from copy import deepcopy
from functools import wraps
from sklearn.utils import check_random_state
import numpy as np
from scipy.optimize import OptimizeResult
from scipy.optimize import minimize as sp_minimize
from sklearn.base import is_regressor
from sklearn.ensemble import GradientBoostingRegressor
from joblib import dump as dump_
from joblib import load as load_
from collections import OrderedDict
from .learning import ExtraTreesRegressor
from .learning import GaussianProcessRegressor
from .learning import GradientBoostingQuantileRegressor
from .learning import RandomForestRegressor
from .learning.gaussian_process.kernels import ConstantKernel
from .learning.gaussian_process.kernels import HammingKernel
from .learning.gaussian_process.kernels import Matern
from .sampler import Sobol, Lhs, Hammersly, Halton, Grid
from .sampler import InitialPointGenerator
from .space import Space, Categorical, Integer, Real, Dimension
__all__ = (
"load",
"dump",
)
def create_result(Xi, yi, space=None, rng=None, specs=None, models=None):
"""
Initialize an `OptimizeResult` object.
Parameters
----------
Xi : list of lists, shape (n_iters, n_features)
Location of the minimum at every iteration.
yi : array-like, shape (n_iters,)
Minimum value obtained at every iteration.
space : Space instance, optional
Search space.
rng : RandomState instance, optional
State of the random state.
specs : dict, optional
Call specifications.
models : list, optional
List of fit surrogate models.
Returns
-------
res : `OptimizeResult`, scipy object
OptimizeResult instance with the required information.
"""
res = OptimizeResult()
yi = np.asarray(yi)
if np.ndim(yi) == 2:
res.log_time = np.ravel(yi[:, 1])
yi = np.ravel(yi[:, 0])
best = np.argmin(yi)
res.x = Xi[best]
res.fun = yi[best]
res.func_vals = yi
res.x_iters = Xi
res.models = models
res.space = space
res.random_state = rng
res.specs = specs
return res
def eval_callbacks(callbacks, result):
"""Evaluate list of callbacks on result.
The return values of the `callbacks` are ORed together to give the
overall decision on whether or not the optimization procedure should
continue.
Parameters
----------
callbacks : list of callables
Callbacks to evaluate.
result : `OptimizeResult`, scipy object
Optimization result object to be stored.
Returns
-------
decision : bool
Decision of the callbacks whether or not to keep optimizing
"""
stop = False
if callbacks:
for c in callbacks:
decision = c(result)
if decision is not None:
stop = stop or decision
return stop
[docs]def dump(res, filename, store_objective=True, **kwargs):
"""
Store an skopt optimization result into a file.
Parameters
----------
res : `OptimizeResult`, scipy object
Optimization result object to be stored.
filename : string or `pathlib.Path`
The path of the file in which it is to be stored. The compression
method corresponding to one of the supported filename extensions ('.z',
'.gz', '.bz2', '.xz' or '.lzma') will be used automatically.
store_objective : boolean, default=True
Whether the objective function should be stored. Set `store_objective`
to `False` if your objective function (`.specs['args']['func']`) is
unserializable (i.e. if an exception is raised when trying to serialize
the optimization result).
Notice that if `store_objective` is set to `False`, a deep copy of the
optimization result is created, potentially leading to performance
problems if `res` is very large. If the objective function is not
critical, one can delete it before calling `skopt.dump()` and thus
avoid deep copying of `res`.
**kwargs : other keyword arguments
All other keyword arguments will be passed to `joblib.dump`.
"""
if store_objective:
dump_(res, filename, **kwargs)
elif 'func' in res.specs['args']:
# If the user does not want to store the objective and it is indeed
# present in the provided object, then create a deep copy of it and
# remove the objective function before dumping it with joblib.dump.
res_without_func = deepcopy(res)
del res_without_func.specs['args']['func']
dump_(res_without_func, filename, **kwargs)
else:
# If the user does not want to store the objective and it is already
# missing in the provided object, dump it without copying.
dump_(res, filename, **kwargs)
[docs]def load(filename, **kwargs):
"""
Reconstruct a skopt optimization result from a file
persisted with skopt.dump.
.. note::
Notice that the loaded optimization result can be missing
the objective function (`.specs['args']['func']`) if `skopt.dump`
was called with `store_objective=False`.
Parameters
----------
filename : string or `pathlib.Path`
The path of the file from which to load the optimization result.
**kwargs : other keyword arguments
All other keyword arguments will be passed to `joblib.load`.
Returns
-------
res : `OptimizeResult`, scipy object
Reconstructed OptimizeResult instance.
