1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272
|
"""
Customize your Metropolis-Hastings algorithm
============================================
This simple example shows how you can build your own variant
of the Metropolis-Hastings algorithm.
"""
# %%
# We want to sample from the distribution with support :math:`[-3, 3]^2`
# whose PDF :math:`f` is proportional to the Ackley function to the tenth power:
#
# .. math::
# \forall \vect{x} \in [-3, 3]^2 \quad f(\vect{x}) \propto a(\vect{x})^{10},
#
# where :math:`a` is the Ackey function defined in :ref:`use-case-ackley` page.
# In the following we call it the "Ackley distribution".
import openturns as ot
import openturns.viewer as otv
from openturns.usecases import ackley_function
from numpy import exp, format_float_scientific
ot.RandomGenerator.SetSeed(100)
# %%
# Prepare the Metropolis-Hastings algorithm
# -----------------------------------------
# Define the Ackley distribution support and density (up to a constant factor).
am = ackley_function.AckleyModel()
ackley = am.model
power10 = ot.SymbolicFunction("x", "x^10")
ackley_pdf = ot.ComposedFunction(power10, ackley)
logarithm = ot.SymbolicFunction("x", "10 * log(x)")
ackley_logpdf = ot.ComposedFunction(logarithm, ackley)
lb = -3.0
ub = 3.0
support = ot.Interval([lb] * 2, [ub] * 2)
# %%
# Define the proposal distribution as a :class:`~openturns.Histogram`.
# Its ticks (on the X axis of the PDF of the histogram) will remain the same,
# but its frequencies (on the Y axis) will be updated
# during the course of the Metropolis-Hastings algorithm.
n_bins = 50
myticks = ot.RegularGrid(lb, (ub - lb) / n_bins, n_bins + 1).getValues()
frequencies = [1.0] * (myticks.getSize() - 1)
proposal = ot.Histogram(myticks, frequencies)
# %%
# The state of the Markov chain must be converted to an acceptable set
# of parameters for the :class:`~openturns.Histogram` distribution.
# This is the job of the *link function*,
# which we construct with the :class:`~openturns.OpenTURNSPythonFunction` class.
# It takes a state as input and outputs the parameters (ticks and frequencies)
# of the proposal distribution.
# In our case, the ticks will not depend on the inputs,
# but the frequencies will be outputs of the Ackley function.
parameter_dim = proposal.getParameter().getSize()
parameter_desc = proposal.getParameterDescription()
class ConditionalAckley(ot.OpenTURNSPythonFunction):
"""
When executed, this function returns the parameters of a Histogram
which approximates the conditional Ackley distribution obtained
when one of the 2 coordinates is fixed.
To compute the frequencies of the Histogram,
this OpenTURNSPythonFunction computes the values of the Ackley function
on a regular grid on the line parallel to
either the (1, 0) vector (if the second coordinate is fixed)
or the (0, 1) vector (if the first coordinate is fixed)
containing the point passed as input.
The regular grid covers the part of this line which is contained in
the support of the Ackley distribution, implicitly defined as the
smallest square that contains the cartesian product of the regular grid
with itself. For example, if the regular grid covers the interval [-3, 3],
then the support is the square [-3, 3] x [-3, 3].
Parameters
----------
marginal : int
The marginal whose value is *not* fixed.
If 0, then the line of the regular grid is parallel to the (1, 0) vector.
If 1, then the line of the regular grid is parallel to the (0, 1) vector.
ticks : RegularGrid
Ticks of the Histogram distribution.
"""
def __init__(self, marginal, ticks):
super().__init__(2, parameter_dim)
self.setInputDescription(["X0", "X1"]) # input: X0 and X1 coordinates
self.setOutputDescription(parameter_desc) # output: parameters of the Histogram
self._marginal = marginal # parameter which does not vary after initialization
offset = (ticks[1] - ticks[0]) / 2
self._marginal_inputs = ot.Sample.BuildFromPoint(ticks)[0:-1] + offset
# _marginal_inputs contains the varying coordinate of the points in the regular grid
self._size = self._marginal_inputs.getSize()
self._ticks = ticks
def _exec(self, X):
"""
Execute the function on a point X = (X0, X1).
Parameters
----------
X : list of 2 floats
Point through which the line containing the regular grid passes.
Returns
-------
parameters : :class:`~openturns.Point`
Parameters of the :class:`~openturns.Histogram`.
"""
inputs = ot.Sample(self._size, X) # sample of inputs for the Ackley function
# All input points are initialized at the point X passed as argument.
# Replace the varying coordinate with the values of the regular grid.
inputs[:, self._marginal] = self._marginal_inputs
# Compute the Ackley function on these inputs.
outputs = exp(ackley_logpdf(inputs).asPoint())
# The outputs are the unnormalized frequencies of the Histogram
# proposal distribution, but the Histogram.setParameter() method
# expects a full set of parameters.
# The easiest way to provide it is to construct a new Histogram object
# with the adequate frequencies and call its getParameter() method.
return ot.Histogram(self._ticks, outputs).getParameter()
