Update of symbolic likelihoods.

GPy/kern/__init__.py

@@ -3,7 +3,7 @@ from _src.rbf import RBF
 from _src.linear import Linear, LinearFull
 from _src.static import Bias, White
 from _src.brownian import Brownian
-from _src.sympykern import Sympykern
+from _src.symbolic import Symbolic
 from _src.stationary import Exponential, Matern32, Matern52, ExpQuad, RatQuad, Cosine
 from _src.mlp import MLP
 from _src.periodic import PeriodicExponential, PeriodicMatern32, PeriodicMatern52

GPy/kern/_src/symbolic.py

@@ -11,7 +11,7 @@ from kern import Kern
 from ...core.parameterization import Param
 from ...core.parameterization.transformations import Logexp
 
-class Sympykern(Kern):
+class Symbolic(Kern):
     """
     A kernel object, where all the hard work in done by sympy.
 
@@ -26,10 +26,8 @@ class Sympykern(Kern):
      - to handle multiple inputs, call them x_1, z_1, etc
      - to handle multpile correlated outputs, you'll need to add parameters with an index, such as lengthscale_i and lengthscale_j.
     """
-    def __init__(self, input_dim, k=None, output_dim=1, name=None, param=None, active_dims=None):
+    def __init__(self, input_dim, k=None, output_dim=1, name='symbolic', param=None, active_dims=None, operators=None):
 
-        if name is None:
-            name='sympykern'
         if k is None:
             raise ValueError, "You must provide an argument for the covariance function."
         super(Sympykern, self).__init__(input_dim, active_dims, name)
@@ -60,7 +58,6 @@ class Sympykern(Kern):
         # extract parameter names from the covariance
         thetas = sorted([e for e in sp_vars if not (e.name[0:2]=='x_' or e.name[0:2]=='z_')],key=lambda e:e.name)
 
-
         # Look for parameters with index (subscripts), they are associated with different outputs.
         if self.output_dim>1:
             self._sp_theta_i = sorted([e for e in thetas if (e.name[-2:]=='_i')], key=lambda e:e.name)
@@ -117,6 +114,12 @@ class Sympykern(Kern):
             self.arg_list += self._sp_theta_i + self._sp_theta_j
             self.diag_arg_list += self._sp_theta_i
 
+        # Check if there are additional linear operators on the covariance.
+        self._sp_operators = operators
+        # TODO: Deal with linear operators
+        #if self._sp_operators:
+        #    for operator in self._sp_operators:
+                
         # psi_stats aren't yet implemented.
         if False:
             self.compute_psi_stats()
@@ -254,3 +257,176 @@ class Sympykern(Kern):
                     self._reverse_arguments[theta_i.name] = self._arguments[theta_j.name].T
                     self._reverse_arguments[theta_j.name] = self._arguments[theta_i.name].T
 