"""
return load_(filename, **kwargs)
def is_listlike(x):
return isinstance(x, (list, tuple))
def is_2Dlistlike(x):
return np.all([is_listlike(xi) for xi in x])
def check_x_in_space(x, space):
if is_2Dlistlike(x):
if not np.all([p in space for p in x]):
raise ValueError("Not all points are within the bounds of"
" the space.")
if any([len(p) != len(space.dimensions) for p in x]):
raise ValueError("Not all points have the same dimensions as"
" the space.")
elif is_listlike(x):
if x not in space:
raise ValueError("Point (%s) is not within the bounds of"
" the space (%s)."
% (x, space.bounds))
if len(x) != len(space.dimensions):
raise ValueError("Dimensions of point (%s) and space (%s) do not match"
% (x, space.bounds))
[docs]def expected_minimum(res, n_random_starts=20, random_state=None):
"""Compute the minimum over the predictions of the last surrogate model.
Uses `expected_minimum_random_sampling` with `n_random_starts` = 100000,
when the space contains any categorical values.
.. note::
The returned minimum may not necessarily be an accurate
prediction of the minimum of the true objective function.
Parameters
----------
res : `OptimizeResult`, scipy object
The optimization result returned by a `skopt` minimizer.
n_random_starts : int, default=20
The number of random starts for the minimization of the surrogate
model.
random_state : int, RandomState instance, or None (default)
Set random state to something other than None for reproducible
results.
Returns
-------
x : list
location of the minimum.
fun : float
the surrogate function value at the minimum.
"""
if res.space.is_partly_categorical:
return expected_minimum_random_sampling(res, n_random_starts=100000,
random_state=random_state)
def func(x):
reg = res.models[-1]
x = res.space.transform(x.reshape(1, -1))
return reg.predict(x.reshape(1, -1))[0]
xs = [res.x]
if n_random_starts > 0:
xs.extend(res.space.rvs(n_random_starts, random_state=random_state))
best_x = None
best_fun = np.inf
for x0 in xs:
r = sp_minimize(func, x0=x0, bounds=res.space.bounds)
if r.fun < best_fun:
best_x = r.x
best_fun = r.fun
return [v for v in best_x], best_fun
[docs]def expected_minimum_random_sampling(res, n_random_starts=100000,
random_state=None):
"""Minimum search by doing naive random sampling, Returns the parameters
that gave the minimum function value. Can be used when the space
contains any categorical values.
.. note::
The returned minimum may not necessarily be an accurate
prediction of the minimum of the true objective function.
Parameters
----------
res : `OptimizeResult`, scipy object
The optimization result returned by a `skopt` minimizer.
n_random_starts : int, default=100000
The number of random starts for the minimization of the surrogate
model.
random_state : int, RandomState instance, or None (default)
Set random state to something other than None for reproducible
results.
Returns
-------
x : list
location of the minimum.
fun : float
the surrogate function value at the minimum.
"""
# sample points from search space
random_samples = res.space.rvs(n_random_starts, random_state=random_state)
# make estimations with surrogate
model = res.models[-1]
y_random = model.predict(res.space.transform(random_samples))
index_best_objective = np.argmin(y_random)
min_x = random_samples[index_best_objective]
return min_x, y_random[index_best_objective]
def has_gradients(estimator):
"""
Check if an estimator's ``predict`` method provides gradients.
Parameters
----------
estimator :
sklearn BaseEstimator instance.
"""
tree_estimators = (
ExtraTreesRegressor, RandomForestRegressor,
GradientBoostingQuantileRegressor
)
# cook_estimator() returns None for "dummy minimize" aka random values only
if estimator is None:
return False
if isinstance(estimator, tree_estimators):
return False
categorical_gp = False
if hasattr(estimator, "kernel"):
params = estimator.get_params()
categorical_gp = (
isinstance(estimator.kernel, HammingKernel) or
any([isinstance(params[p], HammingKernel) for p in params])
)
return not categorical_gp
[docs]def cook_estimator(base_estimator, space=None, **kwargs):
"""Cook a default estimator.
For the special base_estimator called "DUMMY" the return value is None.
This corresponds to sampling points at random, hence there is no need
for an estimator.
Parameters
----------
base_estimator : "GP", "RF", "ET", "GBRT", "DUMMY" or sklearn regressor
Should inherit from `sklearn.base.RegressorMixin`.
In addition the `predict` method should have an optional `return_std`
argument, which returns `std(Y | x)`` along with `E[Y | x]`.
