def set_probabilities_in_cs(self, cs: ConfigurationSpace,
relied2models: Dict[str, List[str]],
relied2AllModels: Dict[str, List[str]],
all_models: List[str], **kwargs):
estimator = cs.get_hyperparameter("estimator:__choice__")
probabilities = []
model2prob = {}
L = 0
for rely_model in relied2models:
cur_models = relied2models[rely_model]
L += len(cur_models)
for model in cur_models:
model2prob[model] = kwargs[rely_model] / len(cur_models)
p_rest = (1 - sum(model2prob.values())) / (len(all_models) - L)
for model in estimator.choices:
probabilities.append(model2prob.get(model, p_rest))
estimator.probabilities = probabilities
default_estimator_choice = None
for models in relied2models.values():
if models:
default_estimator_choice = models[0]
estimator.default_value = default_estimator_choice
for rely_model, path in RelyModels.info:
forbid_eq_value = path[-1]
path = path[:-1]
forbid_eq_key = ":".join(path + ["__choice__"])
forbid_eq_key_hp = cs.get_hyperparameter(forbid_eq_key)
forbid_in_key = "estimator:__choice__"
hit = relied2AllModels.get(rely_model)
if not hit:
choices = list(forbid_eq_key_hp.choices)
choices.remove(forbid_eq_value)
forbid_eq_key_hp.choices = tuple(choices)
forbid_eq_key_hp.default_value = choices[0]
forbid_eq_key_hp.probabilities = [1 / len(choices)
] * len(choices)
# fixme 最后我放弃了在这上面进行修改，在hdl部分就做了预处理
continue
forbid_in_value = list(set(all_models) - set(hit))
# 只选择了boost模型
if not forbid_in_value:
continue
choices = forbid_eq_key_hp.choices
probabilities = []
p: float = kwargs[rely_model]
p_rest = (1 - p) * (len(choices) - 1)
for choice in choices:
if choice == forbid_eq_value:
probabilities.append(p)
else:
probabilities.append(p_rest)
forbid_eq_key_hp.probabilities = probabilities
cs.add_forbidden_clause(
ForbiddenAndConjunction(
ForbiddenEqualsClause(forbid_eq_key_hp, forbid_eq_value),
ForbiddenInClause(cs.get_hyperparameter(forbid_in_key),
forbid_in_value),
))
def _construct_in_condition(
condition: Dict,
cs: ConfigurationSpace,
) -> InCondition:
return InCondition(
child=cs.get_hyperparameter(condition['child']),
parent=cs.get_hyperparameter(condition['parent']),
values=condition['values'],
)
def _construct_lt_condition(
condition: Dict,
cs: ConfigurationSpace,
) -> LessThanCondition:
return LessThanCondition(
child=cs.get_hyperparameter(condition['child']),
parent=cs.get_hyperparameter(condition['parent']),
value=condition['value'],
)
def _construct_neq_condition(
condition: Dict,
cs: ConfigurationSpace,
) -> NotEqualsCondition:
return NotEqualsCondition(
child=cs.get_hyperparameter(condition['child']),
parent=cs.get_hyperparameter(condition['parent']),
value=condition['value'],
)
def _construct_lt_condition(
condition: Dict,
cs: ConfigurationSpace,
) -> LessThanCondition:
return LessThanCondition(
child=cs.get_hyperparameter(condition['child']),
parent=cs.get_hyperparameter(condition['parent']),
value=condition['value'],
)
def _construct_neq_condition(
condition: Dict,
cs: ConfigurationSpace,
) -> NotEqualsCondition:
return NotEqualsCondition(
child=cs.get_hyperparameter(condition['child']),
parent=cs.get_hyperparameter(condition['parent']),
value=condition['value'],
)
def _construct_in_condition(
condition: Dict,
cs: ConfigurationSpace,
) -> InCondition:
return InCondition(
child=cs.get_hyperparameter(condition['child']),
parent=cs.get_hyperparameter(condition['parent']),
values=condition['values'],
)
def add_params(cs: ConfigurationSpace):
'''
adds parameters to ConfigurationSpace
'''
selector = cs.get_hyperparameter("selector")
regressor = cs.get_hyperparameter("regressor")
if "PairwiseRegressor" in selector.choices:
cond = InCondition(child=regressor, parent=selector, values=["PairwiseRegressor"])
cs.add_condition(cond)
def add_params(cs: ConfigurationSpace):
'''
adds parameters to ConfigurationSpace
'''
selector = cs.get_hyperparameter("selector")
classifier = cs.get_hyperparameter("classifier")
if "MultiClassifier" in selector.choices:
cond = InCondition(child=classifier,
parent=selector,
values=["MultiClassifier"])
cs.add_condition(cond)
def _construct_forbidden_in(
clause: Dict,
cs: ConfigurationSpace,
) -> ForbiddenEqualsClause:
return ForbiddenInClause(hyperparameter=cs.get_hyperparameter(
clause['name']),
values=clause['values'])
def alternative_configuration_recovery(config_list: typing.List[str], cs: ConfigurationSpace):
""" Used to recover ints and bools as categoricals or constants from trajectory """
config_dict = {}
for param in config_list:
k,v = param.split("=")
v = v.strip("'")
hp = cs.get_hyperparameter(k)
if isinstance(hp, FloatHyperparameter):
v = float(v)
elif isinstance(hp, IntegerHyperparameter):
v = int(v)
################# DIFFERENCE: ################
elif isinstance(hp, CategoricalHyperparameter) or isinstance(hp, Constant):
if isinstance(hp.default_value, bool):
v = True if v == 'True' else False
elif isinstance(hp.default_value, int):
v = int(v)
elif isinstance(hp.default_value, float):
v = float(v)
else:
v = v
##############################################
config_dict[k] = v
config = Configuration(configuration_space=cs, values=config_dict)
config.origin = "External Trajectory"
return config
def _convert_dict_to_config(config_list: typing.List[str], cs: ConfigurationSpace):
# CAN BE DONE IN CONFIGSPACE
"""Since we save a configurations in a dictionary str->str we have to
try to figure out the type (int, float, str) of each parameter value
Parameters
----------
config_list: typing.List[str]
Configuration as a list of "str='str'"
cs: ConfigurationSpace
Configuration Space to translate dict object into Confiuration object
"""
config_dict = {}
for param in config_list:
k, v = param.split("=")
v = v.strip("'")
hp = cs.get_hyperparameter(k)
if isinstance(hp, FloatHyperparameter):
v = float(v)
elif isinstance(hp, IntegerHyperparameter):
v = int(v)
config_dict[k] = v
config = Configuration(configuration_space=cs, values=config_dict)
config.origin = "External Trajectory"
return config
def _construct_forbidden_in(
clause: Dict,
cs: ConfigurationSpace,
) -> ForbiddenEqualsClause:
return ForbiddenInClause(
hyperparameter=cs.get_hyperparameter(clause['name']),
values=clause['values']
)
def add_params(cs: ConfigurationSpace):
'''
adds parameters to ConfigurationSpace
'''
try:
classifier = cs.get_hyperparameter("classifier")
classifier.choices.append("RandomForest")
except KeyError:
classifier = CategoricalHyperparameter(
"classifier", choices=["RandomForest"], default="RandomForest")
cs.add_hyperparameter(classifier)
n_estimators = UniformIntegerHyperparameter(
name="rf:n_estimators", lower=10, upper=100, default=10, log=True)
cs.add_hyperparameter(n_estimators)
criterion = CategoricalHyperparameter(
name="rf:criterion", choices=["gini", "entropy"], default="gini")
cs.add_hyperparameter(criterion)
max_features = CategoricalHyperparameter(
name="rf:max_features", choices=["sqrt", "log2", None], default="sqrt")
cs.add_hyperparameter(max_features)
max_depth = UniformIntegerHyperparameter(
name="rf:max_depth", lower=10, upper=2**31, default=2**31, log=True)
cs.add_hyperparameter(max_depth)
min_samples_split = UniformIntegerHyperparameter(
name="rf:min_samples_split", lower=2, upper=100, default=2, log=True)
cs.add_hyperparameter(min_samples_split)
min_samples_leaf = UniformIntegerHyperparameter(
name="rf:min_samples_leaf", lower=2, upper=100, default=10, log=True)
cs.add_hyperparameter(min_samples_leaf)
bootstrap = CategoricalHyperparameter(
name="rf:bootstrap", choices=[True, False], default=True)
cs.add_hyperparameter(bootstrap)
cond = InCondition(
child=n_estimators, parent=classifier, values=["RandomForest"])
cs.add_condition(cond)
cond = InCondition(
child=criterion, parent=classifier, values=["RandomForest"])
cs.add_condition(cond)
cond = InCondition(
child=max_features, parent=classifier, values=["RandomForest"])
cs.add_condition(cond)
cond = InCondition(
child=max_depth, parent=classifier, values=["RandomForest"])
cs.add_condition(cond)
cond = InCondition(
child=min_samples_split, parent=classifier, values=["RandomForest"])
cs.add_condition(cond)
cond = InCondition(
child=min_samples_leaf, parent=classifier, values=["RandomForest"])
cs.add_condition(cond)
cond = InCondition(
child=bootstrap, parent=classifier, values=["RandomForest"])
cs.add_condition(cond)
def add_params(cs: ConfigurationSpace):
'''
adds parameters to ConfigurationSpace
'''
try:
selector = cs.get_hyperparameter("selector")
selector.choices.append("PairwiseClassifier")
except KeyError:
selector = CategoricalHyperparameter(
"selector",
choices=["PairwiseClassifier"],
default="PairwiseClassifier")
cs.add_hyperparameter(selector)
classifier = cs.get_hyperparameter("classifier")
cond = InCondition(child=classifier,
parent=selector,
values=["PairwiseClassifier"])
cs.add_condition(cond)
def _convert_dict_to_config(config_list: typing.List[str], cs: ConfigurationSpace) -> Configuration:
"""Since we save a configurations in a dictionary str->str we have to
try to figure out the type (int, float, str) of each parameter value
Parameters
----------
config_list: typing.List[str]
Configuration as a list of "str='str'"
cs: ConfigurationSpace
Configuration Space to translate dict object into Confiuration object
"""
config_dict = {}
v = '' # type: typing.Union[str, float, int, bool]
for param in config_list:
k, v = param.split("=")
v = v.strip("'")
hp = cs.get_hyperparameter(k)
if isinstance(hp, FloatHyperparameter):
v = float(v)
elif isinstance(hp, IntegerHyperparameter):
v = int(v)
elif isinstance(hp, (CategoricalHyperparameter, Constant)):
# Checking for the correct type requires jumping some hoops
# First, we gather possible interpretations of our string
interpretations = [v] # type: typing.List[typing.Union[str, bool, int, float]]
if v in ["True", "False"]:
# Special Case for booleans (assuming we support them)
# This is important to avoid false positive warnings triggered by 1 == True or "False" == True
interpretations.append(True if v == 'True' else False)
else:
for t in [int, float]:
try:
interpretations.append(t(v))
except ValueError:
