# Copyright 2016 Valentine Svensson, James Hensman, alexggmatthews, Alexis Boukouvalas # Copyright 2017 Artem Artemev @awav # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. r""" Likelihoods are another core component of GPflow. This describes how likely the data is under the assumptions made about the underlying latent functions p(Y|F). Different likelihoods make different assumptions about the distribution of the data, as such different data-types (continuous, binary, ordinal, count) are better modelled with different likelihood assumptions. Use of any likelihood other than Gaussian typically introduces the need to use an approximation to perform inference, if one isn't already needed. A variational inference and MCMC models are included in GPflow and allow approximate inference with non-Gaussian likelihoods. An introduction to these models can be found :ref:`here `. Specific notebooks illustrating non-Gaussian likelihood regressions are available for `classification `_ (binary data), `ordinal `_ and `multiclass `_. Creating new likelihoods ---------- Likelihoods are defined by their log-likelihood. When creating new likelihoods, the :func:`logp ` method (log p(Y|F)), the :func:`conditional_mean `, :func:`conditional_variance `. In order to perform variational inference with non-Gaussian likelihoods a term called ``variational expectations``, ∫ q(F) log p(Y|F) dF, needs to be computed under a Gaussian distribution q(F) ~ N(μ, Σ). The :func:`variational_expectations ` method can be overriden if this can be computed in closed form, otherwise; if the new likelihood inherits :class:`Likelihood ` the default will use Gauss-Hermite numerical integration (works well when F is 1D or 2D), if the new likelihood inherits from :class:`MonteCarloLikelihood ` the integration is done by sampling (can be more suitable when F is higher dimensional). """ import numpy as np import tensorflow as tf from . import logdensities from . import priors from . import settings from . import transforms from .decors import params_as_tensors from .decors import params_as_tensors_for from .params import ParamList from .params import Parameter from .params import Parameterized from .quadrature import hermgauss from .quadrature import ndiagquad, ndiag_mc class Likelihood(Parameterized): def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) self.num_gauss_hermite_points = 20 def predict_mean_and_var(self, Fmu, Fvar): r""" Given a Normal distribution for the latent function, return the mean of Y if q(f) = N(Fmu, Fvar) and this object represents p(y|f) then this method computes the predictive mean \int\int y p(y|f)q(f) df dy and the predictive variance \int\int y^2 p(y|f)q(f) df dy - [ \int\int y p(y|f)q(f) df dy ]^2 Here, we implement a default Gauss-Hermite quadrature routine, but some likelihoods (e.g. Gaussian) will implement specific cases. """ integrand2 = lambda *X: self.conditional_variance(*X) + tf.square(self.conditional_mean(*X)) E_y, E_y2 = ndiagquad([self.conditional_mean, integrand2], self.num_gauss_hermite_points, Fmu, Fvar) V_y = E_y2 - tf.square(E_y) return E_y, V_y def predict_density(self, Fmu, Fvar, Y): r""" Given a Normal distribution for the latent function, and a datum Y, compute the log predictive density of Y. i.e. if q(f) = N(Fmu, Fvar) and this object represents p(y|f) then this method computes the predictive density \log \int p(y=Y|f)q(f) df Here, we implement a default Gauss-Hermite quadrature routine, but some likelihoods (Gaussian, Poisson) will implement specific cases. """ return