logdensities.py
``````# Copyright 2016 James Hensman, alexggmatthews
#
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#
# Unless required by applicable law or agreed to in writing, software
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and

import tensorflow as tf
import numpy as np

from . import settings

logger = settings.logger()

def gaussian(x, mu, var):
return -0.5 * (np.log(2 * np.pi) + tf.log(var) + tf.square(mu-x) / var)

def lognormal(x, mu, var):
lnx = tf.log(x)
return gaussian(lnx, mu, var) - lnx

def bernoulli(x, p):
return tf.log(tf.where(tf.equal(x, 1), p, 1-p))

def poisson(x, lam):
return x * tf.log(lam) - lam - tf.lgamma(x + 1.)

def exponential(x, scale):
return - x/scale - tf.log(scale)

def gamma(x, shape, scale):
return -shape * tf.log(scale) - tf.lgamma(shape) \
+ (shape - 1.) * tf.log(x) - x / scale

def student_t(x, mean, scale, df):
df = tf.cast(df, settings.float_type)
const = tf.lgamma((df + 1.) * 0.5) - tf.lgamma(df * 0.5) \
- 0.5 * (tf.log(tf.square(scale)) + tf.log(df) + np.log(np.pi))
const = tf.cast(const, settings.float_type)
return const - 0.5 * (df + 1.) * \
tf.log(1. + (1. / df) * (tf.square((x - mean) / scale)))

def beta(x, alpha, beta):
# need to clip x, since log of 0 is nan...
x = tf.clip_by_value(x, 1e-6, 1-1e-6)
return (alpha - 1.) * tf.log(x) + (beta - 1.) * tf.log(1. - x) \
+ tf.lgamma(alpha + beta)\
- tf.lgamma(alpha)\
- tf.lgamma(beta)

def laplace(x, mu, sigma):
return - tf.abs(mu - x) / sigma - tf.log(2. * sigma)

def multivariate_normal(x, mu, L):
"""
Computes the log-density of a multivariate normal.
:param x  : Dx1 or DxN sample(s) for which we want the density
:param mu : Dx1 or DxN mean(s) of the normal distribution
:param L  : DxD Cholesky decomposition of the covariance matrix
:return p : (1,) or (N,) vector of log densities for each of the N x's and/or mu's

x and mu are either vectors or matrices. If both are vectors (N,1):
p[0] = log pdf(x) where x ~ N(mu, LL^T)
If at least one is a matrix, we assume independence over the *columns*:
the number of rows must match the size of L. Broadcasting behaviour:
p[n] = log pdf of:
x[n] ~ N(mu, LL^T) or x ~ N(mu[n], LL^T) or x[n] ~ N(mu[n], LL^T)
"""
mu_ndims = mu.shape.ndims
x_ndims = x.shape.ndims
if x_ndims is not None and x_ndims != 2:
raise ValueError('Shape of x must be 2D.')
if mu_ndims is not None and mu_ndims != 2:
raise ValueError('Shape of mu must be 2D.')

d = x - mu
alpha = tf.matrix_triangular_solve(L, d, lower=True)
num_dims = tf.cast(tf.shape(d)[0], L.dtype)
p = - 0.5 * tf.reduce_sum(tf.square(alpha), 0)
p -= 0.5 * num_dims * np.log(2 * np.pi)
p -= tf.reduce_sum(tf.log(tf.matrix_diag_part(L)))
return p
``````