+if False:
+    class Symcombine(CombinationKernel):
+        """
+        Combine list of given sympy covariances together with the provided operations.
+        """
+        def __init__(self, subkerns, operations, name='sympy_combine'):
+            super(Symcombine, self).__init__(subkerns, name)
+            for subkern, operation in zip(subkerns, operations):
+                self._sp_k += self._k_double_operate(subkern._sp_k, operation)
+
+        #def _double_operate(self, k, operation):
+
+
+        @Cache_this(limit=2, force_kwargs=['which_parts'])
+        def K(self, X, X2=None, which_parts=None):
+            """
+            Combine covariances with a linear operator.
+            """
+            assert X.shape[1] == self.input_dim
+            if which_parts is None:
+                which_parts = self.parts
+            elif not isinstance(which_parts, (list, tuple)):
+                # if only one part is given
+                which_parts = [which_parts]
+            return reduce(np.add, (p.K(X, X2) for p in which_parts))
+
+        @Cache_this(limit=2, force_kwargs=['which_parts'])
+        def Kdiag(self, X, which_parts=None):
+            assert X.shape[1] == self.input_dim
+            if which_parts is None:
+                which_parts = self.parts
+            elif not isinstance(which_parts, (list, tuple)):
+                # if only one part is given
+                which_parts = [which_parts]
+            return reduce(np.add, (p.Kdiag(X) for p in which_parts))
+
+        def update_gradients_full(self, dL_dK, X, X2=None):
+            [p.update_gradients_full(dL_dK, X, X2) for p in self.parts]
+
+        def update_gradients_diag(self, dL_dK, X):
+            [p.update_gradients_diag(dL_dK, X) for p in self.parts]
+
+        def gradients_X(self, dL_dK, X, X2=None):
+            """Compute the gradient of the objective function with respect to X.
+
+            :param dL_dK: An array of gradients of the objective function with respect to the covariance function.
+            :type dL_dK: np.ndarray (num_samples x num_inducing)
+            :param X: Observed data inputs
+            :type X: np.ndarray (num_samples x input_dim)
+            :param X2: Observed data inputs (optional, defaults to X)
+            :type X2: np.ndarray (num_inducing x input_dim)"""
+
+            target = np.zeros(X.shape)
+            [target.__iadd__(p.gradients_X(dL_dK, X, X2)) for p in self.parts]
+            return target
+
+        def gradients_X_diag(self, dL_dKdiag, X):
+            target = np.zeros(X.shape)
+            [target.__iadd__(p.gradients_X_diag(dL_dKdiag, X)) for p in self.parts]
+            return target
+
+        def psi0(self, Z, variational_posterior):
+            return reduce(np.add, (p.psi0(Z, variational_posterior) for p in self.parts))
+
+        def psi1(self, Z, variational_posterior):
+            return reduce(np.add, (p.psi1(Z, variational_posterior) for p in self.parts))
+
+        def psi2(self, Z, variational_posterior):
+            psi2 = reduce(np.add, (p.psi2(Z, variational_posterior) for p in self.parts))
+            #return psi2
+            # compute the "cross" terms
+            from static import White, Bias
+            from rbf import RBF
+            #from rbf_inv import RBFInv
+            from linear import Linear
+            #ffrom fixed import Fixed
+
+            for p1, p2 in itertools.combinations(self.parts, 2):
+                # i1, i2 = p1.active_dims, p2.active_dims
+                # white doesn;t combine with anything
+                if isinstance(p1, White) or isinstance(p2, White):
+                    pass
+                # rbf X bias
+                #elif isinstance(p1, (Bias, Fixed)) and isinstance(p2, (RBF, RBFInv)):
+                elif isinstance(p1,  Bias) and isinstance(p2, (RBF, Linear)):
+                    tmp = p2.psi1(Z, variational_posterior)
+                    psi2 += p1.variance * (tmp[:, :, None] + tmp[:, None, :])
+                #elif isinstance(p2, (Bias, Fixed)) and isinstance(p1, (RBF, RBFInv)):
+                elif isinstance(p2, Bias) and isinstance(p1, (RBF, Linear)):
+                    tmp = p1.psi1(Z, variational_posterior)
+                    psi2 += p2.variance * (tmp[:, :, None] + tmp[:, None, :])
+                elif isinstance(p2, (RBF, Linear)) and isinstance(p1, (RBF, Linear)):
+                    assert np.intersect1d(p1.active_dims, p2.active_dims).size == 0, "only non overlapping kernel dimensions allowed so far"
+                    tmp1 = p1.psi1(Z, variational_posterior)
+                    tmp2 = p2.psi1(Z, variational_posterior)
+                    psi2 += (tmp1[:, :, None] * tmp2[:, None, :]) + (tmp2[:, :, None] * tmp1[:, None, :])
+                else:
+                    raise NotImplementedError, "psi2 cannot be computed for this kernel"
+            return psi2
+
+        def update_gradients_expectations(self, dL_dpsi0, dL_dpsi1, dL_dpsi2, Z, variational_posterior):
+            from static import White, Bias
+            for p1 in self.parts:
+                #compute the effective dL_dpsi1. Extra terms appear becaue of the cross terms in psi2!
+                eff_dL_dpsi1 = dL_dpsi1.copy()
+                for p2 in self.parts:
+                    if p2 is p1:
+                        continue
+                    if isinstance(p2, White):
+                        continue
+                    elif isinstance(p2, Bias):
+                        eff_dL_dpsi1 += dL_dpsi2.sum(1) * p2.variance * 2.
+                    else:# np.setdiff1d(p1.active_dims, ar2, assume_unique): # TODO: Careful, not correct for overlapping active_dims
+                        eff_dL_dpsi1 += dL_dpsi2.sum(1) * p2.psi1(Z, variational_posterior) * 2.
+                p1.update_gradients_expectations(dL_dpsi0, eff_dL_dpsi1, dL_dpsi2, Z, variational_posterior)
+
+        def gradients_Z_expectations(self, dL_dpsi1, dL_dpsi2, Z, variational_posterior):
+            from static import White, Bias
+            target = np.zeros(Z.shape)
+            for p1 in self.parts:
+                #compute the effective dL_dpsi1. extra terms appear becaue of the cross terms in psi2!
+                eff_dL_dpsi1 = dL_dpsi1.copy()
+                for p2 in self.parts:
+                    if p2 is p1:
+                        continue
+                    if isinstance(p2, White):
+                        continue
+                    elif isinstance(p2, Bias):
+                        eff_dL_dpsi1 += dL_dpsi2.sum(1) * p2.variance * 2.
+                    else:
+                        eff_dL_dpsi1 += dL_dpsi2.sum(1) * p2.psi1(Z, variational_posterior) * 2.
+                target += p1.gradients_Z_expectations(eff_dL_dpsi1, dL_dpsi2, Z, variational_posterior)
+            return target
+
+        def gradients_qX_expectations(self, dL_dpsi0, dL_dpsi1, dL_dpsi2, Z, variational_posterior):
+            from static import White, Bias
+            target_mu = np.zeros(variational_posterior.shape)
+            target_S = np.zeros(variational_posterior.shape)
+            for p1 in self._parameters_:
+                #compute the effective dL_dpsi1. extra terms appear becaue of the cross terms in psi2!
+                eff_dL_dpsi1 = dL_dpsi1.copy()
+                for p2 in self._parameters_:
+                    if p2 is p1:
+                        continue
+                    if isinstance(p2, White):
+                        continue
+                    elif isinstance(p2, Bias):
+                        eff_dL_dpsi1 += dL_dpsi2.sum(1) * p2.variance * 2.
+                    else:
+                        eff_dL_dpsi1 += dL_dpsi2.sum(1) * p2.psi1(Z, variational_posterior) * 2.
+                a, b = p1.gradients_qX_expectations(dL_dpsi0, eff_dL_dpsi1, dL_dpsi2, Z, variational_posterior)
+                target_mu += a
+                target_S += b
+            return target_mu, target_S
+
+        def _getstate(self):
+            """
+            Get the current state of the class,
+            here just all the indices, rest can get recomputed
+            """
+            return super(Add, self)._getstate()
+
+        def _setstate(self, state):
+            super(Add, self)._setstate(state)
+
+        def add(self, other, name='sum'):
+            if isinstance(other, Add):
+                other_params = other._parameters_.copy()
+                for p in other_params:
+                    other.remove_parameter(p)
+                self.add_parameters(*other_params)
+            else: self.add_parameter(other)
+            return self

GPy/likelihoods/__init__.py

@@ -6,3 +6,4 @@ from poisson import Poisson
 from student_t import StudentT
 from likelihood import Likelihood
 from mixed_noise import MixedNoise
+from symbolic import Symbolic

GPy/likelihoods/bernoulli.py

@@ -15,7 +15,7 @@ class Bernoulli(Likelihood):
         p(y_{i}|\\lambda(f_{i})) = \\lambda(f_{i})^{y_{i}}(1-f_{i})^{1-y_{i}}
 