If base_estimator is one of ["GP", "RF", "ET", "GBRT", "DUMMY"], a
surrogate model corresponding to the relevant `X_minimize` function
is created.
space : Space instance
Has to be provided if the base_estimator is a gaussian process.
Ignored otherwise.
kwargs : dict
Extra parameters provided to the base_estimator at init time.
"""
if isinstance(base_estimator, str):
base_estimator = base_estimator.upper()
if base_estimator not in ["GP", "ET", "RF", "GBRT", "DUMMY"]:
raise ValueError("Valid strings for the base_estimator parameter "
" are: 'RF', 'ET', 'GP', 'GBRT' or 'DUMMY' not "
"%s." % base_estimator)
elif not is_regressor(base_estimator):
raise ValueError("base_estimator has to be a regressor.")
if base_estimator == "GP":
if space is not None:
space = Space(space)
space = Space(normalize_dimensions(space.dimensions))
n_dims = space.transformed_n_dims
is_cat = space.is_categorical
else:
raise ValueError("Expected a Space instance, not None.")
cov_amplitude = ConstantKernel(1.0, (0.01, 1000.0))
# only special if *all* dimensions are categorical
if is_cat:
other_kernel = HammingKernel(length_scale=np.ones(n_dims))
else:
other_kernel = Matern(
length_scale=np.ones(n_dims),
length_scale_bounds=[(0.01, 100)] * n_dims, nu=2.5)
base_estimator = GaussianProcessRegressor(
kernel=cov_amplitude * other_kernel,
normalize_y=True, noise="gaussian",
n_restarts_optimizer=2)
elif base_estimator == "RF":
base_estimator = RandomForestRegressor(n_estimators=100,
min_samples_leaf=3)
elif base_estimator == "ET":
base_estimator = ExtraTreesRegressor(n_estimators=100,
min_samples_leaf=3)
elif base_estimator == "GBRT":
gbrt = GradientBoostingRegressor(n_estimators=30, loss="quantile")
base_estimator = GradientBoostingQuantileRegressor(base_estimator=gbrt)
elif base_estimator == "DUMMY":
return None
if ('n_jobs' in kwargs.keys()) and not hasattr(base_estimator, 'n_jobs'):
del kwargs['n_jobs']
base_estimator.set_params(**kwargs)
return base_estimator
[docs]def cook_initial_point_generator(generator, **kwargs):
"""Cook a default initial point generator.
For the special generator called "random" the return value is None.
Parameters
----------
generator : "lhs", "sobol", "halton", "hammersly", "grid", "random" \
or InitialPointGenerator instance"
Should inherit from `skopt.sampler.InitialPointGenerator`.
kwargs : dict
Extra parameters provided to the generator at init time.
"""
if generator is None:
generator = "random"
elif isinstance(generator, str):
generator = generator.lower()
if generator not in ["sobol", "halton", "hammersly", "lhs", "random",
"grid"]:
raise ValueError("Valid strings for the generator parameter "
" are: 'sobol', 'lhs', 'halton', 'hammersly',"
"'random', or 'grid' not "
"%s." % generator)
elif not isinstance(generator, InitialPointGenerator):
raise ValueError("generator has to be an InitialPointGenerator."
"Got %s" % (str(type(generator))))
if isinstance(generator, str):
if generator == "sobol":
generator = Sobol()
elif generator == "halton":
generator = Halton()
elif generator == "hammersly":
generator = Hammersly()
elif generator == "lhs":
generator = Lhs()
elif generator == "grid":
generator = Grid()
elif generator == "random":
return None
generator.set_params(**kwargs)
return generator
[docs]def dimensions_aslist(search_space):
"""Convert a dict representation of a search space into a list of
dimensions, ordered by sorted(search_space.keys()).
Parameters
----------
search_space : dict
Represents search space. The keys are dimension names (strings)
and values are instances of classes that inherit from the class
:class:`skopt.space.Dimension` (Real, Integer or Categorical)
Returns
-------
params_space_list: list
list of skopt.space.Dimension instances.
Examples
--------
>>> from skopt.space.space import Real, Integer
>>> from skopt.utils import dimensions_aslist
>>> search_space = {'name1': Real(0,1),
... 'name2': Integer(2,4), 'name3': Real(-1,1)}
>>> dimensions_aslist(search_space)[0]
Real(low=0, high=1, prior='uniform', transform='identity')
>>> dimensions_aslist(search_space)[1]
Integer(low=2, high=4, prior='uniform', transform='identity')
>>> dimensions_aslist(search_space)[2]
Real(low=-1, high=1, prior='uniform', transform='identity')
"""
params_space_list = [
search_space[k] for k in sorted(search_space.keys())
]
return params_space_list
[docs]def point_asdict(search_space, point_as_list):
"""Convert the list representation of a point from a search space
to the dictionary representation, where keys are dimension names
and values are corresponding to the values of dimensions in the list.