continue
# Second, check if it's in the choices / the correct type.
legal = {interpretation for interpretation in interpretations if hp.is_legal(interpretation)}
# Third, issue warnings if the interpretation is ambigious
if len(legal) != 1:
logging.getLogger("smac.trajlogger").warning(
"Ambigous or no interpretation of value {} for hp {} found ({} possible interpretations). "
"Passing string, but this will likely result in an error".format(v, hp.name, len(legal)))
else:
v = legal.pop()
config_dict[k] = v
config = Configuration(configuration_space=cs, values=config_dict)
config.origin = "External Trajectory"
return config
def add_params(cs: ConfigurationSpace):
'''
adds parameters to ConfigurationSpace
'''
try:
selector = cs.get_hyperparameter("selector")
selector.choices.append("PairwiseClassifier")
except KeyError:
selector = CategoricalHyperparameter(
"selector", choices=["PairwiseClassifier"], default="PairwiseClassifier")
cs.add_hyperparameter(selector)
def add_params(cs: ConfigurationSpace):
'''
adds parameters to ConfigurationSpace
'''
try:
regressor = cs.get_hyperparameter("regressor")
regressor.choices.append("RandomForestRegressor")
regressor._num_choices += 1
except KeyError:
regressor = CategoricalHyperparameter(
"regressor", choices=["RandomForestRegressor"], default="RandomForestRegressor")
cs.add_hyperparameter(regressor)
n_estimators = UniformIntegerHyperparameter(
name="rfreg:n_estimators", lower=10, upper=100, default=10, log=True)
cs.add_hyperparameter(n_estimators)
max_features = CategoricalHyperparameter(
name="rfreg:max_features", choices=["sqrt", "log2", None], default="sqrt")
cs.add_hyperparameter(max_features)
max_depth = UniformIntegerHyperparameter(
name="rfreg:max_depth", lower=10, upper=2 ** 31, default=2 ** 31, log=True)
cs.add_hyperparameter(max_depth)
min_samples_split = UniformIntegerHyperparameter(
name="rfreg:min_samples_split", lower=2, upper=100, default=2, log=True)
cs.add_hyperparameter(min_samples_split)
min_samples_leaf = UniformIntegerHyperparameter(
name="rfreg:min_samples_leaf", lower=2, upper=100, default=10, log=True)
cs.add_hyperparameter(min_samples_leaf)
bootstrap = CategoricalHyperparameter(
name="rfreg:bootstrap", choices=[True, False], default=True)
cs.add_hyperparameter(bootstrap)
cond = InCondition(
child=n_estimators, parent=regressor, values=["RandomForestRegressor"])
cs.add_condition(cond)
cond = InCondition(
child=max_features, parent=regressor, values=["RandomForestRegressor"])
cs.add_condition(cond)
cond = InCondition(
child=max_depth, parent=regressor, values=["RandomForestRegressor"])
cs.add_condition(cond)
cond = InCondition(
child=min_samples_split, parent=regressor, values=["RandomForestRegressor"])
cs.add_condition(cond)
cond = InCondition(
child=min_samples_leaf, parent=regressor, values=["RandomForestRegressor"])
cs.add_condition(cond)
cond = InCondition(
child=bootstrap, parent=regressor, values=["RandomForestRegressor"])
cs.add_condition(cond)
def add_params(cs: ConfigurationSpace):
'''
adds parameters to ConfigurationSpace
'''
try:
selector = cs.get_hyperparameter("selector")
selector.choices.append("PairwiseClassifier")
except KeyError:
selector = CategoricalHyperparameter(
"selector",
choices=["PairwiseClassifier"],
default="PairwiseClassifier")
cs.add_hyperparameter(selector)
def get_default_initial_configs(phps: ConfigurationSpace,
n_configs) -> List[Configuration]:
None_name = "None:NoneType"
phps = deepcopy(phps)
for config in phps.get_hyperparameters():
name: str = config.name
if name.startswith("preprocessing") and name.endswith(
"__choice__") and (None_name in config.choices):
config.default_value = None_name
model_choice = phps.get_hyperparameter("estimator:__choice__")
ans = []
for choice in model_choice.choices:
cur_phps = deepcopy(phps)
cur_phps.get_hyperparameter(
"estimator:__choice__").default_value = choice
default = cur_phps.get_default_configuration()
ans.append(default)
if len(ans) < n_configs:
ans.extend(phps.sample_configuration(n_configs - len(ans)))
return ans
def add_forbidden(
conf_space: ConfigurationSpace,
pipeline: List[Tuple[str, autoPyTorchChoice]],
matches: np.ndarray,
dataset_properties: Dict[str, Any],
include: Optional[Dict[str, Any]] = None,
exclude: Optional[Dict[str, Any]] = None
) -> ConfigurationSpace:
# Not sure if this works for 3D
node_i_is_choice = []
node_i_choices_names: List[List[str]] = []
node_i_choices: List[List[Union[autoPyTorchComponent, autoPyTorchChoice]]] = []
all_nodes = []
for node_name, node in pipeline:
all_nodes.append(node)
is_choice = hasattr(node, "get_available_components")
node_i_is_choice.append(is_choice)
node_include = include.get(
node_name) if include is not None else None
node_exclude = exclude.get(
node_name) if exclude is not None else None
if is_choice:
node_i_choices_names.append(
[str(element) for element in
node.get_available_components(
dataset_properties, include=node_include,
exclude=node_exclude).keys()]
)
node_i_choices.append(
list(node.get_available_components(
dataset_properties, include=node_include,
exclude=node_exclude
).values()))
else:
node_i_choices_names.append([node_name])
node_i_choices.append([node])
# Find out all chains of choices. Only in such a chain its possible to
# have several forbidden constraints
choices_chains = []
idx = 0
while idx < len(pipeline):
if node_i_is_choice[idx]:
chain_start = idx
idx += 1
while idx < len(pipeline) and node_i_is_choice[idx]:
idx += 1
chain_stop = idx
choices_chains.append((chain_start, chain_stop))
idx += 1
for choices_chain in choices_chains:
constraints: Set[Tuple] = set()
chain_start = choices_chain[0]
chain_stop = choices_chain[1]
chain_length = chain_stop - chain_start
# Add one to have also have chain_length in the range
for sub_chain_length in range(2, chain_length + 1):
for start_idx in range(chain_start, chain_stop - sub_chain_length + 1):
indices = range(start_idx, start_idx + sub_chain_length)
node_names = [pipeline[idx][0] for idx in indices]
num_node_choices = []
node_choice_names = []
skip_array_shape = []
for idx in indices:
node = all_nodes[idx]
available_components = node.get_available_components(
dataset_properties,
include=node_i_choices_names[idx])
assert len(available_components) > 0, len(available_components)
skip_array_shape.append(len(available_components))
num_node_choices.append(range(len(available_components)))
node_choice_names.append([name for name in available_components])
# Figure out which choices were already abandoned
skip_array = np.zeros(skip_array_shape)
for product in itertools.product(*num_node_choices):
for node_idx, choice_idx in enumerate(product):
node_idx += start_idx
slices_ = tuple(
slice(None) if idx != node_idx else
slice(choice_idx, choice_idx + 1) for idx in
range(len(matches.shape)))
if np.sum(matches[slices_]) == 0:
skip_array[product] = 1
for product in itertools.product(*num_node_choices):
if skip_array[product]:
continue
slices = tuple(
slice(None) if idx not in indices else
slice(product[idx - start_idx],
product[idx - start_idx] + 1) for idx in
range(len(matches.shape)))
if np.sum(matches[slices]) == 0:
constraint = tuple([(node_names[i],
node_choice_names[i][product[i]])
for i in range(len(product))])
# Check if a more general constraint/forbidden clause
# was already added
continue_ = False
for constraint_length in range(2, len(constraint)):
constr_starts = len(constraint) - constraint_length + 1
for constraint_start_idx in range(constr_starts):
constraint_end_idx = constraint_start_idx + constraint_length
sub_constraint = constraint[constraint_start_idx:constraint_end_idx]
if sub_constraint in constraints:
continue_ = True
break
if continue_:
break
if continue_:
continue
constraints.add(constraint)
forbiddens = []
for i in range(len(product)):
forbiddens.append(
ForbiddenEqualsClause(conf_space.get_hyperparameter(
node_names[i] + ":__choice__"),
node_choice_names[i][product[i]]))
forbidden = ForbiddenAndConjunction(*forbiddens)
conf_space.add_forbidden_clause(forbidden)
return conf_space
def read(pcs_string, debug=False):
"""
Reads in a :py:class:`~ConfigSpace.configuration_space.ConfigurationSpace`
definition from a pcs file.
Example
-------
>>> from ConfigSpace.read_and_write import pcs_new
>>> with open('configspace.pcs', 'r') as fh:
>>> restored_conf = pcs_new.read(fh)
Parameters
----------
pcs_string : str
ConfigSpace definition in pcs format
debug : bool
Provides debug information. Defaults to False.
Returns
-------
:py:class:`~ConfigSpace.configuration_space.ConfigurationSpace`
The restored ConfigurationSpace object
"""
configuration_space = ConfigurationSpace()
conditions = []
forbidden = []
# some statistics
ct = 0
cont_ct = 0
cat_ct = 0
ord_ct = 0
line_ct = 0
for line in pcs_string:
line_ct += 1
if "#" in line:
# It contains a comment
pos = line.find("#")
line = line[:pos]
# Remove quotes and whitespaces at beginning and end
line = line.replace('"', "").replace("'", "")
line = line.strip()
if "|" in line:
# It's a condition
try:
c = pp_condition.parseString(line)
conditions.append(c)
except pyparsing.ParseException:
raise NotImplementedError("Could not parse condition: %s" % line)
continue
if "}" not in line and "]" not in line:
continue
if line.startswith("{") and line.endswith("}"):
forbidden.append(line)
continue
if len(line.strip()) == 0:
continue
ct += 1
param = None
create = {"int": UniformIntegerHyperparameter,
"float": UniformFloatHyperparameter,
"categorical": CategoricalHyperparameter,
"ordinal": OrdinalHyperparameter
}
try:
param_list = pp_cont_param.parseString(line)
name = param_list[0]
if param_list[1] == 'integer':
paramtype = 'int'
elif param_list[1] == 'real':
paramtype = 'float'
else:
paramtype = None
if paramtype in ['int', 'float']:
log = param_list[10:]
param_list = param_list[:10]
if len(log) > 0:
log = log[0]
lower = float(param_list[3])
upper = float(param_list[5])
log_on = True if "log" in log else False
default_value = float(param_list[8])
param = create[paramtype](name=name, lower=lower, upper=upper,
q=None, log=log_on, default_value=default_value)
cont_ct += 1
except pyparsing.ParseException:
pass
try:
if "categorical" in line:
param_list = pp_cat_param.parseString(line)
name = param_list[0]
choices = [choice for choice in param_list[3:-4:2]]
default_value = param_list[-2]
param = create["categorical"](name=name, choices=choices, default_value=default_value)
cat_ct += 1
elif "ordinal" in line:
param_list = pp_ord_param.parseString(line)
name = param_list[0]
sequence = [seq for seq in param_list[3:-4:2]]
default_value = param_list[-2]
param = create["ordinal"](name=name, sequence=sequence, default_value=default_value)
ord_ct += 1
except pyparsing.ParseException:
pass
if param is None:
raise NotImplementedError("Could not parse: %s" % line)
configuration_space.add_hyperparameter(param)
for clause in forbidden:
param_list = pp_forbidden_clause.parseString(clause)
tmp_list = []
clause_list = []
for value in param_list[1:]:
if len(tmp_list) < 3:
tmp_list.append(value)
else:
# So far, only equals is supported by SMAC
if tmp_list[1] == '=':
# TODO maybe add a check if the hyperparameter is
# actually in the configuration space
clause_list.append(ForbiddenEqualsClause(
configuration_space.get_hyperparameter(tmp_list[0]),
tmp_list[2]))
else:
raise NotImplementedError()
tmp_list = []
configuration_space.add_forbidden_clause(ForbiddenAndConjunction(
*clause_list))
conditions_per_child = OrderedDict()
for condition in conditions:
child_name = condition[0]
if child_name not in conditions_per_child:
conditions_per_child[child_name] = list()
conditions_per_child[child_name].append(condition)
for child_name in conditions_per_child:
for condition in conditions_per_child[child_name]:
condition = condition[2:]
condition = ' '.join(condition)
if '||' in str(condition):
ors = []
# 1st case we have a mixture of || and &&
if '&&' in str(condition):
ors_combis = []
for cond_parts in str(condition).split('||'):
condition = str(cond_parts).split('&&')
# if length is 1 it must be or
if len(condition) == 1:
element_list = condition[0].split()
ors_combis.append(condition_specification(child_name, element_list, configuration_space))
else:
# now taking care of ands
ands = []
for and_part in condition:
element_list = [element for part in condition for element in and_part.split()]
ands.append(condition_specification(child_name, element_list, configuration_space))
ors_combis.append(AndConjunction(*ands))
mixed_conjunction = OrConjunction(*ors_combis)
configuration_space.add_condition(mixed_conjunction)
else:
# 2nd case: we only have ors
for cond_parts in str(condition).split('||'):
element_list = [element for element in cond_parts.split()]
ors.append(condition_specification(child_name, element_list, configuration_space))
or_conjunction = OrConjunction(*ors)
configuration_space.add_condition(or_conjunction)
else:
# 3rd case: we only have ands
if '&&' in str(condition):
ands = []
for cond_parts in str(condition).split('&&'):
element_list = [element for element in cond_parts.split()]
ands.append(condition_specification(child_name, element_list, configuration_space))
and_conjunction = AndConjunction(*ands)
configuration_space.add_condition(and_conjunction)
else:
# 4th case: we have a normal condition
element_list = [element for element in condition.split()]
normal_condition = condition_specification(child_name, element_list, configuration_space)
configuration_space.add_condition(normal_condition)
return configuration_space
def _get_hyperparameter_search_space(self,
include=None,
exclude=None,
dataset_properties=None):
"""Create the hyperparameter configuration space.