     .. Note::
-        Y is expected to take values in {-1, 1} TODO: {0, 1}??
+        Y takes values in either {-1, 1} or {0, 1}.
         link function should have the domain [0, 1], e.g. probit (default) or Heaviside
 
     .. See also::
@@ -54,10 +54,10 @@ class Bernoulli(Likelihood):
         """
         if Y_i == 1:
             sign = 1.
-        elif Y_i == 0:
+        elif Y_i == 0 or Y_i == -1:
             sign = -1
         else:
-            raise ValueError("bad value for Bernouilli observation (0, 1)")
+            raise ValueError("bad value for Bernoulli observation (0, 1)")
         if isinstance(self.gp_link, link_functions.Probit):
             z = sign*v_i/np.sqrt(tau_i**2 + tau_i)
             Z_hat = std_norm_cdf(z)
@@ -95,15 +95,15 @@ class Bernoulli(Likelihood):
         else:
             return np.nan
 
-    def pdf_link(self, link_f, y, Y_metadata=None):
+    def pdf_link(self, inv_link_f, y, Y_metadata=None):
         """
-        Likelihood function given link(f)
+        Likelihood function given inverse link of f.
 
         .. math::
             p(y_{i}|\\lambda(f_{i})) = \\lambda(f_{i})^{y_{i}}(1-f_{i})^{1-y_{i}}
 
-        :param link_f: latent variables link(f)
+        :param inv_link_f: latent variables inverse link of f.
-        :type link_f: Nx1 array
+        :type inv_link_f: Nx1 array
         :param y: data
         :type y: Nx1 array
         :param Y_metadata: Y_metadata not used in bernoulli
@@ -113,102 +113,106 @@ class Bernoulli(Likelihood):
         .. Note:
             Each y_i must be in {0, 1}
         """
-        assert np.atleast_1d(link_f).shape == np.atleast_1d(y).shape
+        assert np.atleast_1d(inv_link_f).shape == np.atleast_1d(y).shape
-        #objective = (link_f**y) * ((1.-link_f)**(1.-y))
+        #objective = (inv_link_f**y) * ((1.-inv_link_f)**(1.-y))
-        objective = np.where(y, link_f, 1.-link_f)
+        objective = np.where(y, inv_link_f, 1.-inv_link_f)
         return np.exp(np.sum(np.log(objective)))
 
-    def logpdf_link(self, link_f, y, Y_metadata=None):
+    def logpdf_link(self, inv_link_f, y, Y_metadata=None):
         """
-        Log Likelihood function given link(f)
+        Log Likelihood function given inverse link of f.
 
         .. math::
             \\ln p(y_{i}|\\lambda(f_{i})) = y_{i}\\log\\lambda(f_{i}) + (1-y_{i})\\log (1-f_{i})
 
-        :param link_f: latent variables link(f)
+        :param inv_link_f: latent variables inverse link of f.
-        :type link_f: Nx1 array
+        :type inv_link_f: Nx1 array
         :param y: data
         :type y: Nx1 array
         :param Y_metadata: Y_metadata not used in bernoulli
-        :returns: log likelihood evaluated at points link(f)
+        :returns: log likelihood evaluated at points inverse link of f.
         :rtype: float
         """
-        assert np.atleast_1d(link_f).shape == np.atleast_1d(y).shape
+        assert np.atleast_1d(inv_link_f).shape == np.atleast_1d(y).shape
-        #objective = y*np.log(link_f) + (1.-y)*np.log(link_f)
+        #objective = y*np.log(inv_link_f) + (1.-y)*np.log(inv_link_f)
         state = np.seterr(divide='ignore')
-        objective = np.where(y==1, np.log(link_f), np.log(1-link_f))
+        # TODO check y \in {0, 1} or {-1, 1}
+        objective = np.where(y==1, np.log(inv_link_f), np.log(1-inv_link_f))
         np.seterr(**state)
         return np.sum(objective)
 
-    def dlogpdf_dlink(self, link_f, y, Y_metadata=None):
+    def dlogpdf_dlink(self, inv_link_f, y, Y_metadata=None):
         """
-        Gradient of the pdf at y, given link(f) w.r.t link(f)
+        Gradient of the pdf at y, given inverse link of f w.r.t inverse link of f.
 
         .. math::
             \\frac{d\\ln p(y_{i}|\\lambda(f_{i}))}{d\\lambda(f)} = \\frac{y_{i}}{\\lambda(f_{i})} - \\frac{(1 - y_{i})}{(1 - \\lambda(f_{i}))}
 
-        :param link_f: latent variables link(f)
+        :param inv_link_f: latent variables inverse link of f.
-        :type link_f: Nx1 array
+        :type inv_link_f: Nx1 array
         :param y: data
         :type y: Nx1 array
         :param Y_metadata: Y_metadata not used in bernoulli
-        :returns: gradient of log likelihood evaluated at points link(f)
+        :returns: gradient of log likelihood evaluated at points inverse link of f.
         :rtype: Nx1 array
         """
-        assert np.atleast_1d(link_f).shape == np.atleast_1d(y).shape
+        assert np.atleast_1d(inv_link_f).shape == np.atleast_1d(y).shape
-        #grad = (y/link_f) - (1.-y)/(1-link_f)
+        #grad = (y/inv_link_f) - (1.-y)/(1-inv_link_f)
         state = np.seterr(divide='ignore')
-        grad = np.where(y, 1./link_f, -1./(1-link_f))
+        # TODO check y \in {0, 1} or {-1, 1}
+        grad = np.where(y, 1./inv_link_f, -1./(1-inv_link_f))
         np.seterr(**state)
         return grad
 
-    def d2logpdf_dlink2(self, link_f, y, Y_metadata=None):
+    def d2logpdf_dlink2(self, inv_link_f, y, Y_metadata=None):
         """
-        Hessian at y, given link_f, w.r.t link_f the hessian will be 0 unless i == j
+        Hessian at y, given inv_link_f, w.r.t inv_link_f the hessian will be 0 unless i == j
-        i.e. second derivative logpdf at y given link(f_i) link(f_j)  w.r.t link(f_i) and link(f_j)
+        i.e. second derivative logpdf at y given inverse link of f_i and inverse link of f_j  w.r.t inverse link of f_i and inverse link of f_j.
 