.. seealso:: :class:`skopt.utils.point_aslist`
Parameters
----------
search_space : dict
Represents search space. The keys are dimension names (strings)
and values are instances of classes that inherit from the class
:class:`skopt.space.Dimension` (Real, Integer or Categorical)
point_as_list : list
list with parameter values.The order of parameters in the list
is given by sorted(params_space.keys()).
Returns
-------
params_dict : OrderedDict
dictionary with parameter names as keys to which
corresponding parameter values are assigned.
Examples
--------
>>> from skopt.space.space import Real, Integer
>>> from skopt.utils import point_asdict
>>> search_space = {'name1': Real(0,1),
... 'name2': Integer(2,4), 'name3': Real(-1,1)}
>>> point_as_list = [0.66, 3, -0.15]
>>> point_asdict(search_space, point_as_list)
OrderedDict([('name1', 0.66), ('name2', 3), ('name3', -0.15)])
"""
params_dict = OrderedDict()
for k, v in zip(sorted(search_space.keys()), point_as_list):
params_dict[k] = v
return params_dict
[docs]def point_aslist(search_space, point_as_dict):
"""Convert a dictionary representation of a point from a search space to
the list representation. The list of values is created from the values of
the dictionary, sorted by the names of dimensions used as keys.
.. seealso:: :class:`skopt.utils.point_asdict`
Parameters
----------
search_space : dict
Represents search space. The keys are dimension names (strings)
and values are instances of classes that inherit from the class
:class:`skopt.space.Dimension` (Real, Integer or Categorical)
point_as_dict : dict
dict with parameter names as keys to which corresponding
parameter values are assigned.
Returns
-------
point_as_list : list
list with point values.The order of
parameters in the list is given by sorted(params_space.keys()).
Examples
--------
>>> from skopt.space.space import Real, Integer
>>> from skopt.utils import point_aslist
>>> search_space = {'name1': Real(0,1),
... 'name2': Integer(2,4), 'name3': Real(-1,1)}
>>> point_as_dict = {'name1': 0.66, 'name2': 3, 'name3': -0.15}
>>> point_aslist(search_space, point_as_dict)
[0.66, 3, -0.15]
"""
point_as_list = [
point_as_dict[k] for k in sorted(search_space.keys())
]
return point_as_list
def normalize_dimensions(dimensions):
"""Create a ``Space`` where all dimensions are normalized to unit range.
This is particularly useful for Gaussian process based regressors and is
used internally by ``gp_minimize``.
Parameters
----------
dimensions : list, shape (n_dims,)
List of search space dimensions.
Each search dimension can be defined either as
- a `(lower_bound, upper_bound)` tuple (for `Real` or `Integer`
dimensions),
- a `(lower_bound, upper_bound, "prior")` tuple (for `Real`
dimensions),
- as a list of categories (for `Categorical` dimensions), or
- an instance of a `Dimension` object (`Real`, `Integer` or
`Categorical`).
NOTE: The upper and lower bounds are inclusive for `Integer`
dimensions.
"""
space = Space(dimensions)
transformed_dimensions = []
for dimension in space.dimensions:
# check if dimension is of a Dimension instance
if isinstance(dimension, Dimension):
# Change the transformer to normalize
# and add it to the new transformed dimensions
dimension.set_transformer("normalize")
transformed_dimensions.append(
dimension
)
else:
raise RuntimeError("Unknown dimension type "
"(%s)" % type(dimension))
return Space(transformed_dimensions)
def check_list_types(x, types):
"""
Check whether all elements of a list `x` are of the correct type(s)
and raise a ValueError if they are not.
Note that `types` can be either a single object-type or a tuple
of object-types.
Raises `ValueError`, If one or more element in the list `x` is
not of the correct type(s).
Parameters
----------
x : list
List of objects.
types : object or list(object)
Either a single object-type or a tuple of object-types.
"""
# List of the elements in the list that are incorrectly typed.
err = list(filter(lambda a: not isinstance(a, types), x))
# If the list is non-empty then raise an exception.
if len(err) > 0:
msg = "All elements in list must be instances of {}, but found: {}"
msg = msg.format(types, err)
raise ValueError(msg)
def check_dimension_names(dimensions):
"""
Check whether all dimensions have names. Raises `ValueError`,
if one or more dimensions are unnamed.
Parameters
----------
dimensions : list(Dimension)
List of Dimension-objects.