Parameters
----------
include : dict (optional, default=None)
Returns
-------
"""
cs = ConfigurationSpace()
if dataset_properties is None or not isinstance(
dataset_properties, dict):
dataset_properties = dict()
if not 'target_type' in dataset_properties:
dataset_properties['target_type'] = 'classification'
if dataset_properties['target_type'] != 'classification':
dataset_properties['target_type'] = 'classification'
pipeline = self.steps
cs = self._get_base_search_space(cs=cs,
dataset_properties=dataset_properties,
exclude=exclude,
include=include,
pipeline=pipeline)
classifiers = cs.get_hyperparameter('classifier:__choice__').choices
preprocessors = cs.get_hyperparameter(
'preprocessor:__choice__').choices
available_classifiers = pipeline[-1][1].get_available_components(
dataset_properties)
available_preprocessors = pipeline[-2][1].get_available_components(
dataset_properties)
possible_default_classifier = copy.copy(
list(available_classifiers.keys()))
default = cs.get_hyperparameter('classifier:__choice__').default
del possible_default_classifier[possible_default_classifier.index(
default)]
# A classifier which can handle sparse data after the densifier is
# forbidden for memory issues
for key in classifiers:
if SPARSE in available_classifiers[key].get_properties()['input']:
if 'densifier' in preprocessors:
while True:
try:
cs.add_forbidden_clause(
ForbiddenAndConjunction(
ForbiddenEqualsClause(
cs.get_hyperparameter(
'classifier:__choice__'), key),
ForbiddenEqualsClause(
cs.get_hyperparameter(
'preprocessor:__choice__'),
'densifier')))
# Success
break
except ValueError:
# Change the default and try again
try:
default = possible_default_classifier.pop()
except IndexError:
raise ValueError(
"Cannot find a legal default configuration."
)
cs.get_hyperparameter(
'classifier:__choice__').default = default
# which would take too long
# Combinations of non-linear models with feature learning:
classifiers_ = [
"adaboost", "decision_tree", "extra_trees", "gradient_boosting",
"k_nearest_neighbors", "libsvm_svc", "random_forest",
"gaussian_nb", "decision_tree", "xgradient_boosting"
]
feature_learning = ["kitchen_sinks", "nystroem_sampler"]
for c, f in product(classifiers_, feature_learning):
if c not in classifiers:
continue
if f not in preprocessors:
continue
while True:
try:
cs.add_forbidden_clause(
ForbiddenAndConjunction(
ForbiddenEqualsClause(
cs.get_hyperparameter("classifier:__choice__"),
c),
ForbiddenEqualsClause(
cs.get_hyperparameter(
"preprocessor:__choice__"), f)))
break
except KeyError:
break
except ValueError as e:
# Change the default and try again
try:
default = possible_default_classifier.pop()
except IndexError:
raise ValueError(
"Cannot find a legal default configuration.")
cs.get_hyperparameter(
'classifier:__choice__').default = default
# Won't work
# Multinomial NB etc don't use with features learning, pca etc
classifiers_ = ["multinomial_nb"]
preproc_with_negative_X = [
"kitchen_sinks", "pca", "truncatedSVD", "fast_ica", "kernel_pca",
"nystroem_sampler"
]
for c, f in product(classifiers_, preproc_with_negative_X):
if c not in classifiers:
continue
if f not in preprocessors:
continue
while True:
try:
cs.add_forbidden_clause(
ForbiddenAndConjunction(
ForbiddenEqualsClause(
cs.get_hyperparameter(
"preprocessor:__choice__"), f),
ForbiddenEqualsClause(
cs.get_hyperparameter("classifier:__choice__"),
c)))
break
except KeyError:
break
except ValueError:
# Change the default and try again
try:
default = possible_default_classifier.pop()
except IndexError:
raise ValueError(
"Cannot find a legal default configuration.")
cs.get_hyperparameter(
'classifier:__choice__').default = default
self.configuration_space_ = cs
self.dataset_properties_ = dataset_properties
return cs
def add_params(cs: ConfigurationSpace):
'''
adds parameters to ConfigurationSpace
'''
try:
classifier = cs.get_hyperparameter("classifier")
if "XGBoost" not in classifier.choices:
return
num_round = UniformIntegerHyperparameter(name="xgb:num_round",
lower=10,
upper=100,
default_value=50,
log=True)
cs.add_hyperparameter(num_round)
alpha = UniformFloatHyperparameter(name="xgb:alpha",
lower=0,
upper=10,
default_value=1)
cs.add_hyperparameter(alpha)
lambda_ = UniformFloatHyperparameter(name="xgb:lambda",
lower=1,
upper=10,
default_value=1)
cs.add_hyperparameter(lambda_)
colsample_bylevel = UniformFloatHyperparameter(
name="xgb:colsample_bylevel",
lower=0.5,
upper=1,
default_value=1)
cs.add_hyperparameter(colsample_bylevel)
colsample_bytree = UniformFloatHyperparameter(
name="xgb:colsample_bytree",
lower=0.5,
upper=1,
default_value=1)
cs.add_hyperparameter(colsample_bytree)
subsample = UniformFloatHyperparameter(name="xgb:subsample",
lower=0.01,
upper=1,
default_value=1)
cs.add_hyperparameter(subsample)
max_delta_step = UniformFloatHyperparameter(
name="xgb:max_delta_step", lower=0, upper=10, default_value=0)
cs.add_hyperparameter(max_delta_step)
min_child_weight = UniformFloatHyperparameter(
name="xgb:min_child_weight",
lower=0,
upper=20,
default_value=1)
cs.add_hyperparameter(min_child_weight)
max_depth = UniformIntegerHyperparameter(name="xgb:max_depth",
lower=1,
upper=10,
default_value=6)
cs.add_hyperparameter(max_depth)
gamma = UniformFloatHyperparameter(name="xgb:gamma",
lower=0,
upper=10,
default_value=0)
cs.add_hyperparameter(gamma)
eta = UniformFloatHyperparameter(name="xgb:eta",
lower=0,
upper=1,
default_value=0.3)
cs.add_hyperparameter(eta)
cond = InCondition(child=num_round,
parent=classifier,
values=["XGBoost"])
cs.add_condition(cond)
cond = InCondition(child=alpha,
parent=classifier,
values=["XGBoost"])
cs.add_condition(cond)
cond = InCondition(child=lambda_,
parent=classifier,
values=["XGBoost"])
cs.add_condition(cond)
cond = InCondition(child=colsample_bylevel,
parent=classifier,
values=["XGBoost"])
cs.add_condition(cond)
cond = InCondition(child=colsample_bytree,
parent=classifier,
values=["XGBoost"])
cs.add_condition(cond)
cond = InCondition(child=subsample,
parent=classifier,
values=["XGBoost"])
cs.add_condition(cond)
cond = InCondition(child=max_delta_step,
parent=classifier,
values=["XGBoost"])
cs.add_condition(cond)
cond = InCondition(child=min_child_weight,
parent=classifier,
values=["XGBoost"])
cs.add_condition(cond)
cond = InCondition(child=max_depth,
parent=classifier,
values=["XGBoost"])
cs.add_condition(cond)
cond = InCondition(child=gamma,
parent=classifier,
values=["XGBoost"])
cs.add_condition(cond)
cond = InCondition(child=eta,
parent=classifier,
values=["XGBoost"])
cs.add_condition(cond)
except:
return
def read(pcs_string, debug=False):
"""
Read in a :py:class:`~ConfigSpace.configuration_space.ConfigurationSpace`
definition from a pcs file.
Example
-------
.. testsetup:: pcs_new_test
from ConfigSpace import ConfigurationSpace
import ConfigSpace.hyperparameters as CSH
from ConfigSpace.read_and_write import pcs_new
cs = ConfigurationSpace()
cs.add_hyperparameter(CSH.CategoricalHyperparameter('a', choices=[1, 2, 3]))
with open('configspace.pcs_new', 'w') as f:
f.write(pcs_new.write(cs))
.. doctest:: pcs_new_test
>>> from ConfigSpace.read_and_write import pcs_new
>>> with open('configspace.pcs_new', 'r') as fh:
... deserialized_conf = pcs_new.read(fh)
Parameters
----------
pcs_string : str
ConfigSpace definition in pcs format
debug : bool
Provides debug information. Defaults to False.
Returns
-------
:py:class:`~ConfigSpace.configuration_space.ConfigurationSpace`
The deserialized ConfigurationSpace object
"""
configuration_space = ConfigurationSpace()
conditions = []
forbidden = []
# some statistics
ct = 0
cont_ct = 0
cat_ct = 0
ord_ct = 0
line_ct = 0
for line in pcs_string:
line_ct += 1
if "#" in line:
# It contains a comment
pos = line.find("#")
line = line[:pos]
# Remove quotes and whitespaces at beginning and end
line = line.replace('"', "").replace("'", "")
line = line.strip()
if "|" in line:
# It's a condition
try:
c = pp_condition.parseString(line)
conditions.append(c)
except pyparsing.ParseException:
raise NotImplementedError("Could not parse condition: %s" %
line)
continue
if "}" not in line and "]" not in line:
continue
if line.startswith("{") and line.endswith("}"):
forbidden.append(line)
continue
if len(line.strip()) == 0:
continue
ct += 1
param = None
create = {
"int": UniformIntegerHyperparameter,
"float": UniformFloatHyperparameter,
"categorical": CategoricalHyperparameter,
"ordinal": OrdinalHyperparameter
}
try:
param_list = pp_cont_param.parseString(line)
name = param_list[0]
if param_list[1] == 'integer':
paramtype = 'int'
elif param_list[1] == 'real':
paramtype = 'float'
else:
paramtype = None
if paramtype in ['int', 'float']:
log = param_list[10:]
param_list = param_list[:10]
if len(log) > 0:
log = log[0]
lower = float(param_list[3])
upper = float(param_list[5])
log_on = True if "log" in log else False
default_value = float(param_list[8])
param = create[paramtype](name=name,
lower=lower,
upper=upper,
q=None,
log=log_on,
default_value=default_value)
cont_ct += 1
except pyparsing.ParseException:
pass
try:
if "categorical" in line:
param_list = pp_cat_param.parseString(line)
name = param_list[0]
choices = [choice for choice in param_list[3:-4:2]]
default_value = param_list[-2]
param = create["categorical"](
name=name,
choices=choices,
default_value=default_value,
)
cat_ct += 1
elif "ordinal" in line:
param_list = pp_ord_param.parseString(line)
name = param_list[0]
sequence = [seq for seq in param_list[3:-4:2]]
default_value = param_list[-2]
param = create["ordinal"](
name=name,
sequence=sequence,
default_value=default_value,
)
ord_ct += 1
except pyparsing.ParseException:
pass
if param is None:
raise NotImplementedError("Could not parse: %s" % line)
configuration_space.add_hyperparameter(param)
for clause in forbidden:
param_list = pp_forbidden_clause.parseString(clause)
tmp_list = []
clause_list = []
for value in param_list[1:]:
if len(tmp_list) < 3:
tmp_list.append(value)
else:
# So far, only equals is supported by SMAC
if tmp_list[1] == '=':
hp = configuration_space.get_hyperparameter(tmp_list[0])
if isinstance(hp, NumericalHyperparameter):
if isinstance(hp, IntegerHyperparameter):
forbidden_value = int(tmp_list[2])
elif isinstance(hp, FloatHyperparameter):
forbidden_value = float(tmp_list[2])
else:
raise NotImplementedError
if forbidden_value < hp.lower or forbidden_value > hp.upper:
raise ValueError(
f'forbidden_value is set out of the bound, it needs to'
f' be set between [{hp.lower}, {hp.upper}]'
f' but its value is {forbidden_value}')
elif isinstance(
hp,
(CategoricalHyperparameter, OrdinalHyperparameter)):
hp_values = hp.choices if isinstance(hp, CategoricalHyperparameter)\
else hp.sequence
forbidden_value_in_hp_values = tmp_list[2] in hp_values
if forbidden_value_in_hp_values:
forbidden_value = tmp_list[2]
else:
raise ValueError(
f'forbidden_value is set out of the allowed value '
f'sets, it needs to be one member from {hp_values} '
f'but its value is {forbidden_value}')
else:
raise ValueError('Unsupported Hyperparamter sorts')
clause_list.append(
ForbiddenEqualsClause(
configuration_space.get_hyperparameter(
tmp_list[0]), forbidden_value))
else:
raise NotImplementedError()
tmp_list = []
configuration_space.add_forbidden_clause(
ForbiddenAndConjunction(*clause_list))
conditions_per_child = OrderedDict()
for condition in conditions:
child_name = condition[0]
if child_name not in conditions_per_child:
conditions_per_child[child_name] = list()
conditions_per_child[child_name].append(condition)
for child_name in conditions_per_child:
for condition in conditions_per_child[child_name]:
condition = condition[2:]
condition = ' '.join(condition)
if '||' in str(condition):
ors = []
# 1st case we have a mixture of || and &&
if '&&' in str(condition):
ors_combis = []
for cond_parts in str(condition).split('||'):
condition = str(cond_parts).split('&&')
# if length is 1 it must be or
if len(condition) == 1:
element_list = condition[0].split()
ors_combis.append(
condition_specification(
child_name,
element_list,
configuration_space,
))
else:
# now taking care of ands
ands = []
for and_part in condition:
element_list = [
element for part in condition
for element in and_part.split()
]
ands.append(
condition_specification(
child_name,
element_list,
configuration_space,
))
ors_combis.append(AndConjunction(*ands))
mixed_conjunction = OrConjunction(*ors_combis)
configuration_space.add_condition(mixed_conjunction)
else:
# 2nd case: we only have ors
for cond_parts in str(condition).split('||'):
element_list = [
element for element in cond_parts.split()
]
ors.append(
condition_specification(
child_name,
element_list,
configuration_space,
))
or_conjunction = OrConjunction(*ors)
configuration_space.add_condition(or_conjunction)
else:
# 3rd case: we only have ands
if '&&' in str(condition):
ands = []
for cond_parts in str(condition).split('&&'):
element_list = [
element for element in cond_parts.split()
]
ands.append(
condition_specification(
child_name,
element_list,
configuration_space,
))
and_conjunction = AndConjunction(*ands)
configuration_space.add_condition(and_conjunction)
else:
# 4th case: we have a normal condition
element_list = [element for element in condition.split()]
normal_condition = condition_specification(
child_name,
element_list,
configuration_space,
)
configuration_space.add_condition(normal_condition)
return configuration_space
def get_hyperparameter_search_space(cls, include=None, exclude=None,
dataset_properties=None):
"""Return the configuration space for the CASH problem.
