Source code for gpflow.mean_functions

# Copyright 2016-2020 The GPflow Contributors. All Rights Reserved.
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"""
Throughout GPflow, by default, latent functions being modelled with Gaussian
processes are assumed to have zero mean, f ~ GP(0, k(x,x')).

In some cases we may wish to model only the deviation from a fixed function
with a Gaussian process.  For flexibility this fixed function could be both
input dependent and parameterised function, μ(x; θ),
with some unknown parameters θ, resulting in f ~ GP(μ(x;θ), k(x,x')).

The GPflow :class:`MeanFunction <gpflow.mean_functions.MeanFunction>` class
allows this to be done whilst additionally learning parameters of the
parametric function.
"""

from typing import Collection, Optional

import numpy as np
import tensorflow as tf

from .base import Module, Parameter, TensorType
from .config import default_float, default_int


[docs]class MeanFunction(Module): """ The base mean function class. To implement a mean function, write the __call__ method. This takes a tensor X and returns a tensor m(X). In accordance with the GPflow standard, each row of X represents one datum, and each row of Y is computed independently for each row of X. MeanFunction classes can have parameters, see the Linear class for an example. """ def __call__(self, X: TensorType) -> tf.Tensor: raise NotImplementedError("Implement the __call__ method for this mean function") def __add__(self, other: "MeanFunction") -> "MeanFunction": return Additive(self, other) def __mul__(self, other: "MeanFunction") -> "MeanFunction": return Product(self, other)
[docs]class Linear(MeanFunction): """ y_i = A x_i + b """ def __init__(self, A: TensorType = None, b: TensorType = None) -> None: """ A is a matrix which maps each element of X to Y, b is an additive constant. If X has N rows and D columns, and Y is intended to have Q columns, then A must be [D, Q], b must be a vector of length Q. """ MeanFunction.__init__(self) A = np.ones((1, 1), dtype=default_float()) if A is None else A b = np.zeros(1, dtype=default_float()) if b is None else b self.A = Parameter(np.atleast_2d(A)) self.b = Parameter(b) def __call__(self, X: TensorType) -> tf.Tensor: return tf.tensordot(X, self.A, [[-1], [0]]) + self.b
[docs]class Identity(Linear): """ y_i = x_i """ # The many type-ignores in this class is because we replace a field in the super class with a # property, which mypy doesn't like. def __init__(self, input_dim: Optional[int] = None) -> None: Linear.__init__(self) self.input_dim = input_dim def __call__(self, X: TensorType) -> tf.Tensor: return X @property def A(self) -> tf.Tensor: # type: ignore if self.input_dim is None: raise ValueError( "An input_dim needs to be specified when using the " "`Identity` mean function in combination with expectations." ) return tf.eye(self.input_dim, dtype=default_float()) @property def b(self) -> tf.Tensor: # type: ignore if self.input_dim is None: raise ValueError( "An input_dim needs to be specified when using the " "`Identity` mean function in combination with expectations." ) return tf.zeros(self.input_dim, dtype=default_float()) @A.setter # type: ignore def A(self, A: tf.Tensor) -> None: pass @b.setter # type: ignore def b(self, b: tf.Tensor) -> None: pass
[docs]class Constant(MeanFunction): def __init__(self, c: TensorType = None) -> None: super().__init__() c = np.zeros(1) if c is None else c self.c = Parameter(c) def __call__(self, X: TensorType) -> tf.Tensor: tile_shape = tf.concat( [tf.shape(X)[:-1], [1]], axis=0, ) reshape_shape = tf.concat( [tf.ones(shape=(tf.rank(X) - 1), dtype=default_int()), [-1]], axis=0, ) return tf.tile(tf.reshape(self.c, reshape_shape), tile_shape)
[docs]class Zero(Constant): def __init__(self, output_dim: int = 1) -> None: Constant.__init__(self) self.output_dim = output_dim del self.c def __call__(self, X: TensorType) -> tf.Tensor: output_shape = tf.concat([tf.shape(X)[:-1], [self.output_dim]], axis=0) return tf.zeros(output_shape, dtype=X.dtype)
[docs]class SwitchedMeanFunction(MeanFunction): """ This class enables to use different (independent) mean_functions respective to the data 'label'. We assume the 'label' is stored in the extra column of X. """ def __init__(self, meanfunction_list: Collection[MeanFunction]) -> None: super().__init__() for m in meanfunction_list: assert isinstance(m, MeanFunction) self.meanfunctions = meanfunction_list def __call__(self, X: TensorType) -> tf.Tensor: ind = tf.gather(tf.transpose(X), tf.shape(X)[1] - 1) # ind = X[:,-1] ind = tf.cast(ind, tf.int32) X = tf.transpose( tf.gather(tf.transpose(X), tf.range(0, tf.shape(X)[1] - 1)) ) # X = X[:,:-1] # split up X into chunks corresponding to the relevant likelihoods x_list = tf.dynamic_partition(X, ind, len(self.meanfunctions)) # apply the likelihood-function to each section of the data results = [m(x) for x, m in zip(x_list, self.meanfunctions)] # stitch the results back together partitions = tf.dynamic_partition(tf.range(0, tf.size(ind)), ind, len(self.meanfunctions)) return tf.dynamic_stitch(partitions, results)
[docs]class Additive(MeanFunction): def __init__(self, first_part: MeanFunction, second_part: MeanFunction) -> None: MeanFunction.__init__(self) self.add_1 = first_part self.add_2 = second_part def __call__(self, X: TensorType) -> tf.Tensor: return tf.add(self.add_1(X), self.add_2(X))
[docs]class Product(MeanFunction): def __init__(self, first_part: MeanFunction, second_part: MeanFunction): MeanFunction.__init__(self) self.prod_1 = first_part self.prod_2 = second_part def __call__(self, X: TensorType) -> tf.Tensor: return tf.multiply(self.prod_1(X), self.prod_2(X))