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
|
"""
==========================================
Comparing initial point generation methods
==========================================
Holger Nahrstaedt 2020
.. currentmodule:: skopt
Bayesian optimization or sequential model-based optimization uses a surrogate
model to model the expensive to evaluate function `func`. There are several
choices for what kind of surrogate model to use. This notebook compares the
performance of:
* Halton sequence,
* Hammersly sequence,
* Sobol' sequence and
* Latin hypercube sampling
as initial points. The purely random point generation is used as
a baseline.
"""
print(__doc__)
import numpy as np
np.random.seed(123)
import matplotlib.pyplot as plt
from skopt.benchmarks import hart6 as hart6_
#############################################################################
# Toy model
# =========
#
# We will use the :class:`benchmarks.hart6` function as toy model for the expensive function.
# In a real world application this function would be unknown and expensive
# to evaluate.
# redefined `hart6` to allow adding arbitrary "noise" dimensions
def hart6(x, noise_level=0.0):
return hart6_(x[:6]) + noise_level * np.random.randn()
from skopt.benchmarks import branin as _branin
def branin(x, noise_level=0.0):
return _branin(x) + noise_level * np.random.randn()
#############################################################################
import time
from matplotlib.pyplot import cm
from skopt import gp_minimize
def plot_convergence(
result_list, true_minimum=None, yscale=None, title="Convergence plot"
):
ax = plt.gca()
ax.set_title(title)
ax.set_xlabel("Number of calls $n$")
ax.set_ylabel(r"$\min f(x)$ after $n$ calls")
ax.grid()
if yscale is not None:
ax.set_yscale(yscale)
colors = cm.hsv(np.linspace(0.25, 1.0, len(result_list)))
for results, color in zip(result_list, colors):
name, results = results
n_calls = len(results[0].x_iters)
iterations = range(1, n_calls + 1)
mins = [[np.min(r.func_vals[:i]) for i in iterations] for r in results]
ax.plot(iterations, np.mean(mins, axis=0), c=color, label=name)
# ax.errorbar(iterations, np.mean(mins, axis=0),
# yerr=np.std(mins, axis=0), c=color, label=name)
if true_minimum:
ax.axhline(true_minimum, linestyle="--", color="r", lw=1, label="True minimum")
ax.legend(loc="best")
return ax
def run(minimizer, initial_point_generator, n_initial_points=10, n_repeats=1):
return [
minimizer(
func,
bounds,
n_initial_points=n_initial_points,
initial_point_generator=initial_point_generator,
n_calls=n_calls,
random_state=n,
)
for n in range(n_repeats)
]
def run_measure(initial_point_generator, n_initial_points=10):
start = time.time()
# n_repeats must set to a much higher value to obtain meaningful results.
n_repeats = 1
res = run(
gp_minimize,
initial_point_generator,
n_initial_points=n_initial_points,
n_repeats=n_repeats,
)
duration = time.time() - start
print("%s: %.2f s" % (initial_point_generator, duration))
return res
#############################################################################
# Objective
# =========
#
# The objective of this example is to find one of these minima in as
# few iterations as possible. One iteration is defined as one call
# to the :class:`benchmarks.hart6` function.
#
# We will evaluate each model several times using a different seed for the
# random number generator. Then compare the average performance of these
# models. This makes the comparison more robust against models that get
# "lucky".
from functools import partial
example = "hart6"
if example == "hart6":
func = partial(hart6, noise_level=0.1)
bounds = [
(0.0, 1.0),
] * 6
true_minimum = -3.32237
n_calls = 30
n_initial_points = 10
yscale = None
title = "Convergence plot - hart6"
else:
func = partial(branin, noise_level=2.0)
bounds = [(-5.0, 10.0), (0.0, 15.0)]
true_minimum = 0.397887
n_calls = 30
n_initial_points = 10
yscale = "log"
title = "Convergence plot - branin"
#############################################################################
from skopt.utils import cook_initial_point_generator
# Random search
dummy_res = run_measure("random", n_initial_points)
lhs = cook_initial_point_generator("lhs", lhs_type="classic", criterion=None)
lhs_res = run_measure(lhs, n_initial_points)
lhs2 = cook_initial_point_generator("lhs", criterion="maximin")
lhs2_res = run_measure(lhs2, n_initial_points)
sobol = cook_initial_point_generator("sobol", randomize=False, min_skip=1, max_skip=100)
sobol_res = run_measure(sobol, n_initial_points)
halton_res = run_measure("halton", n_initial_points)
hammersly_res = run_measure("hammersly", n_initial_points)
grid_res = run_measure("grid", n_initial_points)
#############################################################################
# Note that this can take a few minutes.
plot = plot_convergence(
[
("random", dummy_res),
("lhs", lhs_res),
("lhs_maximin", lhs2_res),
("sobol'", sobol_res),
("halton", halton_res),
("hammersly", hammersly_res),
("grid", grid_res),
],
true_minimum=true_minimum,
yscale=yscale,
title=title,
)
plt.show()
#############################################################################
# This plot shows the value of the minimum found (y axis) as a function
# of the number of iterations performed so far (x axis). The dashed red line
# indicates the true value of the minimum of the :class:`benchmarks.hart6`
# function.
#############################################################################
# Test with different n_random_starts values
lhs2 = cook_initial_point_generator("lhs", criterion="maximin")
lhs2_15_res = run_measure(lhs2, 12)
lhs2_20_res = run_measure(lhs2, 14)
lhs2_25_res = run_measure(lhs2, 16)
#############################################################################
# n_random_starts = 10 produces the best results
plot = plot_convergence(
[
("random - 10", dummy_res),
("lhs_maximin - 10", lhs2_res),
("lhs_maximin - 12", lhs2_15_res),
("lhs_maximin - 14", lhs2_20_res),
("lhs_maximin - 16", lhs2_25_res),
],
true_minimum=true_minimum,
yscale=yscale,
title=title,
)
plt.show()
|