Parameters
----------
include_estimators : list of str
If include_estimators is given, only the regressors specified
are used. Specify them by their module name; e.g., to include
only the SVM use :python:`include_regressors=['svr']`.
Cannot be used together with :python:`exclude_regressors`.
exclude_estimators : list of str
If exclude_estimators is given, only the regressors specified
are used. Specify them by their module name; e.g., to include
all regressors except the SVM use
:python:`exclude_regressors=['svr']`.
Cannot be used together with :python:`include_regressors`.
include_preprocessors : list of str
If include_preprocessors is given, only the preprocessors specified
are used. Specify them by their module name; e.g., to include
only the PCA use :python:`include_preprocessors=['pca']`.
Cannot be used together with :python:`exclude_preprocessors`.
exclude_preprocessors : list of str
If include_preprocessors is given, only the preprocessors specified
are used. Specify them by their module name; e.g., to include
all preprocessors except the PCA use
:python:`exclude_preprocessors=['pca']`.
Cannot be used together with :python:`include_preprocessors`.
Returns
-------
cs : ConfigSpace.configuration_space.Configuration
The configuration space describing the SimpleRegressionClassifier.
"""
cs = ConfigurationSpace()
if dataset_properties is None or not isinstance(dataset_properties, dict):
dataset_properties = dict()
if not 'target_type' in dataset_properties:
dataset_properties['target_type'] = 'regression'
if dataset_properties['target_type'] != 'regression':
dataset_properties['target_type'] = 'regression'
if 'sparse' not in dataset_properties:
# This dataset is probaby dense
dataset_properties['sparse'] = False
pipeline = cls._get_pipeline()
cs = cls._get_hyperparameter_search_space(cs, dataset_properties,
exclude, include, pipeline)
regressors = cs.get_hyperparameter('regressor:__choice__').choices
preprocessors = cs.get_hyperparameter('preprocessor:__choice__').choices
available_regressors = pipeline[-1][1].get_available_components(
dataset_properties)
available_preprocessors = pipeline[-2][1].get_available_components(
dataset_properties)
possible_default_regressor = copy.copy(list(
available_regressors.keys()))
default = cs.get_hyperparameter('regressor:__choice__').default
del possible_default_regressor[
possible_default_regressor.index(default)]
# A regressor which can handle sparse data after the densifier
for key in regressors:
if SPARSE in available_regressors[key].get_properties(dataset_properties=None)['input']:
if 'densifier' in preprocessors:
while True:
try:
cs.add_forbidden_clause(
ForbiddenAndConjunction(
ForbiddenEqualsClause(
cs.get_hyperparameter(
'regressor:__choice__'), key),
ForbiddenEqualsClause(
cs.get_hyperparameter(
'preprocessor:__choice__'), 'densifier')
))
break
except ValueError:
# Change the default and try again
try:
default = possible_default_regressor.pop()
except IndexError:
raise ValueError(
"Cannot find a legal default configuration.")
cs.get_hyperparameter(
'regressor:__choice__').default = default
# which would take too long
# Combinations of tree-based models with feature learning:
regressors_ = ["adaboost", "decision_tree", "extra_trees",
"gaussian_process", "gradient_boosting",
"k_nearest_neighbors", "random_forest", "xgradient_boosting"]
feature_learning_ = ["kitchen_sinks", "kernel_pca", "nystroem_sampler"]
for r, f in product(regressors_, feature_learning_):
if r not in regressors:
continue
if f not in preprocessors:
continue
while True:
try:
cs.add_forbidden_clause(ForbiddenAndConjunction(
ForbiddenEqualsClause(cs.get_hyperparameter(
"regressor:__choice__"), r),
ForbiddenEqualsClause(cs.get_hyperparameter(
"preprocessor:__choice__"), f)))
break
except KeyError:
break
except ValueError:
# Change the default and try again
try:
default = possible_default_regressor.pop()
except IndexError:
raise ValueError(
"Cannot find a legal default configuration.")
cs.get_hyperparameter(
'regressor:__choice__').default = default
return cs
def get_hyperspace(data_info,
include_estimators=None, include_preprocessors=None):
if data_info is None or not isinstance(data_info, dict):
data_info = dict()
if 'is_sparse' not in data_info:
# This dataset is probaby dense
data_info['is_sparse'] = False
sparse = data_info['is_sparse']
task_type = data_info['task']
multilabel = (task_type == MULTILABEL_CLASSIFICATION)
multiclass = (task_type == MULTICLASS_CLASSIFICATION)
if task_type in CLASSIFICATION_TASKS:
data_info['multilabel'] = multilabel
data_info['multiclass'] = multiclass
data_info['target_type'] = 'classification'
pipe_type = 'classifier'
# Components match to be forbidden
components_ = ["adaboost", "decision_tree", "extra_trees",
"gradient_boosting", "k_nearest_neighbors",
"libsvm_svc", "random_forest", "gaussian_nb",
"decision_tree"]
feature_learning_ = ["kitchen_sinks", "nystroem_sampler"]
elif task_type in REGRESSION_TASKS:
data_info['target_type'] = 'regression'
pipe_type = 'regressor'
# Components match to be forbidden
components_ = ["adaboost", "decision_tree", "extra_trees",
"gaussian_process", "gradient_boosting",
"k_nearest_neighbors", "random_forest"]
feature_learning_ = ["kitchen_sinks", "kernel_pca", "nystroem_sampler"]
else:
raise NotImplementedError()
include, exclude = dict(), dict()
if include_preprocessors is not None:
include["preprocessor"] = include_preprocessors
if include_estimators is not None:
include[pipe_type] = include_estimators
cs = ConfigurationSpace()
# Construct pipeline
# FIXME OrderedDIct?
pipeline = get_pipeline(data_info['task'])
# TODO include, exclude, pipeline
keys = [pair[0] for pair in pipeline]
for key in include:
if key not in keys:
raise ValueError('Invalid key in include: %s; should be one '
'of %s' % (key, keys))
for key in exclude:
if key not in keys:
raise ValueError('Invalid key in exclude: %s; should be one '
'of %s' % (key, keys))
# Construct hyperspace
# TODO What's the 'signed' stands for?
if 'signed' not in data_info:
# This dataset probably contains unsigned data
data_info['signed'] = False
match = check_pipeline(pipeline, data_info,
include=include, exclude=exclude)
# Now we have only legal combinations at this step of the pipeline
# Simple sanity checks
assert np.sum(match) != 0, "No valid pipeline found."
assert np.sum(match) <= np.size(match), \
"'matches' is not binary; %s <= %d, %s" % \
(str(np.sum(match)), np.size(match), str(match.shape))
# Iterate each dimension of the matches array (each step of the
# pipeline) to see if we can add a hyperparameter for that step
for node_idx, n_ in enumerate(pipeline):
node_name, node = n_
is_choice = hasattr(node, "get_available_components")
# if the node isn't a choice we can add it immediately because it
# must be active (if it wouldn't, np.sum(matches) would be zero
if not is_choice:
cs.add_configuration_space(node_name,
node.get_hyperparameter_search_space(data_info))
# If the node isn't a choice, we have to figure out which of it's
# choices are actually legal choices
else:
choices_list = find_active_choices(match, node, node_idx,data_info,
include=include.get(node_name),
exclude=exclude.get(node_name))
cs.add_configuration_space(node_name,
node.get_hyperparameter_search_space(data_info,
include=choices_list))
# And now add forbidden parameter configurations
# According to matches
if np.sum(match) < np.size(match):
cs = add_forbidden(conf_space=cs, pipeline=pipeline, matches=match,
dataset_properties=data_info, include=include, exclude=exclude)
components = cs.get_hyperparameter('%s:__choice__' % pipe_type).choices
availables = pipeline[-1][1].get_available_components(data_info)
preprocessors = cs.get_hyperparameter('preprocessor:__choice__').choices
#available_preprocessors = pipeline[-2][1].get_available_components(data_info)
possible_default = copy.copy(list(availables.keys()))
default = cs.get_hyperparameter('%s:__choice__' % pipe_type).default
del possible_default[possible_default.index(default)]
# A classifier which can handle sparse data after the densifier is
# forbidden for memory issues
for key in components:
# TODO regression dataset_properties=None
if SPARSE in availables[key].get_properties()['input']:
if 'densifier' in preprocessors:
while True:
try:
cs.add_forbidden_clause(
ForbiddenAndConjunction(
ForbiddenEqualsClause(
cs.get_hyperparameter(
'%s:__choice__' % pipe_type), key),
ForbiddenEqualsClause(
cs.get_hyperparameter(
'preprocessor:__choice__'), 'densifier')
))
# Success
break
except ValueError:
# Change the default and try again
try:
default = possible_default.pop()
except IndexError:
raise ValueError("Cannot find a legal default configuration.")
cs.get_hyperparameter('%s:__choice__' % pipe_type).default = default
# which would take too long
# Combinations of non-linear models with feature learning:
for c, f in itertools.product(components_, feature_learning_):
if c not in components:
continue
if f not in preprocessors:
continue
while True:
try:
cs.add_forbidden_clause(ForbiddenAndConjunction(
ForbiddenEqualsClause(cs.get_hyperparameter(
"%s:__choice__" % pipe_type), c),
ForbiddenEqualsClause(cs.get_hyperparameter(
"preprocessor:__choice__"), f)))
break
except KeyError:
break
except ValueError as e:
# Change the default and try again
try:
default = possible_default.pop()
except IndexError:
raise ValueError(
"Cannot find a legal default configuration.")
cs.get_hyperparameter('%s:__choice__' % pipe_type).default = default
if task_type in CLASSIFICATION_TASKS:
# Won't work
# Multinomial NB etc don't use with features learning, pca etc
components_ = ["multinomial_nb"]
preproc_with_negative_X = ["kitchen_sinks", "pca", "truncatedSVD",
"fast_ica", "kernel_pca", "nystroem_sampler"]
for c, f in itertools.product(components_, preproc_with_negative_X):
if c not in components:
continue
if f not in preprocessors:
continue
while True:
try:
cs.add_forbidden_clause(ForbiddenAndConjunction(
ForbiddenEqualsClause(cs.get_hyperparameter(
"preprocessor:__choice__"), f),
ForbiddenEqualsClause(cs.get_hyperparameter(
"classifier:__choice__"), c)))
break
except KeyError:
break
except ValueError:
# Change the default and try again
try:
default = possible_default.pop()
except IndexError:
raise ValueError(
"Cannot find a legal default configuration.")
cs.get_hyperparameter('classifier:__choice__').default = default
return cs
def get_hyperparameter_search_space(cls, include=None, exclude=None,
dataset_properties=None):
"""Create the hyperparameter configuration space.