 
         .. math::
             \\frac{d^{2}\\ln p(y_{i}|\\lambda(f_{i}))}{d\\lambda(f)^{2}} = \\frac{-y_{i}}{\\lambda(f)^{2}} - \\frac{(1-y_{i})}{(1-\\lambda(f))^{2}}
 
-        :param link_f: latent variables link(f)
+        :param inv_link_f: latent variables inverse link of f.
-        :type link_f: Nx1 array
+        :type inv_link_f: Nx1 array
         :param y: data
         :type y: Nx1 array
         :param Y_metadata: Y_metadata not used in bernoulli
-        :returns: Diagonal of log hessian matrix (second derivative of log likelihood evaluated at points link(f))
+        :returns: Diagonal of log hessian matrix (second derivative of log likelihood evaluated at points inverse link of f.
         :rtype: Nx1 array
 
         .. Note::
             Will return diagonal of hessian, since every where else it is 0, as the likelihood factorizes over cases
-            (the distribution for y_i depends only on link(f_i) not on link(f_(j!=i))
+            (the distribution for y_i depends only on inverse link of f_i not on inverse link of f_(j!=i)
         """
-        assert np.atleast_1d(link_f).shape == np.atleast_1d(y).shape
+        assert np.atleast_1d(inv_link_f).shape == np.atleast_1d(y).shape
-        #d2logpdf_dlink2 = -y/(link_f**2) - (1-y)/((1-link_f)**2)
+        #d2logpdf_dlink2 = -y/(inv_link_f**2) - (1-y)/((1-inv_link_f)**2)
         state = np.seterr(divide='ignore')
-        d2logpdf_dlink2 = np.where(y, -1./np.square(link_f), -1./np.square(1.-link_f))
+        # TODO check y \in {0, 1} or {-1, 1}
+        d2logpdf_dlink2 = np.where(y, -1./np.square(inv_link_f), -1./np.square(1.-inv_link_f))
         np.seterr(**state)
         return d2logpdf_dlink2
 
-    def d3logpdf_dlink3(self, link_f, y, Y_metadata=None):
+    def d3logpdf_dlink3(self, inv_link_f, y, Y_metadata=None):
         """
-        Third order derivative log-likelihood function at y given link(f) w.r.t link(f)
+        Third order derivative log-likelihood function at y given inverse link of f w.r.t inverse link of f
 
         .. math::
             \\frac{d^{3} \\ln p(y_{i}|\\lambda(f_{i}))}{d^{3}\\lambda(f)} = \\frac{2y_{i}}{\\lambda(f)^{3}} - \\frac{2(1-y_{i}}{(1-\\lambda(f))^{3}}
 
-        :param link_f: latent variables link(f)
+        :param inv_link_f: latent variables passed through inverse link of f.
-        :type link_f: Nx1 array
+        :type inv_link_f: Nx1 array
         :param y: data
         :type y: Nx1 array
         :param Y_metadata: Y_metadata not used in bernoulli
-        :returns: third derivative of log likelihood evaluated at points link(f)
+        :returns: third derivative of log likelihood evaluated at points inverse_link(f)
         :rtype: Nx1 array
         """
-        assert np.atleast_1d(link_f).shape == np.atleast_1d(y).shape
+        assert np.atleast_1d(inv_link_f).shape == np.atleast_1d(y).shape
-        #d3logpdf_dlink3 = 2*(y/(link_f**3) - (1-y)/((1-link_f)**3))
+        #d3logpdf_dlink3 = 2*(y/(inv_link_f**3) - (1-y)/((1-inv_link_f)**3))
         state = np.seterr(divide='ignore')
-        d3logpdf_dlink3 = np.where(y, 2./(link_f**3), -2./((1.-link_f)**3))
+        # TODO check y \in {0, 1} or {-1, 1}
+        d3logpdf_dlink3 = np.where(y, 2./(inv_link_f**3), -2./((1.-inv_link_f)**3))
         np.seterr(**state)
         return d3logpdf_dlink3
 

GPy/likelihoods/likelihood.py

@@ -16,20 +16,20 @@ class Likelihood(Parameterized):
     Likelihood base class, used to defing p(y|f).
 
     All instances use _inverse_ link functions, which can be swapped out. It is
-    expected that inherriting classes define a default inverse link function
+    expected that inheriting classes define a default inverse link function
 
-    To use this class, inherrit and define missing functionality.
+    To use this class, inherit and define missing functionality.
 
-    Inherriting classes *must* implement:
+    Inheriting classes *must* implement:
        pdf_link : a bound method which turns the output of the link function into the pdf
        logpdf_link : the logarithm of the above
 
-    To enable use with EP, inherriting classes *must* define:
+    To enable use with EP, inheriting classes *must* define:
        TODO: a suitable derivative function for any parameters of the class
     It is also desirable to define:
        moments_match_ep : a function to compute the EP moments If this isn't defined, the moments will be computed using 1D quadrature.
 
