
     Poisson likelihood
-    Y is expected to take values in {0,1,2,...}
 
     .. math::
         L(x) = \\exp(\\lambda) * \\frac{\\lambda^Y_i}{Y_i!}
 
+    ..Note: Y is expected to take values in {0,1,2,...}
     """
     def __init__(self,gp_link=None,analytical_mean=False,analytical_variance=False):
-        #self.discrete = True
-        #self.support_limits = (0,np.inf)
-
-        #self.analytical_mean = False
         super(Poisson, self).__init__(gp_link,analytical_mean,analytical_variance)
 
     def _preprocess_values(self,Y): #TODO
-        #self.scale = .5*Y.max()
-        #self.shift = Y.mean()
-        return Y #(Y - self.shift)/self.scale
+        return Y
 
     def _mass(self,gp,obs):
         """
         Mass (or density) function
         """
-        #obs = obs*self.scale + self.shift
         return stats.poisson.pmf(obs,self.gp_link.transf(gp))
 
     def _nlog_mass(self,gp,obs):
@@ -51,15 +44,6 @@ class Poisson(NoiseDistribution):
         transf = self.gp_link.transf(gp)
         return obs * ((self.gp_link.dtransf_df(gp)/transf)**2 - d2_df/transf) + d2_df
 
-    def _dnlog_mass_dobs(self,obs,gp): #TODO not needed
-        return special.psi(obs+1) -  np.log(self.gp_link.transf(gp))
-
-    def _d2nlog_mass_dobs2(self,obs,gp=None): #TODO not needed
-        return special.polygamma(1,obs)
-
-    def _d2nlog_mass_dcross(self,obs,gp): #TODO not needed
-        return -self.gp_link.dtransf_df(gp)/self.gp_link.transf(gp)
-
     def _mean(self,gp):
         """
         Mass (or density) function