Parameters
----------
include : dict (optional, default=None)
Returns
-------
"""
cs = ConfigurationSpace()
if dataset_properties is None or not isinstance(dataset_properties, dict):
dataset_properties = dict()
if not 'target_type' in dataset_properties:
dataset_properties['target_type'] = 'classification'
if dataset_properties['target_type'] != 'classification':
dataset_properties['target_type'] = 'classification'
pipeline = cls._get_pipeline()
cs = cls._get_hyperparameter_search_space(cs, dataset_properties,
exclude, include, pipeline)
classifiers = cs.get_hyperparameter('classifier:__choice__').choices
preprocessors = cs.get_hyperparameter('preprocessor:__choice__').choices
available_classifiers = pipeline[-1][1].get_available_components(
dataset_properties)
available_preprocessors = pipeline[-2][1].get_available_components(
dataset_properties)
possible_default_classifier = copy.copy(list(
available_classifiers.keys()))
default = cs.get_hyperparameter('classifier:__choice__').default
del possible_default_classifier[possible_default_classifier.index(default)]
# A classifier which can handle sparse data after the densifier is
# forbidden for memory issues
for key in classifiers:
if SPARSE in available_classifiers[key].get_properties()['input']:
if 'densifier' in preprocessors:
while True:
try:
cs.add_forbidden_clause(
ForbiddenAndConjunction(
ForbiddenEqualsClause(
cs.get_hyperparameter(
'classifier:__choice__'), key),
ForbiddenEqualsClause(
cs.get_hyperparameter(
'preprocessor:__choice__'), 'densifier')
))
# Success
break
except ValueError:
# Change the default and try again
try:
default = possible_default_classifier.pop()
except IndexError:
raise ValueError("Cannot find a legal default configuration.")
cs.get_hyperparameter(
'classifier:__choice__').default = default
# which would take too long
# Combinations of non-linear models with feature learning:
classifiers_ = ["adaboost", "decision_tree", "extra_trees",
"gradient_boosting", "k_nearest_neighbors",
"libsvm_svc", "random_forest", "gaussian_nb",
"decision_tree", "xgradient_boosting"]
feature_learning = ["kitchen_sinks", "nystroem_sampler"]
for c, f in product(classifiers_, feature_learning):
if c not in classifiers:
continue
if f not in preprocessors:
continue
while True:
try:
cs.add_forbidden_clause(ForbiddenAndConjunction(
ForbiddenEqualsClause(cs.get_hyperparameter(
"classifier:__choice__"), c),
ForbiddenEqualsClause(cs.get_hyperparameter(
"preprocessor:__choice__"), f)))
break
except KeyError:
break
except ValueError as e:
# Change the default and try again
try:
default = possible_default_classifier.pop()
except IndexError:
raise ValueError(
"Cannot find a legal default configuration.")
cs.get_hyperparameter(
'classifier:__choice__').default = default
# Won't work
# Multinomial NB etc don't use with features learning, pca etc
classifiers_ = ["multinomial_nb"]
preproc_with_negative_X = ["kitchen_sinks", "pca", "truncatedSVD",
"fast_ica", "kernel_pca", "nystroem_sampler"]
for c, f in product(classifiers_, preproc_with_negative_X):
if c not in classifiers:
continue
if f not in preprocessors:
continue
while True:
try:
cs.add_forbidden_clause(ForbiddenAndConjunction(
ForbiddenEqualsClause(cs.get_hyperparameter(
"preprocessor:__choice__"), f),
ForbiddenEqualsClause(cs.get_hyperparameter(
"classifier:__choice__"), c)))
break
except KeyError:
break
except ValueError:
# Change the default and try again
try:
default = possible_default_classifier.pop()
except IndexError:
raise ValueError(
"Cannot find a legal default configuration.")
cs.get_hyperparameter(
'classifier:__choice__').default = default
return cs
def read(pcs_string, debug=False):
"""
Reads in a :py:class:`~ConfigSpace.configuration_space.ConfigurationSpace`
definition from a pcs file.
Example
-------
>>> from ConfigSpace.read_and_write import pcs
>>> with open('configspace.pcs', 'r') as fh:
>>> restored_conf = pcs_new.read(fh)
Parameters
----------
pcs_string : str
ConfigSpace definition in pcs format
debug : bool
Provides debug information. Defaults to False.
Returns
-------
:py:class:`~ConfigSpace.configuration_space.ConfigurationSpace`
The restored ConfigurationSpace object
"""
configuration_space = ConfigurationSpace()
conditions = []
forbidden = []
# some statistics
ct = 0
cont_ct = 0
cat_ct = 0
line_ct = 0
for line in pcs_string:
line_ct += 1
if "#" in line:
# It contains a comment
pos = line.find("#")
line = line[:pos]
# Remove quotes and whitespaces at beginning and end
line = line.replace('"', "").replace("'", "")
line = line.strip()
if "|" in line:
# It's a condition
try:
c = pp_condition.parseString(line)
conditions.append(c)
except pyparsing.ParseException:
raise NotImplementedError("Could not parse condition: %s" % line)
continue
if "}" not in line and "]" not in line:
continue
if line.startswith("{") and line.endswith("}"):
forbidden.append(line)
continue
if len(line.strip()) == 0:
continue
ct += 1
param = None
create = {"int": UniformIntegerHyperparameter,
"float": UniformFloatHyperparameter,
"categorical": CategoricalHyperparameter}
try:
param_list = pp_cont_param.parseString(line)
il = param_list[9:]
if len(il) > 0:
il = il[0]
param_list = param_list[:9]
name = param_list[0]
lower = float(param_list[2])
upper = float(param_list[4])
paramtype = "int" if "i" in il else "float"
log = True if "l" in il else False
default_value = float(param_list[7])
param = create[paramtype](name=name, lower=lower, upper=upper,
q=None, log=log, default_value=default_value)
cont_ct += 1
except pyparsing.ParseException:
pass
try:
param_list = pp_cat_param.parseString(line)
name = param_list[0]
choices = [c for c in param_list[2:-4:2]]
default_value = param_list[-2]
param = create["categorical"](name=name, choices=choices,
default_value=default_value)
cat_ct += 1
except pyparsing.ParseException:
pass
if param is None:
raise NotImplementedError("Could not parse: %s" % line)
configuration_space.add_hyperparameter(param)
for clause in forbidden:
# TODO test this properly!
# TODO Add a try/catch here!
# noinspection PyUnusedLocal
param_list = pp_forbidden_clause.parseString(clause)
tmp_list = []
clause_list = []
for value in param_list[1:]:
if len(tmp_list) < 3:
tmp_list.append(value)
else:
# So far, only equals is supported by SMAC
if tmp_list[1] == '=':
# TODO maybe add a check if the hyperparameter is
# actually in the configuration space
clause_list.append(ForbiddenEqualsClause(
configuration_space.get_hyperparameter(tmp_list[0]),
tmp_list[2]))
else:
raise NotImplementedError()
tmp_list = []
configuration_space.add_forbidden_clause(ForbiddenAndConjunction(
*clause_list))
# Now handle conditions
# If there are two conditions for one child, these two conditions are an
# AND-conjunction of conditions, thus we have to connect them
conditions_per_child = OrderedDict()
for condition in conditions:
child_name = condition[0]
if child_name not in conditions_per_child:
conditions_per_child[child_name] = list()
conditions_per_child[child_name].append(condition)
for child_name in conditions_per_child:
condition_objects = []
for condition in conditions_per_child[child_name]:
child = configuration_space.get_hyperparameter(child_name)
parent_name = condition[2]
parent = configuration_space.get_hyperparameter(parent_name)
restrictions = condition[5:-1:2]
# TODO: cast the type of the restriction!
if len(restrictions) == 1:
condition = EqualsCondition(child, parent, restrictions[0])
else:
condition = InCondition(child, parent, values=restrictions)
condition_objects.append(condition)
# Now we have all condition objects for this child, so we can build a
# giant AND-conjunction of them (if number of conditions >= 2)!
if len(condition_objects) > 1:
and_conjunction = AndConjunction(*condition_objects)
configuration_space.add_condition(and_conjunction)
else:
configuration_space.add_condition(condition_objects[0])
return configuration_space
def _get_hyperparameter_search_space(self, include=None, exclude=None,
dataset_properties=None):
"""Return the configuration space for the CASH problem.
Parameters
----------
include_estimators : list of str
If include_estimators is given, only the regressors specified
are used. Specify them by their module name; e.g., to include
only the SVM use :python:`include_regressors=['svr']`.
Cannot be used together with :python:`exclude_regressors`.
exclude_estimators : list of str
If exclude_estimators is given, only the regressors specified
are used. Specify them by their module name; e.g., to include
all regressors except the SVM use
:python:`exclude_regressors=['svr']`.
Cannot be used together with :python:`include_regressors`.
include_preprocessors : list of str
If include_preprocessors is given, only the preprocessors specified
are used. Specify them by their module name; e.g., to include
only the PCA use :python:`include_preprocessors=['pca']`.
Cannot be used together with :python:`exclude_preprocessors`.
exclude_preprocessors : list of str
If include_preprocessors is given, only the preprocessors specified
are used. Specify them by their module name; e.g., to include
all preprocessors except the PCA use
:python:`exclude_preprocessors=['pca']`.
Cannot be used together with :python:`include_preprocessors`.
Returns
-------
cs : ConfigSpace.configuration_space.Configuration
The configuration space describing the SimpleRegressionClassifier.
"""
cs = ConfigurationSpace()
if dataset_properties is None or not isinstance(dataset_properties, dict):
dataset_properties = dict()
if not 'target_type' in dataset_properties:
dataset_properties['target_type'] = 'regression'
if dataset_properties['target_type'] != 'regression':
dataset_properties['target_type'] = 'regression'
if 'sparse' not in dataset_properties:
# This dataset is probaby dense
dataset_properties['sparse'] = False
cs = self._get_base_search_space(
cs=cs, dataset_properties=dataset_properties,
exclude=exclude, include=include, pipeline=self.steps)
regressors = cs.get_hyperparameter('regressor:__choice__').choices
preprocessors = cs.get_hyperparameter('feature_preprocessor:__choice__').choices
available_regressors = self._final_estimator.get_available_components(
dataset_properties)
possible_default_regressor = copy.copy(list(
available_regressors.keys()))
default = cs.get_hyperparameter('regressor:__choice__').default_value
del possible_default_regressor[
possible_default_regressor.index(default)]
# A regressor which can handle sparse data after the densifier is
# forbidden for memory issues
for key in regressors:
if SPARSE in available_regressors[key].get_properties(dataset_properties=None)['input']:
if 'densifier' in preprocessors:
while True:
try:
cs.add_forbidden_clause(
ForbiddenAndConjunction(
ForbiddenEqualsClause(
cs.get_hyperparameter(
'regressor:__choice__'), key),
ForbiddenEqualsClause(
cs.get_hyperparameter(
'feature_preprocessor:__choice__'), 'densifier')
))
# Success
break
except ValueError:
# Change the default and try again
try:
default = possible_default_regressor.pop()
except IndexError:
raise ValueError(
"Cannot find a legal default configuration.")
cs.get_hyperparameter(
'regressor:__choice__').default_value = default
# which would take too long
# Combinations of tree-based models with feature learning:
regressors_ = ["adaboost", "decision_tree", "extra_trees",
"gaussian_process", "gradient_boosting",
"k_nearest_neighbors", "random_forest", "xgradient_boosting"]
feature_learning_ = ["kitchen_sinks", "kernel_pca", "nystroem_sampler"]
for r, f in product(regressors_, feature_learning_):
if r not in regressors:
continue
if f not in preprocessors:
continue
while True:
try:
cs.add_forbidden_clause(ForbiddenAndConjunction(
ForbiddenEqualsClause(cs.get_hyperparameter(
"regressor:__choice__"), r),
ForbiddenEqualsClause(cs.get_hyperparameter(
"feature_preprocessor:__choice__"), f)))
break
except KeyError:
break
except ValueError:
# Change the default and try again
try:
default = possible_default_regressor.pop()
except IndexError:
raise ValueError(
"Cannot find a legal default configuration.")