-    To enable use with Laplace approximation, inherriting classes *must* define:
+    To enable use with Laplace approximation, inheriting classes *must* define:
        Some derivative functions *AS TODO*
 
     For exact Gaussian inference, define *JH TODO*
@@ -159,7 +159,7 @@ class Likelihood(Parameterized):
 
     def predictive_variance(self, mu,variance, predictive_mean=None, Y_metadata=None):
         """
-        Numerical approximation to the predictive variance: V(Y_star)
+        Approximation to the predictive variance: V(Y_star)
 
         The following variance decomposition is used:
         V(Y_star) = E( V(Y_star|f_star) ) + V( E(Y_star|f_star) )
@@ -208,28 +208,28 @@ class Likelihood(Parameterized):
         # V(Y_star) = E[ V(Y_star|f_star) ] + E(Y_star**2|f_star) - E[Y_star|f_star]**2
         return exp_var + var_exp
 
-    def pdf_link(self, link_f, y, Y_metadata=None):
+    def pdf_link(self, inv_link_f, y, Y_metadata=None):
         raise NotImplementedError
 
-    def logpdf_link(self, link_f, y, Y_metadata=None):
+    def logpdf_link(self, inv_link_f, y, Y_metadata=None):
         raise NotImplementedError
 
-    def dlogpdf_dlink(self, link_f, y, Y_metadata=None):
+    def dlogpdf_dlink(self, inv_link_f, y, Y_metadata=None):
         raise NotImplementedError
 
-    def d2logpdf_dlink2(self, link_f, y, Y_metadata=None):
+    def d2logpdf_dlink2(self, inv_link_f, y, Y_metadata=None):
         raise NotImplementedError
 
-    def d3logpdf_dlink3(self, link_f, y, Y_metadata=None):
+    def d3logpdf_dlink3(self, inv_link_f, y, Y_metadata=None):
         raise NotImplementedError
 
-    def dlogpdf_link_dtheta(self, link_f, y, Y_metadata=None):
+    def dlogpdf_link_dtheta(self, inv_link_f, y, Y_metadata=None):
         raise NotImplementedError
 
-    def dlogpdf_dlink_dtheta(self, link_f, y, Y_metadata=None):
+    def dlogpdf_dlink_dtheta(self, inv_link_f, y, Y_metadata=None):
         raise NotImplementedError
 
-    def d2logpdf_dlink2_dtheta(self, link_f, y, Y_metadata=None):
+    def d2logpdf_dlink2_dtheta(self, inv_link_f, y, Y_metadata=None):
         raise NotImplementedError
 
     def pdf(self, f, y, Y_metadata=None):
@@ -247,8 +247,8 @@ class Likelihood(Parameterized):
         :returns: likelihood evaluated for this point
         :rtype: float
         """
-        link_f = self.gp_link.transf(f)
+        inv_link_f = self.gp_link.transf(f)
-        return self.pdf_link(link_f, y, Y_metadata=Y_metadata)
+        return self.pdf_link(inv_link_f, y, Y_metadata=Y_metadata)
 
     def logpdf(self, f, y, Y_metadata=None):
         """
@@ -265,8 +265,8 @@ class Likelihood(Parameterized):
         :returns: log likelihood evaluated for this point
         :rtype: float
         """
-        link_f = self.gp_link.transf(f)
+        inv_link_f = self.gp_link.transf(f)
-        return self.logpdf_link(link_f, y, Y_metadata=Y_metadata)
+        return self.logpdf_link(inv_link_f, y, Y_metadata=Y_metadata)
 
     def dlogpdf_df(self, f, y, Y_metadata=None):
         """
@@ -284,8 +284,8 @@ class Likelihood(Parameterized):
         :returns: derivative of log likelihood evaluated for this point
         :rtype: 1xN array
         """
-        link_f = self.gp_link.transf(f)
+        inv_link_f = self.gp_link.transf(f)
-        dlogpdf_dlink = self.dlogpdf_dlink(link_f, y, Y_metadata=Y_metadata)
+        dlogpdf_dlink = self.dlogpdf_dlink(inv_link_f, y, Y_metadata=Y_metadata)
         dlink_df = self.gp_link.dtransf_df(f)
         return chain_1(dlogpdf_dlink, dlink_df)
 
@@ -305,10 +305,10 @@ class Likelihood(Parameterized):
         :returns: second derivative of log likelihood evaluated for this point (diagonal only)
         :rtype: 1xN array
         """
-        link_f = self.gp_link.transf(f)
+        inv_link_f = self.gp_link.transf(f)
-        d2logpdf_dlink2 = self.d2logpdf_dlink2(link_f, y, Y_metadata=Y_metadata)
+        d2logpdf_dlink2 = self.d2logpdf_dlink2(inv_link_f, y, Y_metadata=Y_metadata)
         dlink_df = self.gp_link.dtransf_df(f)
-        dlogpdf_dlink = self.dlogpdf_dlink(link_f, y, Y_metadata=Y_metadata)
+        dlogpdf_dlink = self.dlogpdf_dlink(inv_link_f, y, Y_metadata=Y_metadata)
         d2link_df2 = self.gp_link.d2transf_df2(f)
         return chain_2(d2logpdf_dlink2, dlink_df, dlogpdf_dlink, d2link_df2)
 
@@ -328,12 +328,12 @@ class Likelihood(Parameterized):
         :returns: third derivative of log likelihood evaluated for this point
         :rtype: float
         """
-        link_f = self.gp_link.transf(f)
+        inv_link_f = self.gp_link.transf(f)
-        d3logpdf_dlink3 = self.d3logpdf_dlink3(link_f, y, Y_metadata=Y_metadata)
+        d3logpdf_dlink3 = self.d3logpdf_dlink3(inv_link_f, y, Y_metadata=Y_metadata)
         dlink_df = self.gp_link.dtransf_df(f)
-        d2logpdf_dlink2 = self.d2logpdf_dlink2(link_f, y, Y_metadata=Y_metadata)
+        d2logpdf_dlink2 = self.d2logpdf_dlink2(inv_link_f, y, Y_metadata=Y_metadata)
         d2link_df2 = self.gp_link.d2transf_df2(f)
-        dlogpdf_dlink = self.dlogpdf_dlink(link_f, y, Y_metadata=Y_metadata)
+        dlogpdf_dlink = self.dlogpdf_dlink(inv_link_f, y, Y_metadata=Y_metadata)
         d3link_df3 = self.gp_link.d3transf_df3(f)
         return chain_3(d3logpdf_dlink3, dlink_df, d2logpdf_dlink2, d2link_df2, dlogpdf_dlink, d3link_df3)
 