# %%
# The 2 components of the state of the Markov chain will be updated
# one after the other, not simultaneously.
# We define 2 :class:`~openturns.UserDefinedMetropolisHastings` algorithms
# encapsulated within a :class:`~openturns.Gibbs` algorithm,
# so we need 2 link functions, each corresponding to one of the marginals
# of the Ackley distribution.
#
# Note that thanks to the :class:`~openturns.OpenTURNSPythonFunction` class,
# we were able to only code one template to be used by two different functions
# instead of directly coding two functions with the :class:`~openturns.PythonFunction` class.
link_function_0 = ot.Function(ConditionalAckley(0, myticks))
link_function_1 = ot.Function(ConditionalAckley(1, myticks))
# %%
# Let us illustrate the first of these functions.
# We can start by evaluating it at :math:`(0.5, 1.5)`.
# Let :math:`(X_0, X_1)` be a bidimensional random variable
# following the Ackley distribution.
# The output is the set of parameters for a :class:`~openturns.Histogram`
# distribution that approximates the distribution of :math:`X_0`
# conditional on :math:`X_1 = 1.5`.
# Let us update the Histogram we created before with this set of parameters.
par = link_function_0([0.5, 1.5])
proposal.setParameter(par)
print(par)
# %%
# The `link_function_0` function computes histogram frequencies proportional
# to the values of the unnormalized Ackley distribution PDF
# along the :math:`X_1 = 1.5` line.
title = "Ackley PDF (up to a constant factor) and $X_1 = 1.5$ cross-section"
graph = ot.Graph(title, "$X_0$", "$X_1$", True)
line = ot.Curve([[-3, 1.5], [3, 1.5]], "black", "dashed", 2)
graph.add(line)
contour = ackley_pdf.draw([lb] * 2, [ub] * 2).getDrawable(0).getImplementation()
contour.setLabels(
[format_float_scientific(float(v), precision=1) for v in contour.getLabels()]
)
contour.setColorMapNorm("log")
graph.add(contour)
view = otv.View(graph)
# %%
# Let us compare the histogram to the unnormalized PDF
# (we still need to rescale it to make it appear properly on the graph).
scaling = ot.SymbolicFunction("x", "1.3e-10 * x")
scaled_ackley_pdf = ot.ComposedFunction(scaling, ackley_pdf)
graph = proposal.drawPDF()
graph.setXTitle("")
graph.add(scaled_ackley_pdf.draw(0, 0, [0.0, 1.5], -3.0, 3.0, 100))
graph.setTitle("Conditional distribution of $X_0$ given $X_1 = 1.5$")
_ = otv.View(graph)
# %%
# Let us now do the same think with `link_function_1`.
# This time, the relevant cross-section is along the line :math:`X_1 = 0.5`.
par = link_function_1([0.5, 1.5])
proposal.setParameter(par)
print(par)
title = "Ackley PDF (up to a constant factor) and $X_0 = 0.5$ cross-section"
graph = ot.Graph(title, "$X_0$", "$X_1$", True)
line = ot.Curve([[0.5, -3], [0.5, 3]], "black", "dashed", 2)
graph.add(line)
graph.setLegendPosition("upper right")
contour = ackley_pdf.draw([lb] * 2, [ub] * 2).getDrawable(0).getImplementation()
contour.setLabels(
[format_float_scientific(float(v), precision=1) for v in contour.getLabels()]
)
contour.setColorMapNorm("log")
graph.add(contour)
view = otv.View(graph)
scaling = ot.SymbolicFunction("x", "3.1e-10 * x")
scaled_ackley_pdf = ot.ComposedFunction(scaling, ackley_pdf)
graph = proposal.drawPDF()
graph.setXTitle("")
graph.add(scaled_ackley_pdf.draw(1, 0, [0.5, 0.0], -3.0, 3.0, 100))
graph.setTitle("Conditional distribution of $X_1$ given $X_0 = 0.5$")
_ = otv.View(graph)
# %%
# We now choose the initial state of the Markov chain.
initialState = [0.1] * 2
# %%
# Sample from the Ackley distribution
# -----------------------------------
# We can finally define the two Metropolis-Hastings algorithms
# and the Gibbs algorithm which encapsulates them.
gmh_0 = ot.UserDefinedMetropolisHastings(
ackley_logpdf, support, initialState, proposal, link_function_0, [0]
)
gmh_1 = ot.UserDefinedMetropolisHastings(
ackley_logpdf, support, initialState, proposal, link_function_1, [1]
)
gibbs = ot.Gibbs([gmh_0, gmh_1])
sample = gibbs.getSample(100)
# %%
# Print the acceptance rates of the two Metropolis-Hastings samplers
mhlist = gibbs.getMetropolisHastingsCollection()
rate_gmh_0 = mhlist[0].getAcceptanceRate()
rate_gmh_1 = mhlist[1].getAcceptanceRate()
print("Acceptance rates: {} and {}".format(rate_gmh_0, rate_gmh_1))
# %%
# Draw the contour plot of the Ackley distribution PDF (up to a multiplicative constant)
# and the MCMC sample: we can see the sample is accurate.
title = "Ackley PDF (up to a constant factor) and Metropolis-Hastings sample"
graph = ot.Graph(title, "$X_0$", "$X_1$", True)
contour = ackley_pdf.draw([lb] * 2, [ub] * 2).getDrawable(0).getImplementation()
contour.setLabels(
[format_float_scientific(float(v), precision=1) for v in contour.getLabels()]
)
print(contour.getLabels())
contour.setColorMapNorm("log")
graph.add(contour)
graph.add(ot.Cloud(sample, "black", "plus"))
view = otv.View(graph)
# %%
# Display all figures
otv.View.ShowAll()
|