cs.get_hyperparameter(
'regressor:__choice__').default_value = default
self.configuration_space_ = cs
self.dataset_properties_ = dataset_properties
return cs
class AutoFolio(object):
def __init__(self, random_seed: int=12345):
''' Constructor
Arguments
---------
random_seed: int
random seed for numpy and random packages
'''
np.random.seed(random_seed) # fix seed
random.seed(random_seed)
# I don't know the reason, but without an initial print with
# logging.info we don't get any output
logging.info("Init AutoFolio")
self._root_logger = logging.getLogger()
self.logger = logging.getLogger("AutoFolio")
self.cs = None
self.overwrite_args = None
def run_cli(self):
'''
main method of AutoFolio based on command line interface
'''
cmd_parser = CMDParser()
args_, self.overwrite_args = cmd_parser.parse()
self._root_logger.setLevel(args_.verbose)
if args_.load:
self.read_model_and_predict(
model_fn=args_.load, feature_vec=list(map(float, args_.feature_vec)))
else:
scenario = ASlibScenario()
if args_.scenario:
scenario.read_scenario(args_.scenario)
elif args_.performance_csv and args_.feature_csv:
scenario.read_from_csv(perf_fn=args_.performance_csv,
feat_fn=args_.feature_csv,
objective=args_.objective,
runtime_cutoff=args_.runtime_cutoff,
maximize=args_.maximize)
self.cs = self.get_cs(scenario)
if args_.tune:
config = self.get_tuned_config(scenario)
else:
config = self.cs.get_default_configuration()
self.logger.debug(config)
if args_.save:
feature_pre_pipeline, pre_solver, selector = self.fit(
scenario=scenario, config=config)
self._save_model(
args_.save, scenario, feature_pre_pipeline, pre_solver, selector, config)
else:
self.run_cv(config=config, scenario=scenario, folds=10)
def _save_model(self, out_fn: str, scenario: ASlibScenario, feature_pre_pipeline: list, pre_solver: Aspeed, selector, config: Configuration):
'''
save all pipeline objects for predictions
Arguments
---------
out_fn: str
filename of output file
scenario: AslibScenario
ASlib scenario with all the data
feature_pre_pipeline: list
list of preprocessing objects
pre_solver: Aspeed
aspeed object with pre-solving schedule
selector: autofolio.selector.*
fitted selector object
config: Configuration
parameter setting configuration
'''
scenario.logger = None
for fpp in feature_pre_pipeline:
fpp.logger = None
if pre_solver:
pre_solver.logger = None
selector.logger = None
model = [scenario, feature_pre_pipeline, pre_solver, selector, config]
with open(out_fn, "bw") as fp:
pickle.dump(model, fp)
def read_model_and_predict(self, model_fn: str, feature_vec: list):
'''
reads saved model from disk and predicts the selected algorithm schedule for a given feature vector
Arguments
--------
model_fn: str
file name of saved model
feature_vec: list
instance feature vector as a list of floats
'''
with open(model_fn, "br") as fp:
scenario, feature_pre_pipeline, pre_solver, selector, config = pickle.load(
fp)
for fpp in feature_pre_pipeline:
fpp.logger = logging.getLogger("Feature Preprocessing")
if pre_solver:
pre_solver.logger = logging.getLogger("Aspeed PreSolving")
selector.logger = logging.getLogger("Selector")
# saved scenario is adapted to given feature vector
feature_vec = np.array([feature_vec])
scenario.feature_data = pd.DataFrame(
feature_vec, index=["pseudo_instance"], columns=scenario.feature_names)
scenario.instances = ["pseudo_instance"]
pred = self.predict(scenario=scenario, config=config,
feature_pre_pipeline=feature_pre_pipeline, pre_solver=pre_solver, selector=selector)
print("Selected Schedule [(algorithm, budget)]: %s" % (
pred["pseudo_instance"]))
def get_cs(self, scenario: ASlibScenario):
'''
returns the parameter configuration space of AutoFolio
(based on the automl config space: https://github.com/automl/ConfigSpace)
Arguments
---------
scenario: autofolio.data.aslib_scenario.ASlibScenario
aslib scenario at hand
'''
self.cs = ConfigurationSpace()
# add feature steps as binary parameters
for fs in scenario.feature_steps:
fs_param = CategoricalHyperparameter(name="fgroup_%s" % (
fs), choices=[True, False], default=fs in scenario.feature_steps_default)
self.cs.add_hyperparameter(fs_param)
# preprocessing
PCAWrapper.add_params(self.cs)
ImputerWrapper.add_params(self.cs)
StandardScalerWrapper.add_params(self.cs)
# Pre-Solving
if scenario.performance_type[0] == "runtime":
Aspeed.add_params(
cs=self.cs, cutoff=scenario.algorithm_cutoff_time)
# classifiers
RandomForest.add_params(self.cs)
# selectors
PairwiseClassifier.add_params(self.cs)
return self.cs
def get_tuned_config(self, scenario: ASlibScenario):
'''
uses SMAC3 to determine a well-performing configuration in the configuration space self.cs on the given scenario
Arguments
---------
scenario: ASlibScenario
ASlib Scenario at hand
Returns
-------
Configuration
best incumbent configuration found by SMAC
'''
taf = ExecuteTAFunc(functools.partial(self.run_cv, scenario=scenario))
ac_scenario = Scenario({"run_obj": "quality", # we optimize quality
# at most 10 function evaluations
"runcount-limit": 10,
"cs": self.cs, # configuration space
"deterministic": "true"
})
# necessary to use stats options related to scenario information
AC_Stats.scenario = ac_scenario
# Optimize
self.logger.info(
">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>")
self.logger.info("Start Configuration")
self.logger.info(
">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>")
smbo = SMBO(scenario=ac_scenario, tae_runner=taf,
rng=np.random.RandomState(42))
smbo.run(max_iters=999)
AC_Stats.print_stats()
self.logger.info("Final Incumbent: %s" % (smbo.incumbent))
return smbo.incumbent
def run_cv(self, config: Configuration, scenario: ASlibScenario, folds=10):
'''
run a cross fold validation based on the given data from cv.arff
Arguments
---------
scenario: autofolio.data.aslib_scenario.ASlibScenario
aslib scenario at hand
config: Configuration
parameter configuration to use for preprocessing
folds: int
number of cv-splits
'''
try:
if scenario.performance_type[0] == "runtime":
cv_stat = Stats(runtime_cutoff=scenario.algorithm_cutoff_time)
else:
cv_stat = Stats(runtime_cutoff=0)
for i in range(1, folds + 1):
self.logger.info("CV-Iteration: %d" % (i))
test_scenario, training_scenario = scenario.get_split(indx=i)
feature_pre_pipeline, pre_solver, selector = self.fit(
scenario=training_scenario, config=config)
schedules = self.predict(
test_scenario, config, feature_pre_pipeline, pre_solver, selector)
val = Validator()
if scenario.performance_type[0] == "runtime":
stats = val.validate_runtime(
schedules=schedules, test_scenario=test_scenario)
elif scenario.performance_type[0] == "solution_quality":
stats = val.validate_quality(
schedules=schedules, test_scenario=test_scenario)
else:
raise ValueError("Unknown performance_type[0]")
cv_stat.merge(stat=stats)
self.logger.info(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>")
self.logger.info("CV Stats")
par10 = cv_stat.show()
except ValueError:
traceback.print_exc()
if not scenario.maximize[0]:
par10 = scenario.algorithm_cutoff_time * 10
else:
par10 = scenario.algorithm_cutoff_time * -10
if scenario.maximize[0]:
par10 *= -1
return par10
def fit(self, scenario: ASlibScenario, config: Configuration):
'''
fit AutoFolio on given ASlib Scenario
Arguments
---------
scenario: autofolio.data.aslib_scenario.ASlibScenario
aslib scenario at hand
config: Configuration
parameter configuration to use for preprocessing
Returns
-------
list of fitted feature preproccessing objects
pre-solving object
fitted selector
'''
self.logger.info("Given Configuration: %s" % (config))
if self.overwrite_args:
config = self._overwrite_configuration(
config=config, overwrite_args=self.overwrite_args)
self.logger.info("Overwritten Configuration: %s" % (config))
scenario, feature_pre_pipeline = self.fit_transform_feature_preprocessing(
scenario, config)
pre_solver = self.fit_pre_solving(scenario, config)
selector = self.fit_selector(scenario, config)
return feature_pre_pipeline, pre_solver, selector
def _overwrite_configuration(self, config: Configuration, overwrite_args: list):
'''
overwrites a given configuration with some new settings
Arguments
---------
config: Configuration
initial configuration to be adapted
overwrite_args: list
new parameter settings as a list of strings
Returns
-------
Configuration
'''
def pairwise(iterable):
a, b = tee(iterable)
next(b, None)
return zip(a, b)
dict_conf = config.get_dictionary()
for param, value in pairwise(overwrite_args):
if dict_conf.get(param):
if type(self.cs.get_hyperparameter(param)) is UniformIntegerHyperparameter:
dict_conf[param] = int(value)
elif type(self.cs.get_hyperparameter(param)) is UniformFloatHyperparameter:
dict_conf[param] = float(value)
elif value == "True":
dict_conf[param] = True
elif value == "False":
dict_conf[param] = False
else:
dict_conf[param] = value
else:
self.logger.warn(
"Unknown given parameter: %s %s" % (param, value))
config = Configuration(self.cs, values=dict_conf)
return config
def fit_transform_feature_preprocessing(self, scenario: ASlibScenario, config: Configuration):
'''
performs feature preprocessing on a given ASlib scenario wrt to a given configuration
Arguments
---------
scenario: autofolio.data.aslib_scenario.ASlibScenario
aslib scenario at hand
config: Configuration
parameter configuration to use for preprocessing
Returns
-------
list of fitted feature preproccessing objects
'''
pipeline = []
fgf = FeatureGroupFiltering()
scenario = fgf.fit_transform(scenario, config)
imputer = ImputerWrapper()
scenario = imputer.fit_transform(scenario, config)
scaler = StandardScalerWrapper()
scenario = scaler.fit_transform(scenario, config)
pca = PCAWrapper()
scenario = pca.fit_transform(scenario, config)
return scenario, [fgf, imputer, scaler, pca]
def fit_pre_solving(self, scenario: ASlibScenario, config: Configuration):
'''
fits an pre-solving schedule using Aspeed [Hoos et al, 2015 TPLP)
Arguments
---------
scenario: autofolio.data.aslib_scenario.ASlibScenario
aslib scenario at hand
config: Configuration
parameter configuration to use for preprocessing
Returns
-------
instance of Aspeed() with a fitted pre-solving schedule if performance_type of scenario is runtime; else None
'''
if scenario.performance_type[0] == "runtime":
aspeed = Aspeed()
aspeed.fit(scenario=scenario, config=config)
return aspeed
else:
return None
def fit_selector(self, scenario: ASlibScenario, config: Configuration):
'''
fits an algorithm selector for a given scenario wrt a given configuration
Arguments
---------
scenario: autofolio.data.aslib_scenario.ASlibScenario
aslib scenario at hand
config: Configuration
parameter configuration
'''
if config.get("selector") == "PairwiseClassifier":
clf_class = None
if config.get("classifier") == "RandomForest":
clf_class = RandomForest
selector = PairwiseClassifier(classifier_class=clf_class)
selector.fit(scenario=scenario, config=config)
return selector
def predict(self, scenario: ASlibScenario, config: Configuration, feature_pre_pipeline: list, pre_solver: Aspeed, selector):
'''
predicts algorithm schedules wrt a given config
and given pipelines
Arguments
---------
scenario: autofolio.data.aslib_scenario.ASlibScenario
aslib scenario at hand
config: Configuration
parameter configuration
feature_pre_pipeline: list
list of fitted feature preprocessors
pre_solver: Aspeed
pre solver object with a saved static schedule
selector: autofolio.selector.*
fitted selector object
'''
self.logger.info("Predict on Test")
for f_pre in feature_pre_pipeline:
scenario = f_pre.transform(scenario)
if pre_solver:
pre_solving_schedule = pre_solver.predict(scenario=scenario)
else:
pre_solving_schedule = {}
pred_schedules = selector.predict(scenario=scenario)
# combine schedules
if pre_solving_schedule:
return dict((inst, pre_solving_schedule.get(inst, []) + schedule) for inst, schedule in pred_schedules.items())
else:
return pred_schedules
class AutoFolio(object):
def __init__(self, random_seed: int=12345):
''' Constructor
Arguments
---------
random_seed: int
random seed for numpy and random packages
'''
np.random.seed(random_seed) # fix seed
random.seed(random_seed)
# I don't know the reason, but without an initial print with
# logging.info we don't get any output
logging.info("Init AutoFolio")
self._root_logger = logging.getLogger()
self.logger = logging.getLogger("AutoFolio")
self.cs = None
self.overwrite_args = None
def run_cli(self):
'''
main method of AutoFolio based on command line interface
'''
cmd_parser = CMDParser()
args_, self.overwrite_args = cmd_parser.parse()
self._root_logger.setLevel(args_.verbose)
if args_.load:
pred = self.read_model_and_predict(
model_fn=args_.load, feature_vec=list(map(float, args_.feature_vec.split(" "))))
print("Selected Schedule [(algorithm, budget)]: %s" % (pred))
else:
scenario = ASlibScenario()
if args_.scenario:
scenario.read_scenario(args_.scenario)
elif args_.performance_csv and args_.feature_csv:
scenario.read_from_csv(perf_fn=args_.performance_csv,
feat_fn=args_.feature_csv,
objective=args_.objective,
runtime_cutoff=args_.runtime_cutoff,
maximize=args_.maximize,
cv_fn=args_.cv_csv)
else:
raise ValueError("Missing inputs to read scenario data.")