@@ -342,10 +342,10 @@ class Likelihood(Parameterized):
         TODO: Doc strings
         """
         if self.size > 0:
-            link_f = self.gp_link.transf(f)
+            inv_link_f = self.gp_link.transf(f)
-            return self.dlogpdf_link_dtheta(link_f, y, Y_metadata=Y_metadata)
+            return self.dlogpdf_link_dtheta(inv_link_f, y, Y_metadata=Y_metadata)
         else:
-            #Is no parameters so return an empty array for its derivatives
+            # There are no parameters so return an empty array for derivatives
             return np.zeros([1, 0])
 
     def dlogpdf_df_dtheta(self, f, y, Y_metadata=None):
@@ -353,12 +353,12 @@ class Likelihood(Parameterized):
         TODO: Doc strings
         """
         if self.size > 0:
-            link_f = self.gp_link.transf(f)
+            inv_link_f = self.gp_link.transf(f)
             dlink_df = self.gp_link.dtransf_df(f)
-            dlogpdf_dlink_dtheta = self.dlogpdf_dlink_dtheta(link_f, y, Y_metadata=Y_metadata)
+            dlogpdf_dlink_dtheta = self.dlogpdf_dlink_dtheta(inv_link_f, y, Y_metadata=Y_metadata)
             return chain_1(dlogpdf_dlink_dtheta, dlink_df)
         else:
-            #Is no parameters so return an empty array for its derivatives
+            # There are no parameters so return an empty array for derivatives
             return np.zeros([f.shape[0], 0])
 
     def d2logpdf_df2_dtheta(self, f, y, Y_metadata=None):
@@ -366,14 +366,14 @@ class Likelihood(Parameterized):
         TODO: Doc strings
         """
         if self.size > 0:
-            link_f = self.gp_link.transf(f)
+            inv_link_f = self.gp_link.transf(f)
             dlink_df = self.gp_link.dtransf_df(f)
             d2link_df2 = self.gp_link.d2transf_df2(f)
-            d2logpdf_dlink2_dtheta = self.d2logpdf_dlink2_dtheta(link_f, y, Y_metadata=Y_metadata)
+            d2logpdf_dlink2_dtheta = self.d2logpdf_dlink2_dtheta(inv_link_f, y, Y_metadata=Y_metadata)
-            dlogpdf_dlink_dtheta = self.dlogpdf_dlink_dtheta(link_f, y, Y_metadata=Y_metadata)
+            dlogpdf_dlink_dtheta = self.dlogpdf_dlink_dtheta(inv_link_f, y, Y_metadata=Y_metadata)
             return chain_2(d2logpdf_dlink2_dtheta, dlink_df, dlogpdf_dlink_dtheta, d2link_df2)
         else:
-            #Is no parameters so return an empty array for its derivatives
+            # There are no parameters so return an empty array for derivatives
             return np.zeros([f.shape[0], 0])
 
     def _laplace_gradients(self, f, y, Y_metadata=None):
@@ -411,7 +411,10 @@ class Likelihood(Parameterized):
         #compute the quantiles by sampling!!!
         N_samp = 1000
         s = np.random.randn(mu.shape[0], N_samp)*np.sqrt(var) + mu
+        #ss_f = s.flatten()
+        #ss_y = self.samples(ss_f, Y_metadata)
         ss_y = self.samples(s, Y_metadata)
+        #ss_y = ss_y.reshape(mu.shape[0], N_samp)
 
         return [np.percentile(ss_y ,q, axis=1)[:,None] for q in quantiles]
 

GPy/likelihoods/student_t.py

@@ -26,8 +26,8 @@ class StudentT(Likelihood):
             gp_link = link_functions.Identity()
 
         super(StudentT, self).__init__(gp_link, name='Student_T')
-
+        # sigma2 is not a noise parameter, it is a squared scale.
-        self.sigma2 = Param('t_noise', float(sigma2), Logexp())
+        self.sigma2 = Param('t_scale2', float(sigma2), Logexp())
         self.v = Param('deg_free', float(deg_free))
         self.add_parameter(self.sigma2)
         self.add_parameter(self.v)
@@ -46,23 +46,23 @@ class StudentT(Likelihood):
         self.sigma2.gradient = grads[0]
         self.v.gradient = grads[1]
 
-    def pdf_link(self, link_f, y, Y_metadata=None):
+    def pdf_link(self, inv_link_f, y, Y_metadata=None):
         """
         Likelihood function given link(f)
 
         .. math::
             p(y_{i}|\\lambda(f_{i})) = \\frac{\\Gamma\\left(\\frac{v+1}{2}\\right)}{\\Gamma\\left(\\frac{v}{2}\\right)\\sqrt{v\\pi\\sigma^{2}}}\\left(1 + \\frac{1}{v}\\left(\\frac{(y_{i} - \\lambda(f_{i}))^{2}}{\\sigma^{2}}\\right)\\right)^{\\frac{-v+1}{2}}
 
-        :param link_f: latent variables link(f)
+        :param inv_link_f: latent variables link(f)
-        :type link_f: Nx1 array
+        :type inv_link_f: Nx1 array
         :param y: data
         :type y: Nx1 array
         :param Y_metadata: Y_metadata which is not used in student t distribution
         :returns: likelihood evaluated for this point
         :rtype: float
         """
-        assert np.atleast_1d(link_f).shape == np.atleast_1d(y).shape
+        assert np.atleast_1d(inv_link_f).shape == np.atleast_1d(y).shape
-        e = y - link_f
+        e = y - inv_link_f
         #Careful gamma(big_number) is infinity!
         objective = ((np.exp(gammaln((self.v + 1)*0.5) - gammaln(self.v * 0.5))
                      / (np.sqrt(self.v * np.pi * self.sigma2)))
@@ -70,15 +70,15 @@ class StudentT(Likelihood):
                     )
         return np.prod(objective)
 
-    def logpdf_link(self, link_f, y, Y_metadata=None):
+    def logpdf_link(self, inv_link_f, y, Y_metadata=None):
         """
         Log Likelihood Function given link(f)
 