ndiagquad(self.logp, self.num_gauss_hermite_points, Fmu, Fvar, logspace=True, Y=Y) def variational_expectations(self, Fmu, Fvar, Y): r""" Compute the expected log density of the data, given a Gaussian distribution for the function values. if q(f) = N(Fmu, Fvar) and this object represents p(y|f) then this method computes \int (\log p(y|f)) q(f) df. Here, we implement a default Gauss-Hermite quadrature routine, but some likelihoods (Gaussian, Poisson) will implement specific cases. """ return ndiagquad(self.logp, self.num_gauss_hermite_points, Fmu, Fvar, Y=Y) class Gaussian(Likelihood): def __init__(self, variance=1.0, **kwargs): super().__init__(**kwargs) self.variance = Parameter( variance, transform=transforms.positive, dtype=settings.float_type) @params_as_tensors def logp(self, F, Y): return logdensities.gaussian(Y, F, self.variance) @params_as_tensors def conditional_mean(self, F): # pylint: disable=R0201 return tf.identity(F) @params_as_tensors def conditional_variance(self, F): return tf.fill(tf.shape(F), tf.squeeze(self.variance)) @params_as_tensors def predict_mean_and_var(self, Fmu, Fvar): return tf.identity(Fmu), Fvar + self.variance @params_as_tensors def predict_density(self, Fmu, Fvar, Y): return logdensities.gaussian(Y, Fmu, Fvar + self.variance) @params_as_tensors def variational_expectations(self, Fmu, Fvar, Y): return -0.5 * np.log(2 * np.pi) - 0.5 * tf.log(self.variance) \ - 0.5 * (tf.square(Y - Fmu) + Fvar) / self.variance class Poisson(Likelihood): """ Poisson likelihood for use with count data, where the rate is given by the (transformed) GP. let g(.) be the inverse-link function, then this likelihood represents p(y_i | f_i) = Poisson(y_i | g(f_i) * binsize) Note:binsize For use in a Log Gaussian Cox process (doubly stochastic model) where the rate function of an inhomogeneous Poisson process is given by a GP. The intractable likelihood can be approximated by gridding the space (into bins of size 'binsize') and using this Poisson likelihood. """ def __init__(self, invlink=tf.exp, binsize=1., **kwargs): super().__init__(**kwargs) self.invlink = invlink self.binsize = np.double(binsize) def logp(self, F, Y): return logdensities.poisson(Y, self.invlink(F) * self.binsize) def conditional_variance(self, F): return self.invlink(F) * self.binsize def conditional_mean(self, F): return self.invlink(F) * self.binsize def variational_expectations(self, Fmu, Fvar, Y): if self.invlink is tf.exp: return Y * Fmu - tf.exp(Fmu + Fvar / 2) * self.binsize \ - tf.lgamma(Y + 1) + Y * tf.log(self.binsize) return super(Poisson, self).variational_expectations(Fmu, Fvar, Y) class Exponential(Likelihood): def __init__(self, invlink=tf.exp, **kwargs): super().__init__(**kwargs) self.invlink = invlink def logp(self, F, Y): return logdensities.exponential(Y, self.invlink(F)) def conditional_mean(self, F): return self.invlink(F) def conditional_variance(self, F): return tf.square(self.invlink(F)) def variational_expectations(self, Fmu, Fvar, Y): if self.invlink is tf.exp: return - tf.exp(-Fmu + Fvar / 2) * Y - Fmu return super().variational_expectations(Fmu, Fvar, Y) class StudentT(Likelihood): def __init__(self, scale=1.0, df=3.0, **kwargs): """ :param scale float: scale parameter :param df float: degrees of freedom """ super().