test_scenario = None
if args_.performance_test_csv and args_.feature_test_csv:
test_scenario = ASlibScenario()
test_scenario.read_from_csv(perf_fn=args_.performance_test_csv,
feat_fn=args_.feature_test_csv,
objective=args_.objective,
runtime_cutoff=args_.runtime_cutoff,
maximize=args_.maximize,
cv_fn=None)
config = {}
if args_.config is not None:
self.logger.info("Reading yaml config file")
config = yaml.load(open(args_.config))
if not config.get("wallclock_limit"):
config["wallclock_limit"] = args_.wallclock_limit
if not config.get("runcount_limit"):
config["runcount_limit"] = args_.runcount_limit
if not config.get("output-dir"):
config["output-dir"] = args_.output_dir
self.cs = self.get_cs(scenario, config)
if args_.outer_cv:
self._outer_cv(scenario, config, args_.outer_cv_fold,
args_.out_template, smac_seed=args_.smac_seed)
return 0
if args_.tune:
config = self.get_tuned_config(scenario,
wallclock_limit=args_.wallclock_limit,
runcount_limit=args_.runcount_limit,
autofolio_config=config,
seed=args_.smac_seed)
else:
config = self.cs.get_default_configuration()
self.logger.debug(config)
if args_.save:
feature_pre_pipeline, pre_solver, selector = self.fit(
scenario=scenario, config=config)
self._save_model(
args_.save, scenario, feature_pre_pipeline, pre_solver, selector, config)
else:
self.run_cv(config=config, scenario=scenario, folds=int(scenario.cv_data.max().max()))
if test_scenario is not None:
stats = self.run_fold(config=config,
fold=0,
return_fit=False,
scenario=scenario,
test_scenario=test_scenario)
def _outer_cv(self, scenario: ASlibScenario, autofolio_config:dict=None,
outer_cv_fold:int=None, out_template:str=None,
smac_seed:int=42):
'''
Evaluate on a scenario using an "outer" cross-fold validation
scheme. In particular, this ensures that SMAC does not use the test
set during hyperparameter optimization.
Arguments
---------
scenario: ASlibScenario
ASlib Scenario at hand
autofolio_config: dict, or None
An optional dictionary of configuration options
outer_cv_fold: int, or None
If given, then only the single outer-cv fold is processed
out_template: str, or None
If given, the learned configurations are written to the
specified locations. The string is considered a template, and
"%fold%" will be replaced with the fold.
smac_seed:int
random seed for SMAC
Returns
-------
stats: validate.Stats
Performance over all outer-cv folds
'''
import string
outer_stats = None
# For each outer split
outer_cv_folds = range(1, 11)
if outer_cv_fold is not None:
outer_cv_folds = range(outer_cv_fold, outer_cv_fold+1)
for cv_fold in outer_cv_folds:
# Use ‘ASlibScenario.get_split()’ to get the outer split
outer_testing, outer_training = scenario.get_split(cv_fold)
msg = ">>>>> Outer CV fold: {} <<<<<".format(cv_fold)
self.logger.info(msg)
# Use ASlibScenario.create_cv_splits() to get an inner-cv
outer_training.create_cv_splits(n_folds=10)
# Use ‘AutoFolio.get_tuned_config()’ to tune on inner-cv
config = self.get_tuned_config(
outer_training,
autofolio_config=autofolio_config,
seed=smac_seed
)
# Use `AutoFolio.run_fold()’ to get the performance on the outer split
stats, fit, schedule = self.run_fold(
config,
scenario,
cv_fold,
return_fit=True
)
feature_pre_pipeline, pre_solver, selector = fit
if outer_stats is None:
outer_stats = stats
else:
outer_stats.merge(stats)
# save the model, if given an output location
if out_template is not None:
out_template_ = string.Template(out_template)
model_fn = out_template_.substitute(fold=cv_fold, type="pkl")
msg = "Writing model to: {}".format(model_fn)
self.logger.info(msg)
self._save_model(
model_fn,
scenario,
feature_pre_pipeline,
pre_solver,
selector,
config
)
# convert the schedule to a data frame
schedule_df = pd.Series(schedule, name="solver")
schedule_df.index.name = "instance"
schedule_df = schedule_df.reset_index()
# just keep the solver name; we don't care about the time
# x[0] gets the first pair in the schedule list
# and x[0][0] gets the name of the solver from that pair
schedule_df['solver'] = schedule_df['solver'].apply(lambda x: x[0][0])
selections_fn = out_template_.substitute(fold=cv_fold, type="csv")
msg = "Writing solver choices to: {}".format(selections_fn)
self.logger.info(msg)
schedule_df.to_csv(selections_fn, index=False)
self.logger.info(">>>>> Final Stats <<<<<")
outer_stats.show()
def _save_model(self, out_fn: str, scenario: ASlibScenario, feature_pre_pipeline: list, pre_solver: Aspeed, selector, config: Configuration):
'''
save all pipeline objects for predictions
Arguments
---------
out_fn: str
filename of output file
scenario: AslibScenario
ASlib scenario with all the data
feature_pre_pipeline: list
list of preprocessing objects
pre_solver: Aspeed
aspeed object with pre-solving schedule
selector: autofolio.selector.*
fitted selector object
config: Configuration
parameter setting configuration
'''
scenario.logger = None
for fpp in feature_pre_pipeline:
fpp.logger = None
if pre_solver:
pre_solver.logger = None
selector.logger = None
model = [scenario, feature_pre_pipeline, pre_solver, selector, config]
with open(out_fn, "bw") as fp:
pickle.dump(model, fp)
def read_model_and_predict(self, model_fn: str, feature_vec: list):
'''
reads saved model from disk and predicts the selected algorithm schedule for a given feature vector
Arguments
--------
model_fn: str
file name of saved model
feature_vec: list
instance feature vector as a list of floats
Returns
-------
list of tuple
Selected schedule [(algorithm, budget)]
'''
with open(model_fn, "br") as fp:
scenario, feature_pre_pipeline, pre_solver, selector, config = pickle.load(
fp)
for fpp in feature_pre_pipeline:
fpp.logger = logging.getLogger("Feature Preprocessing")
if pre_solver:
pre_solver.logger = logging.getLogger("Aspeed PreSolving")
selector.logger = logging.getLogger("Selector")
# saved scenario is adapted to given feature vector
feature_vec = np.array([feature_vec])
scenario.feature_data = pd.DataFrame(
feature_vec, index=["pseudo_instance"], columns=scenario.features)
scenario.instances = ["pseudo_instance"]
pred = self.predict(scenario=scenario, config=config,
feature_pre_pipeline=feature_pre_pipeline, pre_solver=pre_solver, selector=selector)
return pred["pseudo_instance"]
def get_cs(self, scenario: ASlibScenario, autofolio_config:dict=None):
'''
returns the parameter configuration space of AutoFolio
(based on the automl config space: https://github.com/automl/ConfigSpace)
Arguments
---------
scenario: aslib_scenario.aslib_scenario.ASlibScenario
aslib scenario at hand
autofolio_config: dict, or None
An optional dictionary of configuration options
'''
self.cs = ConfigurationSpace()
# only allow the feature groups specified in the config file
# by default, though, all of the feature groups are allowed.
allowed_feature_groups = autofolio_config.get("allowed_feature_groups",
scenario.feature_steps)
if len(allowed_feature_groups) == 0:
msg = "Please ensure at least one feature group is allowed"
raise ValueError(msg)
if len(allowed_feature_groups) == 1:
choices = [True] # if we only have one feature group, it has to be active
else:
choices = [True, False]
default = True
for fs in allowed_feature_groups:
fs_param = CategoricalHyperparameter(name="fgroup_%s" % (fs),
choices=choices, default_value=default)
self.cs.add_hyperparameter(fs_param)
# preprocessing
if autofolio_config.get("pca", True):
PCAWrapper.add_params(self.cs)
if autofolio_config.get("impute", True):
ImputerWrapper.add_params(self.cs)
if autofolio_config.get("scale", True):
StandardScalerWrapper.add_params(self.cs)
# Pre-Solving
if scenario.performance_type[0] == "runtime":
if autofolio_config.get("presolve", True):
Aspeed.add_params(
cs=self.cs, cutoff=scenario.algorithm_cutoff_time)
if autofolio_config.get("classifier"):
# fix parameter
cls_choices = [autofolio_config["classifier"]]
cls_def = autofolio_config["classifier"]
else:
cls_choices = ["RandomForest","XGBoost"]
cls_def = "RandomForest"
classifier = CategoricalHyperparameter(
"classifier", choices=cls_choices,
default_value=cls_def)
self.cs.add_hyperparameter(classifier)
RandomForest.add_params(self.cs)
XGBoost.add_params(self.cs)
if autofolio_config.get("regressor"):
# fix parameter
reg_choices = [autofolio_config["regressor"]]
reg_def = autofolio_config["regressor"]
else:
reg_choices = ["RandomForestRegressor"]
reg_def = "RandomForestRegressor"
regressor = CategoricalHyperparameter(
"regressor", choices=reg_choices, default_value=reg_def)
self.cs.add_hyperparameter(regressor)
RandomForestRegressor.add_params(self.cs)
# selectors
if autofolio_config.get("selector"):
# fix parameter
sel_choices = [autofolio_config["selector"]]
sel_def = autofolio_config["selector"]
else:
sel_choices = ["PairwiseClassifier","PairwiseRegressor"]
sel_def = "PairwiseClassifier"
selector = CategoricalHyperparameter(
"selector", choices=sel_choices, default_value=sel_def)
self.cs.add_hyperparameter(selector)
PairwiseClassifier.add_params(self.cs)
PairwiseRegression.add_params(self.cs)
self.logger.debug(self.cs)
return self.cs
def get_tuned_config(self, scenario: ASlibScenario,
runcount_limit:int=42,
wallclock_limit:int=300,
autofolio_config:dict=dict(),
seed:int=42):
'''
uses SMAC3 to determine a well-performing configuration in the configuration space self.cs on the given scenario
Arguments
---------
scenario: ASlibScenario
ASlib Scenario at hand
runcount_limit: int
runcount_limit for SMAC scenario
wallclock_limit: int
wallclock limit in sec for SMAC scenario
(overwritten by autofolio_config)
autofolio_config: dict, or None
An optional dictionary of configuration options
seed: int
random seed for SMAC
Returns
-------
Configuration
best incumbent configuration found by SMAC
'''
wallclock_limit = autofolio_config.get("wallclock_limit", wallclock_limit)
runcount_limit = autofolio_config.get("runcount_limit", runcount_limit)
taf = functools.partial(self.called_by_smac, scenario=scenario)
max_fold = scenario.cv_data.max().max()
max_fold = int(max_fold)
ac_scenario = Scenario({"run_obj": "quality", # we optimize quality
"runcount-limit": runcount_limit,
"cs": self.cs, # configuration space
"deterministic": "true",
"instances": [[str(i)] for i in range(1, max_fold+1)],
"wallclock-limit": wallclock_limit,
"output-dir" : "" if not autofolio_config.get("output-dir",None) else autofolio_config.get("output-dir")
})
# necessary to use stats options related to scenario information
AC_Stats.scenario = ac_scenario
# Optimize
self.logger.info(
">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>")
self.logger.info("Start Configuration")
self.logger.info(
">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>")
smac = SMAC(scenario=ac_scenario, tae_runner=taf,
rng=np.random.RandomState(seed))
incumbent = smac.optimize()
self.logger.info("Final Incumbent: %s" % (incumbent))
return incumbent
def called_by_smac(self, config: Configuration, scenario: ASlibScenario, instance:str=None, seed:int=1):
'''
run a cross fold validation based on the given data from cv.arff
Arguments
---------
config: Configuration
parameter configuration to use for preprocessing
scenario: aslib_scenario.aslib_scenario.ASlibScenario
aslib scenario at hand
instance: str
cv-fold index
seed: int
random seed (not used)
Returns
-------
float: average performance
'''
if instance is None:
perf = self.run_cv(config=config, scenario=scenario)
else:
try:
stats = self.run_fold(config=config, scenario=scenario, fold=int(instance))
perf = stats.show()
except ValueError:
if scenario.performance_type[0] == "runtime":
perf = scenario.algorithm_cutoff_time * 20
else:
# try to impute a worst case perf
perf = scenario.performance_data.max().max()
if scenario.maximize[0]:
perf *= -1
return perf
def run_cv(self, config: Configuration, scenario: ASlibScenario, folds:int=10):