"""
# List of the dimensions that have no names.
err_dims = list(filter(lambda dim: dim.name is None, dimensions))
# If the list is non-empty then raise an exception.
if len(err_dims) > 0:
msg = "All dimensions must have names, but found: {}"
msg = msg.format(err_dims)
raise ValueError(msg)
[docs]def use_named_args(dimensions):
"""
Wrapper / decorator for an objective function that uses named arguments
to make it compatible with optimizers that use a single list of parameters.
Your objective function can be defined as being callable using named
arguments: `func(foo=123, bar=3.0, baz='hello')` for a search-space
with dimensions named `['foo', 'bar', 'baz']`. But the optimizer
will only pass a single list `x` of unnamed arguments when calling
the objective function: `func(x=[123, 3.0, 'hello'])`. This wrapper
converts your objective function with named arguments into one that
accepts a list as argument, while doing the conversion automatically.
The advantage of this is that you don't have to unpack the list of
arguments `x` yourself, which makes the code easier to read and
also reduces the risk of bugs if you change the number of dimensions
or their order in the search-space.
Examples
--------
>>> # Define the search-space dimensions. They must all have names!
>>> from skopt.space import Real
>>> from skopt import forest_minimize
>>> from skopt.utils import use_named_args
>>> dim1 = Real(name='foo', low=0.0, high=1.0)
>>> dim2 = Real(name='bar', low=0.0, high=1.0)
>>> dim3 = Real(name='baz', low=0.0, high=1.0)
>>>
>>> # Gather the search-space dimensions in a list.
>>> dimensions = [dim1, dim2, dim3]
>>>
>>> # Define the objective function with named arguments
>>> # and use this function-decorator to specify the
>>> # search-space dimensions.
>>> @use_named_args(dimensions=dimensions)
... def my_objective_function(foo, bar, baz):
... return foo ** 2 + bar ** 4 + baz ** 8
>>>
>>> # Not the function is callable from the outside as
>>> # `my_objective_function(x)` where `x` is a list of unnamed arguments,
>>> # which then wraps your objective function that is callable as
>>> # `my_objective_function(foo, bar, baz)`.
>>> # The conversion from a list `x` to named parameters `foo`,
>>> # `bar`, `baz`
>>> # is done automatically.
>>>
>>> # Run the optimizer on the wrapped objective function which is called
>>> # as `my_objective_function(x)` as expected by `forest_minimize()`.
>>> result = forest_minimize(func=my_objective_function,
... dimensions=dimensions,
... n_calls=20, base_estimator="ET",
... random_state=4)
>>>
>>> # Print the best-found results in same format as the expected result.
>>> print("Best fitness: " + str(result.fun))
Best fitness: 0.1948080835239698
>>> print("Best parameters: {}".format(result.x))
Best parameters: [0.44134853091052617, 0.06570954323368307, 0.17586123323419825]
Parameters
----------
dimensions : list(Dimension)
List of `Dimension`-objects for the search-space dimensions.
Returns
-------
wrapped_func : callable
Wrapped objective function.
"""
def decorator(func):
"""
This uses more advanced Python features to wrap `func` using a
function-decorator, which are not explained so well in the
official Python documentation.
A good video tutorial explaining how this works is found here:
https://www.youtube.com/watch?v=KlBPCzcQNU8
Parameters
----------
func : callable
Function to minimize. Should take *named arguments*
and return the objective value.
"""
# Ensure all dimensions are correctly typed.
check_list_types(dimensions, Dimension)
# Ensure all dimensions have names.
check_dimension_names(dimensions)
@wraps(func)
def wrapper(x):
"""
This is the code that will be executed every time the
wrapped / decorated `func` is being called.
It takes `x` as a single list of parameters and
converts them to named arguments and calls `func` with them.
Parameters
----------
x : list
A single list of parameters e.g. `[123, 3.0, 'linear']`
which will be converted to named arguments and passed
to `func`.
Returns
-------
objective_value
The objective value returned by `func`.
"""
# Ensure the number of dimensions match
# the number of parameters in the list x.
if len(x) != len(dimensions):
msg = "Mismatch in number of search-space dimensions. " \
"len(dimensions)=={} and len(x)=={}"
msg = msg.format(len(dimensions), len(x))
raise ValueError(msg)
# Create a dict where the keys are the names of the dimensions
# and the values are taken from the list of parameters x.
arg_dict = {dim.name: value for dim, value in zip(dimensions, x)}
# Call the wrapped objective function with the named arguments.
objective_value = func(**arg_dict)
return objective_value
return wrapper
return decorator