__init__(**kwargs) self.df = df self.scale = Parameter(scale, transform=transforms.positive, dtype=settings.float_type) @params_as_tensors def logp(self, F, Y): return logdensities.student_t(Y, F, self.scale, self.df) @params_as_tensors def conditional_mean(self, F): return tf.identity(F) @params_as_tensors def conditional_variance(self, F): var = self.scale ** 2 * (self.df / (self.df - 2.0)) return tf.fill(tf.shape(F), tf.squeeze(var)) def inv_probit(x): jitter = 1e-3 # ensures output is strictly between 0 and 1 return 0.5 * (1.0 + tf.erf(x / np.sqrt(2.0))) * (1 - 2 * jitter) + jitter class Bernoulli(Likelihood): def __init__(self, invlink=inv_probit, **kwargs): super().__init__(**kwargs) self.invlink = invlink def logp(self, F, Y): return logdensities.bernoulli(Y, self.invlink(F)) def predict_mean_and_var(self, Fmu, Fvar): if self.invlink is inv_probit: p = inv_probit(Fmu / tf.sqrt(1 + Fvar)) return p, p - tf.square(p) else: # for other invlink, use quadrature return super().predict_mean_and_var(Fmu, Fvar) def predict_density(self, Fmu, Fvar, Y): p = self.predict_mean_and_var(Fmu, Fvar)[0] return logdensities.bernoulli(Y, p) def conditional_mean(self, F): return self.invlink(F) def conditional_variance(self, F): p = self.conditional_mean(F) return p - tf.square(p) class Gamma(Likelihood): """ Use the transformed GP to give the *scale* (inverse rate) of the Gamma """ def __init__(self, invlink=tf.exp, **kwargs): super().__init__(**kwargs) self.invlink = invlink self.shape = Parameter(1.0, transform=transforms.positive) @params_as_tensors def logp(self, F, Y): return logdensities.gamma(Y, self.shape, self.invlink(F)) @params_as_tensors def conditional_mean(self, F): return self.shape * self.invlink(F) @params_as_tensors def conditional_variance(self, F): scale = self.invlink(F) return self.shape * tf.square(scale) @params_as_tensors def variational_expectations(self, Fmu, Fvar, Y): if self.invlink is tf.exp: return -self.shape * Fmu - tf.lgamma(self.shape) \ + (self.shape - 1.) * tf.log(Y) - Y * tf.exp(-Fmu + Fvar / 2.) else: return super().variational_expectations(Fmu, Fvar, Y) class Beta(Likelihood): """ This uses a reparameterisation of the Beta density. We have the mean of the Beta distribution given by the transformed process: m = sigma(f) and a scale parameter. The familiar alpha, beta parameters are given by m = alpha / (alpha + beta) scale = alpha + beta so: alpha = scale * m beta = scale * (1-m) """ def __init__(self, invlink=inv_probit, scale=1.0, **kwargs): super().__init__(**kwargs) self.scale = Parameter(scale, transform=transforms.positive) self.invlink = invlink @params_as_tensors def logp(self, F, Y): mean = self.invlink(F) alpha = mean * self.scale beta = self.scale - alpha return logdensities.beta(Y, alpha, beta) @params_as_tensors def conditional_mean(self, F): return self.invlink(F) @params_as_tensors def conditional_variance(self, F): mean = self.invlink(F) return (mean - tf.square(mean)) / (self.scale + 1.) class RobustMax(Parameterized): """ This class represent a multi-class inverse-link function. Given a vector f=[f_1, f_2, ... f_k], the result of the mapping is y = [y_1 ... y_k] with y_i = (1-eps) i == argmax(f) eps/(k-1) otherwise. """ def __init__(self, num_classes, epsilon=1e-3, **kwargs): super().__init__(**kwargs) self.epsilon = Parameter(epsilon, transforms.Logistic(), trainable=False, dtype=settings.float_type, prior=priors.Beta(0.2, 5.)) self.num_classes = num_classes @params_as_tensors def __call__(self, F): i = tf.argmax(F, 1) return tf.one_hot(i, self.num_classes, tf.squeeze(1. - self.epsilon), tf.squeeze(self._eps_K1)) @property @params_as_tensors def _eps_K1(self): return self.epsilon / (self.num_classes - 1.) def prob_is_largest(self, Y, mu, var, gh_x, gh_w): Y = tf.cast(Y, tf.int64) # work out what the mean and variance is of the indicated latent function. oh_on = tf.cast(tf.one_hot(tf.reshape(Y, (-1,)), self.num_classes, 1., 0.), settings.float_type) mu_selected = tf.reduce_sum(oh_on * mu, 1) var_selected = tf.reduce_sum(oh_on * var, 1) # generate Gauss Hermite grid X = tf.reshape(mu_selected, (-1, 1)) + gh_x * tf.reshape( tf.sqrt(tf.clip_by_value(2. * var_selected, 1e-10, np.inf)), (-1, 1)) # compute the CDF of the Gaussian between the latent functions and the grid (including the selected function) dist = (tf.expand_dims(X, 1) - tf.expand_dims(mu, 2)) / tf.expand_dims( tf.sqrt(tf.clip_by_value(var, 1e-10, np.inf)), 2) cdfs = 0.5 * (1.0 + tf.erf(dist / np.sqrt(2.0))) cdfs = cdfs * (1 - 2e-4) + 1e-4 # blank out all the distances on the selected latent function oh_off = tf.cast(tf.one_hot(tf.reshape(Y, (-1,)), self.num_classes, 0., 1.), settings.float_type) cdfs = cdfs * tf.expand_dims(oh_off, 2) + tf.expand_dims(oh_on, 2) # take the product over the latent functions, and the sum over the GH grid. return tf.matmul(tf.reduce_prod(cdfs, reduction_indices=[1]), tf.reshape(gh_w / np.sqrt(np.pi), (-1, 1))) class MultiClass(Likelihood): def __init__(self, num_classes, invlink=None, **kwargs): """ A likelihood that can do multi-way classification. Currently the only valid choice of inverse-link function (invlink) is an instance of RobustMax. """ super().__init__(**kwargs) self.num_classes = num_classes if invlink is None: invlink = RobustMax(self.num_classes) elif not isinstance(invlink, RobustMax): raise NotImplementedError self.invlink = invlink def logp(self, F, Y): if isinstance(self.invlink, RobustMax): with params_as_tensors_for(self.invlink): hits = tf.equal(tf.expand_dims(tf.argmax(F, 1), 1), tf.cast(Y, tf.int64)) yes = tf.ones(tf.shape(Y), dtype=settings.float_type) - self.invlink.epsilon no = tf.zeros(tf.shape(Y), dtype=settings.float_type) + self.invlink._eps_K1 p = tf.where(hits, yes, no) return tf.log(p) else: raise NotImplementedError def variational_expectations(self, Fmu, Fvar, Y): if isinstance(self.invlink, RobustMax): with params_as_tensors_for(self.invlink): gh_x, gh_w = hermgauss(self.num_gauss_hermite_points) p = self.invlink.prob_is_largest(Y, Fmu, Fvar, gh_x, gh_w) ve = p * tf.log(1. - self.invlink.epsilon) + (1. - p) * tf.log(self.invlink._eps_K1) return ve else: raise NotImplementedError def predict_mean_and_var(self, Fmu, Fvar): if isinstance(self.invlink, RobustMax): # To compute this, we'll compute the density for each possible output possible_outputs = [tf.fill(tf.stack([tf.shape(Fmu)[0], 1]), np.array(i, dtype=np.int64)) for i in range(self.num_classes)] ps = [self._predict_non_logged_density(Fmu, Fvar, po) for po in possible_outputs] ps = tf.transpose(tf.stack([tf.reshape(p, (-1,)) for p in ps])) return ps, ps - tf.square(ps) else: raise NotImplementedError def predict_density(self, Fmu, Fvar, Y): return tf.log(self._predict_non_logged_density(Fmu, Fvar, Y)) def _predict_non_logged_density(self, Fmu, Fvar, Y): if isinstance(self.invlink, RobustMax): with params_as_tensors_for(self.invlink): gh_x, gh_w = hermgauss(self.num_gauss_hermite_points) p = self.invlink.prob_is_largest(Y, Fmu, Fvar, gh_x, gh_w) den = p * (1. - self.invlink.epsilon) + (1. - p) * (self.invlink._eps_K1) return den else: raise NotImplementedError def conditional_mean(self, F): return self.invlink(F) def conditional_variance(self, F): p = self.conditional_mean(F) return p - tf.square(p) class SwitchedLikelihood(Likelihood): def __init__(self, likelihood_list, **kwargs): """ In this likelihood, we assume at extra column of Y, which contains integers that specify a likelihood from the list of likelihoods. """ super().