         .. math::
             \\ln p(y_{i}|\lambda(f_{i})) = \\ln \\Gamma\\left(\\frac{v+1}{2}\\right) - \\ln \\Gamma\\left(\\frac{v}{2}\\right) - \\ln \\sqrt{v \\pi\\sigma^{2}} - \\frac{v+1}{2}\\ln \\left(1 + \\frac{1}{v}\\left(\\frac{(y_{i} - \lambda(f_{i}))^{2}}{\\sigma^{2}}\\right)\\right)
 
-        :param link_f: latent variables (link(f))
+        :param inv_link_f: latent variables (link(f))
-        :type link_f: Nx1 array
+        :type inv_link_f: Nx1 array
         :param y: data
         :type y: Nx1 array
         :param Y_metadata: Y_metadata which is not used in student t distribution
@@ -86,11 +86,11 @@ class StudentT(Likelihood):
         :rtype: float
 
         """
-        assert np.atleast_1d(link_f).shape == np.atleast_1d(y).shape
+        assert np.atleast_1d(inv_link_f).shape == np.atleast_1d(y).shape
-        e = y - link_f
+        e = y - inv_link_f
         #FIXME:
-        #Why does np.log(1 + (1/self.v)*((y-link_f)**2)/self.sigma2) suppress the divide by zero?!
+        #Why does np.log(1 + (1/self.v)*((y-inv_link_f)**2)/self.sigma2) suppress the divide by zero?!
-        #But np.log(1 + (1/float(self.v))*((y-link_f)**2)/self.sigma2) throws it correctly
+        #But np.log(1 + (1/float(self.v))*((y-inv_link_f)**2)/self.sigma2) throws it correctly
         #print - 0.5*(self.v + 1)*np.log(1 + (1/np.float(self.v))*((e**2)/self.sigma2))
         objective = (+ gammaln((self.v + 1) * 0.5)
                     - gammaln(self.v * 0.5)
@@ -99,15 +99,15 @@ class StudentT(Likelihood):
                     )
         return np.sum(objective)
 
-    def dlogpdf_dlink(self, link_f, y, Y_metadata=None):
+    def dlogpdf_dlink(self, inv_link_f, y, Y_metadata=None):
         """
         Gradient of the log likelihood function at y, given link(f) w.r.t link(f)
 
         .. math::
             \\frac{d \\ln p(y_{i}|\lambda(f_{i}))}{d\\lambda(f)} = \\frac{(v+1)(y_{i}-\lambda(f_{i}))}{(y_{i}-\lambda(f_{i}))^{2} + \\sigma^{2}v}
 
-        :param link_f: latent variables (f)
+        :param inv_link_f: latent variables (f)
-        :type link_f: Nx1 array
+        :type inv_link_f: Nx1 array
         :param y: data
         :type y: Nx1 array
         :param Y_metadata: Y_metadata which is not used in student t distribution
@@ -115,12 +115,12 @@ class StudentT(Likelihood):
         :rtype: Nx1 array
 
         """
-        assert np.atleast_1d(link_f).shape == np.atleast_1d(y).shape
+        assert np.atleast_1d(inv_link_f).shape == np.atleast_1d(y).shape
-        e = y - link_f
+        e = y - inv_link_f
         grad = ((self.v + 1) * e) / (self.v * self.sigma2 + (e**2))
         return grad
 
-    def d2logpdf_dlink2(self, link_f, y, Y_metadata=None):
+    def d2logpdf_dlink2(self, inv_link_f, y, Y_metadata=None):
         """
         Hessian at y, given link(f), w.r.t link(f)
         i.e. second derivative logpdf at y given link(f_i) and link(f_j)  w.r.t link(f_i) and link(f_j)
@@ -129,8 +129,8 @@ class StudentT(Likelihood):
         .. math::
             \\frac{d^{2} \\ln p(y_{i}|\lambda(f_{i}))}{d^{2}\\lambda(f)} = \\frac{(v+1)((y_{i}-\lambda(f_{i}))^{2} - \\sigma^{2}v)}{((y_{i}-\lambda(f_{i}))^{2} + \\sigma^{2}v)^{2}}
 
-        :param link_f: latent variables link(f)
+        :param inv_link_f: latent variables inv_link(f)
-        :type link_f: Nx1 array
+        :type inv_link_f: Nx1 array
         :param y: data
         :type y: Nx1 array
         :param Y_metadata: Y_metadata which is not used in student t distribution
@@ -141,90 +141,90 @@ class StudentT(Likelihood):
             Will return diagonal of hessian, since every where else it is 0, as the likelihood factorizes over cases
             (the distribution for y_i depends only on link(f_i) not on link(f_(j!=i))
         """
-        assert np.atleast_1d(link_f).shape == np.atleast_1d(y).shape
+        assert np.atleast_1d(inv_link_f).shape == np.atleast_1d(y).shape
-        e = y - link_f
+        e = y - inv_link_f
         hess = ((self.v + 1)*(e**2 - self.v*self.sigma2)) / ((self.sigma2*self.v + e**2)**2)
         return hess
 
-    def d3logpdf_dlink3(self, link_f, y, Y_metadata=None):
+    def d3logpdf_dlink3(self, inv_link_f, y, Y_metadata=None):
         """
         Third order derivative log-likelihood function at y given link(f) w.r.t link(f)
 
         .. math::
             \\frac{d^{3} \\ln p(y_{i}|\lambda(f_{i}))}{d^{3}\\lambda(f)} = \\frac{-2(v+1)((y_{i} - \lambda(f_{i}))^3 - 3(y_{i} - \lambda(f_{i})) \\sigma^{2} v))}{((y_{i} - \lambda(f_{i})) + \\sigma^{2} v)^3}
 