__init__(**kwargs) for l in likelihood_list: assert isinstance(l, Likelihood) self.likelihood_list = ParamList(likelihood_list) self.num_likelihoods = len(self.likelihood_list) def _partition_and_stitch(self, args, func_name): """ args is a list of tensors, to be passed to self.likelihoods. args[-1] is the 'Y' argument, which contains the indexes to self.likelihoods. This function splits up the args using dynamic_partition, calls the relevant function on the likelihoods, and re-combines the result. """ # get the index from Y Y = args[-1] ind = Y[:, -1] ind = tf.cast(ind, tf.int32) Y = Y[:, :-1] args[-1] = Y # split up the arguments into chunks corresponding to the relevant likelihoods args = zip(*[tf.dynamic_partition(X, ind, self.num_likelihoods) for X in args]) # apply the likelihood-function to each section of the data with params_as_tensors_for(self, convert=False): funcs = [getattr(lik, func_name) for lik in self.likelihood_list] results = [f(*args_i) for f, args_i in zip(funcs, args)] # stitch the results back together partitions = tf.dynamic_partition(tf.range(0, tf.size(ind)), ind, self.num_likelihoods) results = tf.dynamic_stitch(partitions, results) return results def logp(self, F, Y): return self._partition_and_stitch([F, Y], 'logp') def predict_density(self, Fmu, Fvar, Y): return self._partition_and_stitch([Fmu, Fvar, Y], 'predict_density') def variational_expectations(self, Fmu, Fvar, Y): return self._partition_and_stitch([Fmu, Fvar, Y], 'variational_expectations') def predict_mean_and_var(self, Fmu, Fvar): mvs = [lik.predict_mean_and_var(Fmu, Fvar) for lik in self.likelihood_list] mu_list, var_list = zip(*mvs) mu = tf.concat(mu_list, 1) var = tf.concat(var_list, 1) return mu, var class Ordinal(Likelihood): """ A likelihood for doing ordinal regression. The data are integer values from 0 to K, and the user must specify (K-1) 'bin edges' which define the points at which the labels switch. Let the bin edges be [a_0, a_1, ... a_{K-1}], then the likelihood is p(Y=0|F) = phi((a_0 - F) / sigma) p(Y=1|F) = phi((a_1 - F) / sigma) - phi((a_0 - F) / sigma) p(Y=2|F) = phi((a_2 - F) / sigma) - phi((a_1 - F) / sigma) ... p(Y=K|F) = 1 - phi((a_{K-1} - F) / sigma) where phi is the cumulative density function of a Gaussian (the inverse probit function) and sigma is a parameter to be learned. A reference is: @article{chu2005gaussian, title={Gaussian processes for ordinal regression}, author={Chu, Wei and Ghahramani, Zoubin}, journal={Journal of Machine Learning Research}, volume={6}, number={Jul}, pages={1019--1041}, year={2005} } """ def __init__(self, bin_edges, **kwargs): """ bin_edges is a numpy array specifying at which function value the output label should switch. If the possible Y values are 0...K, then the size of bin_edges should be (K-1). """ super().__init__(**kwargs) self.bin_edges = bin_edges self.num_bins = bin_edges.size + 1 self.sigma = Parameter(1.0, transform=transforms.positive) @params_as_tensors def logp(self, F, Y): Y = tf.cast(Y, tf.int64) scaled_bins_left = tf.concat([self.bin_edges / self.sigma, np.array([np.inf])], 0) scaled_bins_right = tf.concat([np.array([-np.inf]), self.bin_edges / self.sigma], 0) selected_bins_left = tf.gather(scaled_bins_left, Y) selected_bins_right = tf.gather(scaled_bins_right, Y) return tf.log(inv_probit(selected_bins_left - F / self.sigma) - inv_probit(selected_bins_right - F / self.sigma) + 1e-6) @params_as_tensors def _make_phi(self, F): """ A helper function for making predictions. Constructs a probability matrix where each row output the probability of the corresponding label, and the rows match the entries of F. Note that a matrix of F values is flattened. """ scaled_bins_left = tf.concat([self.bin_edges / self.sigma, np.array([np.inf])], 0) scaled_bins_right = tf.concat([np.array([-np.inf]), self.bin_edges / self.sigma], 0) return inv_probit(scaled_bins_left - tf.reshape(F, (-1, 1)) / self.sigma) \ - inv_probit(scaled_bins_right - tf.reshape(F, (-1, 1)) / self.sigma) def conditional_mean(self, F): phi = self._make_phi(F) Ys = tf.reshape(np.arange(self.num_bins, dtype=np.float64), (-1, 1)) return tf.reshape(tf.matmul(phi, Ys), tf.shape(F)) def conditional_variance(self, F): phi = self._make_phi(F) Ys = tf.reshape(np.arange(self.num_bins, dtype=np.float64), (-1, 1)) E_y = tf.matmul(phi, Ys) E_y2 = tf.matmul(phi, tf.square(Ys)) return tf.reshape(E_y2 - tf.square(E_y), tf.shape(F)) class MonteCarloLikelihood(Likelihood): def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) self.num_monte_carlo_points = 100 del self.num_gauss_hermite_points def _mc_quadrature(self, funcs, Fmu, Fvar, logspace: bool = False, epsilon=None, **Ys): return ndiag_mc(funcs, self.num_monte_carlo_points, Fmu, Fvar, logspace, epsilon, **Ys) def predict_mean_and_var(self, Fmu, Fvar, epsilon=None): r""" Given a Normal distribution for the latent function, return the mean of Y if q(f) = N(Fmu, Fvar) and this object represents p(y|f) then this method computes the predictive mean \int\int y p(y|f)q(f) df dy and the predictive variance \int\int y^2 p(y|f)q(f) df dy - [ \int\int y p(y|f)q(f) df dy ]^2 Here, we implement a default Monte Carlo routine. """ integrand2 = lambda *X: self.conditional_variance(*X) + tf.square(self.conditional_mean(*X)) E_y, E_y2 = self._mc_quadrature([self.conditional_mean, integrand2], Fmu, Fvar, epsilon=epsilon) V_y = E_y2 - tf.square(E_y) return E_y, V_y # N x D def predict_density(self, Fmu, Fvar, Y, epsilon=None): r""" Given a Normal distribution for the latent function, and a datum Y, compute the log predictive density of Y. i.e. if q(f) = N(Fmu, Fvar) and this object represents p(y|f) then this method computes the predictive density \log \int p(y=Y|f)q(f) df Here, we implement a default Monte Carlo routine. """ return self._mc_quadrature(self.logp, Fmu, Fvar, Y=Y, logspace=True, epsilon=epsilon) def variational_expectations(self, Fmu, Fvar, Y, epsilon=None): r""" Compute the expected log density of the data, given a Gaussian distribution for the function values. if q(f) = N(Fmu, Fvar) - Fmu: N x D Fvar: N x D and this object represents p(y|f) - Y: N x 1 then this method computes \int (\log p(y|f)) q(f) df. Here, we implement a default Monte Carlo quadrature routine. """ return self._mc_quadrature(self.logp, Fmu, Fvar, Y=Y, epsilon=epsilon) class GaussianMC(MonteCarloLikelihood, Gaussian): """ Stochastic version of Gaussian likelihood for comparison. """ pass class SoftMax(MonteCarloLikelihood): """ The soft-max multi-class likelihood. """ def __init__(self, num_classes, **kwargs): super().__init__(**kwargs) self.num_classes = num_classes def logp(self, F, Y): with tf.control_dependencies( [ tf.assert_equal(tf.shape(Y)[1], 1), tf.assert_equal(tf.cast(tf.shape(F)[1], settings.int_type), tf.cast(self.num_classes, settings.int_type)) ]): if Y.dtype != np.int32: Y = tf.cast(Y, np.int32) return -tf.nn.sparse_softmax_cross_entropy_with_logits(logits=F, labels=Y[:, 0])[:, None] def conditional_mean(self, F): return tf.nn.softmax(F) def conditional_variance(self, F): p = self.conditional_mean(F) return p - tf.square(p)