-        :param link_f: latent variables link(f)
+        :param inv_link_f: latent variables link(f)
-        :type link_f: Nx1 array
+        :type inv_link_f: Nx1 array
         :param y: data
         :type y: Nx1 array
         :param Y_metadata: Y_metadata which is not used in student t distribution
         :returns: third derivative of likelihood evaluated at points f
         :rtype: Nx1 array
         """
-        assert np.atleast_1d(link_f).shape == np.atleast_1d(y).shape
+        assert np.atleast_1d(inv_link_f).shape == np.atleast_1d(y).shape
-        e = y - link_f
+        e = y - inv_link_f
         d3lik_dlink3 = ( -(2*(self.v + 1)*(-e)*(e**2 - 3*self.v*self.sigma2)) /
                        ((e**2 + self.sigma2*self.v)**3)
                     )
         return d3lik_dlink3
 
-    def dlogpdf_link_dvar(self, link_f, y, Y_metadata=None):
+    def dlogpdf_link_dvar(self, inv_link_f, y, Y_metadata=None):
         """
         Gradient of the log-likelihood function at y given f, w.r.t variance parameter (t_noise)
 
         .. math::
             \\frac{d \\ln p(y_{i}|\lambda(f_{i}))}{d\\sigma^{2}} = \\frac{v((y_{i} - \lambda(f_{i}))^{2} - \\sigma^{2})}{2\\sigma^{2}(\\sigma^{2}v + (y_{i} - \lambda(f_{i}))^{2})}
 
-        :param link_f: latent variables link(f)
+        :param inv_link_f: latent variables link(f)
-        :type link_f: Nx1 array
+        :type inv_link_f: Nx1 array
         :param y: data
         :type y: Nx1 array
         :param Y_metadata: Y_metadata which is not used in student t distribution
         :returns: derivative of likelihood evaluated at points f w.r.t variance parameter
         :rtype: float
         """
-        assert np.atleast_1d(link_f).shape == np.atleast_1d(y).shape
+        assert np.atleast_1d(inv_link_f).shape == np.atleast_1d(y).shape
-        e = y - link_f
+        e = y - inv_link_f
         dlogpdf_dvar = self.v*(e**2 - self.sigma2)/(2*self.sigma2*(self.sigma2*self.v + e**2))
         return np.sum(dlogpdf_dvar)
 
-    def dlogpdf_dlink_dvar(self, link_f, y, Y_metadata=None):
+    def dlogpdf_dlink_dvar(self, inv_link_f, y, Y_metadata=None):
         """
         Derivative of the dlogpdf_dlink w.r.t variance parameter (t_noise)
 
         .. math::
             \\frac{d}{d\\sigma^{2}}(\\frac{d \\ln p(y_{i}|\lambda(f_{i}))}{df}) = \\frac{-2\\sigma v(v + 1)(y_{i}-\lambda(f_{i}))}{(y_{i}-\lambda(f_{i}))^2 + \\sigma^2 v)^2}
 
-        :param link_f: latent variables link_f
+        :param inv_link_f: latent variables inv_link_f
-        :type link_f: Nx1 array
+        :type inv_link_f: Nx1 array
         :param y: data
         :type y: Nx1 array
         :param Y_metadata: Y_metadata which is not used in student t distribution
         :returns: derivative of likelihood evaluated at points f w.r.t variance parameter
         :rtype: Nx1 array
         """
-        assert np.atleast_1d(link_f).shape == np.atleast_1d(y).shape
+        assert np.atleast_1d(inv_link_f).shape == np.atleast_1d(y).shape
-        e = y - link_f
+        e = y - inv_link_f
         dlogpdf_dlink_dvar = (self.v*(self.v+1)*(-e))/((self.sigma2*self.v + e**2)**2)
         return dlogpdf_dlink_dvar
 
-    def d2logpdf_dlink2_dvar(self, link_f, y, Y_metadata=None):
+    def d2logpdf_dlink2_dvar(self, inv_link_f, y, Y_metadata=None):
         """
         Gradient of the hessian (d2logpdf_dlink2) w.r.t variance parameter (t_noise)
 
         .. math::
             \\frac{d}{d\\sigma^{2}}(\\frac{d^{2} \\ln p(y_{i}|\lambda(f_{i}))}{d^{2}f}) = \\frac{v(v+1)(\\sigma^{2}v - 3(y_{i} - \lambda(f_{i}))^{2})}{(\\sigma^{2}v + (y_{i} - \lambda(f_{i}))^{2})^{3}}
 
-        :param link_f: latent variables link(f)
+        :param inv_link_f: latent variables link(f)
-        :type link_f: Nx1 array
+        :type inv_link_f: Nx1 array
         :param y: data
         :type y: Nx1 array
         :param Y_metadata: Y_metadata which is not used in student t distribution
         :returns: derivative of hessian evaluated at points f and f_j w.r.t variance parameter
         :rtype: Nx1 array
         """
-        assert np.atleast_1d(link_f).shape == np.atleast_1d(y).shape
+        assert np.atleast_1d(inv_link_f).shape == np.atleast_1d(y).shape
-        e = y - link_f
+        e = y - inv_link_f
         d2logpdf_dlink2_dvar = ( (self.v*(self.v+1)*(self.sigma2*self.v - 3*(e**2)))
                               / ((self.sigma2*self.v + (e**2))**3)
                            )
@@ -246,11 +246,12 @@ class StudentT(Likelihood):
         return np.hstack((d2logpdf_dlink2_dvar, d2logpdf_dlink2_dv))
 
     def predictive_mean(self, mu, sigma, Y_metadata=None):
-        return self.gp_link.transf(mu) # only true in link is monotoci, which it is.
+        # The comment here confuses mean and median. 
+        return self.gp_link.transf(mu) # only true if link is monotonic, which it is.
 
     def predictive_variance(self, mu,variance, predictive_mean=None, Y_metadata=None):
-        if self.deg_free <2.:
+        if self.deg_free<=2.:
-            return np.empty(mu.shape)*np.nan #not defined for small degress fo freedom
+            return np.empty(mu.shape)*np.nan # does not exist for degrees of freedom <= 2.
         else:
             return super(StudentT, self).predictive_variance(mu, variance, predictive_mean, Y_metadata)