'''
run a cross fold validation based on the given data from cv.arff
Arguments
---------
scenario: aslib_scenario.aslib_scenario.ASlibScenario
aslib scenario at hand
config: Configuration
parameter configuration to use for preprocessing
folds: int
number of cv-splits
seed: int
random seed (not used)
'''
#TODO: use seed and instance in an appropriate way
try:
if scenario.performance_type[0] == "runtime":
cv_stat = Stats(runtime_cutoff=scenario.algorithm_cutoff_time)
else:
cv_stat = Stats(runtime_cutoff=0)
for i in range(1, folds + 1):
self.logger.info("CV-Iteration: %d" % (i))
stats = self.run_fold(config=config,
scenario=scenario,
fold=i)
cv_stat.merge(stat=stats)
self.logger.info(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>")
self.logger.info("CV Stats")
par10 = cv_stat.show()
except ValueError:
traceback.print_exc()
par10 = scenario.algorithm_cutoff_time * 10
if scenario.maximize[0]:
par10 *= -1
return par10
def run_fold(self, config: Configuration, scenario:ASlibScenario, fold:int, test_scenario=None, return_fit:bool=False):
'''
run a given fold of cross validation
Arguments
---------
scenario: aslib_scenario.aslib_scenario.ASlibScenario
aslib scenario at hand
config: Configuration
parameter configuration to use for preprocessing
fold: int
fold id
test_scenario:aslib_scenario.aslib_scenario.ASlibScenario
aslib scenario with test data for validation
generated from <scenario> if None
return_fit: bool
optionally, the learned preprocessing options, presolver and
selector can be returned
Returns
-------
Stats()
(pre_pipeline, pre_solver, selector):
only present if return_fit is True
the pipeline components fit with the configuration options
schedule: dict of string -> list of (solver, cutoff) pairs
only present if return_fit is True
the solver choices for each instance
'''
if test_scenario is None:
self.logger.info("CV-Iteration: %d" % (fold))
test_scenario, training_scenario = scenario.get_split(indx=fold)
else:
self.logger.info("Validation on test data")
training_scenario = scenario
feature_pre_pipeline, pre_solver, selector = self.fit(
scenario=training_scenario, config=config)
schedules = self.predict(
test_scenario, config, feature_pre_pipeline, pre_solver, selector)
val = Validator()
if scenario.performance_type[0] == "runtime":
stats = val.validate_runtime(
schedules=schedules, test_scenario=test_scenario, train_scenario=training_scenario)
elif scenario.performance_type[0] == "solution_quality":
stats = val.validate_quality(
schedules=schedules, test_scenario=test_scenario, train_scenario=training_scenario)
else:
raise ValueError("Unknown: %s" %(scenario.performance_type[0]))
if return_fit:
return stats, (feature_pre_pipeline, pre_solver, selector), schedules
else:
return stats
def fit(self, scenario: ASlibScenario, config: Configuration):
'''
fit AutoFolio on given ASlib Scenario
Arguments
---------
scenario: aslib_scenario.aslib_scenario.ASlibScenario
aslib scenario at hand
config: Configuration
parameter configuration to use for preprocessing
Returns
-------
list of fitted feature preproccessing objects
pre-solving object
fitted selector
'''
self.logger.info("Given Configuration: %s" % (config))
if self.overwrite_args:
config = self._overwrite_configuration(
config=config, overwrite_args=self.overwrite_args)
self.logger.info("Overwritten Configuration: %s" % (config))
scenario, feature_pre_pipeline = self.fit_transform_feature_preprocessing(
scenario, config)
pre_solver = self.fit_pre_solving(scenario, config)
selector = self.fit_selector(scenario, config)
return feature_pre_pipeline, pre_solver, selector
def _overwrite_configuration(self, config: Configuration, overwrite_args: list):
'''
overwrites a given configuration with some new settings
Arguments
---------
config: Configuration
initial configuration to be adapted
overwrite_args: list
new parameter settings as a list of strings
Returns
-------
Configuration
'''
def pairwise(iterable):
a, b = tee(iterable)
next(b, None)
return zip(a, b)
dict_conf = config.get_dictionary()
for param, value in pairwise(overwrite_args):
try:
ok = self.cs.get_hyperparameter(param)
except KeyError:
ok = None
if ok is not None:
if type(self.cs.get_hyperparameter(param)) is UniformIntegerHyperparameter:
dict_conf[param] = int(value)
elif type(self.cs.get_hyperparameter(param)) is UniformFloatHyperparameter:
dict_conf[param] = float(value)
elif value == "True":
dict_conf[param] = True
elif value == "False":
dict_conf[param] = False
else:
dict_conf[param] = value
else:
self.logger.warn(
"Unknown given parameter: %s %s" % (param, value))
config = Configuration(self.cs, values=dict_conf, allow_inactive_with_values=True)
return config
def fit_transform_feature_preprocessing(self, scenario: ASlibScenario, config: Configuration):
'''
performs feature preprocessing on a given ASlib scenario wrt to a given configuration
Arguments
---------
scenario: aslib_scenario.aslib_scenario.ASlibScenario
aslib scenario at hand
config: Configuration
parameter configuration to use for preprocessing
Returns
-------
list of fitted feature preproccessing objects
'''
pipeline = []
fgf = FeatureGroupFiltering()
scenario = fgf.fit_transform(scenario, config)
imputer = ImputerWrapper()
scenario = imputer.fit_transform(scenario, config)
scaler = StandardScalerWrapper()
scenario = scaler.fit_transform(scenario, config)
pca = PCAWrapper()
scenario = pca.fit_transform(scenario, config)
return scenario, [fgf, imputer, scaler, pca]
def fit_pre_solving(self, scenario: ASlibScenario, config: Configuration):
'''
fits an pre-solving schedule using Aspeed [Hoos et al, 2015 TPLP)
Arguments
---------
scenario: aslib_scenario.aslib_scenario.ASlibScenario
aslib scenario at hand
config: Configuration
parameter configuration to use for preprocessing
Returns
-------
instance of Aspeed() with a fitted pre-solving schedule if performance_type of scenario is runtime; else None
'''
if scenario.performance_type[0] == "runtime":
aspeed = Aspeed()
aspeed.fit(scenario=scenario, config=config)
return aspeed
else:
return None
def fit_selector(self, scenario: ASlibScenario, config: Configuration):
'''
fits an algorithm selector for a given scenario wrt a given configuration
Arguments
---------
scenario: aslib_scenario.aslib_scenario.ASlibScenario
aslib scenario at hand
config: Configuration
parameter configuration
'''
if config.get("selector") == "PairwiseClassifier":
clf_class = None
if config.get("classifier") == "RandomForest":
clf_class = RandomForest
if config.get("classifier") == "XGBoost":
clf_class = XGBoost
selector = PairwiseClassifier(classifier_class=clf_class)
selector.fit(scenario=scenario, config=config)
if config.get("selector") == "MultiClassifier":
clf_class = None
if config.get("classifier") == "RandomForest":
clf_class = RandomForest
if config.get("classifier") == "XGBoost":
clf_class = XGBoost
selector = MultiClassifier(classifier_class=clf_class)
selector.fit(scenario=scenario, config=config)
if config.get("selector") == "IndRegressor":
reg_class = None
if config.get("regressor") == "RandomForestRegressor":
reg_class = RandomForestRegressor
selector = IndRegression(regressor_class=reg_class)
selector.fit(scenario=scenario, config=config)
if config.get("selector") == "JointRegressor":
reg_class = None
if config.get("regressor") == "RandomForestRegressor":
reg_class = RandomForestRegressor
selector = JointRegression(regressor_class=reg_class)
selector.fit(scenario=scenario, config=config)
if config.get("selector") == "PairwiseRegressor":
reg_class = None
if config.get("regressor") == "RandomForestRegressor":
reg_class = RandomForestRegressor
selector = PairwiseRegression(regressor_class=reg_class)
selector.fit(scenario=scenario, config=config)
return selector
def predict(self, scenario: ASlibScenario, config: Configuration, feature_pre_pipeline: list, pre_solver: Aspeed, selector):
'''
predicts algorithm schedules wrt a given config
and given pipelines
Arguments
---------
scenario: aslib_scenario.aslib_scenario.ASlibScenario
aslib scenario at hand
config: Configuration
parameter configuration
feature_pre_pipeline: list
list of fitted feature preprocessors
pre_solver: Aspeed
pre solver object with a saved static schedule
selector: autofolio.selector.*
fitted selector object
'''
self.logger.info("Predict on Test")
for f_pre in feature_pre_pipeline:
scenario = f_pre.transform(scenario)
if pre_solver:
pre_solving_schedule = pre_solver.predict(scenario=scenario)
else:
pre_solving_schedule = {}
pred_schedules = selector.predict(scenario=scenario)
# combine schedules
if pre_solving_schedule:
return dict((inst, pre_solving_schedule.get(inst, []) + schedule) for inst, schedule in pred_schedules.items())
else:
return pred_schedules
from copy import copy, deepcopy
from pickle import dumps, loads
from ConfigSpace.configuration_space import ConfigurationSpace
from ConfigSpace.hyperparameters import CategoricalHyperparameter
weights = [0.25, 0.5, 0.25]
hp = CategoricalHyperparameter("B", ["1", "2", "3"], weights=weights)
sub_cs = ConfigurationSpace()
sub_cs.add_hyperparameter(hp)
cs = ConfigurationSpace()
cs.add_configuration_space("A", sub_cs)
print(deepcopy(sub_cs).get_hyperparameter("B").probabilities, weights)
print(copy(sub_cs).get_hyperparameter("B").probabilities, weights)
print(loads(dumps(sub_cs)).get_hyperparameter("B").probabilities, weights)
print(cs.get_hyperparameter("A:B").probabilities, weights)
print(deepcopy(cs).get_hyperparameter("A:B").probabilities, weights)
print(copy(cs).get_hyperparameter("A:B").probabilities, weights)
print(loads(dumps(cs)).get_hyperparameter("A:B").probabilities, weights)
def generate_csv_data(NUM_EVALUATIONS, NUM_BUDGETS, ALLINONE, SEPARATE):
if not os.path.exists(ALLINONE):
os.makedirs(ALLINONE)
if not os.path.exists(SEPARATE):
os.makedirs(SEPARATE)
config_space = ConfigurationSpace()
config_space.add_hyperparameters([UniformFloatHyperparameter('random_parameter_1', 0, 1.2),
UniformIntegerHyperparameter('random_parameter_2', -10, 10),
UniformIntegerHyperparameter('random_parameter_3', 1, 1000)])
trajectory = []
runhistory = []
lowest_cost = np.inf
start_time = time.time()
if NUM_BUDGETS <= 1:
budgets = [0 for _ in range(NUM_EVALUATIONS)]
else:
budgets = [50 + 50 * (i // (NUM_EVALUATIONS / NUM_BUDGETS)) for i in range(NUM_EVALUATIONS)]
for i, budget in enumerate(budgets):
if i == 0:
random1 = config_space.get_hyperparameter('random_parameter_1').default_value
random2 = config_space.get_hyperparameter('random_parameter_2').default_value
random3 = config_space.get_hyperparameter('random_parameter_3').default_value
else:
random1 = np.random.uniform(0.1, 1.1)
random2 = np.random.randint(-10, 10)
random3 = np.random.randint(1, 1000)
cost = np.random.uniform(np.abs(NUM_EVALUATIONS - i - np.random.randint(50)),
10 * np.log(NUM_EVALUATIONS - i)) * random1
new_time = time.time() - start_time
status = 'SUCCESS'
seed = 42 # should be: np.random.randint(1, 10000000) but seeds are currently not supported with budgets.
if lowest_cost > cost:
lowest_cost = cost
trajectory.append([new_time, new_time, i, cost, random1, random2, random3])
runhistory.append([cost, new_time, status, budget, seed, random1, random2, random3])
with open(os.path.join(ALLINONE, 'runhistory.csv'), 'w', newline='') as f:
writer = csv.writer(f, delimiter=',')
writer.writerow(['cost', 'time', 'status', 'budget', 'seed', 'random_parameter_1', 'random_parameter_2', 'random_parameter_3'])
for run in runhistory:
writer.writerow(run)
with open(os.path.join(SEPARATE, 'runhistory.csv'), 'w', newline='') as rh,\
open(os.path.join(SEPARATE, 'configurations.csv'), 'w', newline='') as configs:
rh_writer = csv.writer(rh, delimiter=',')
configs_writer = csv.writer(configs, delimiter=',')
rh_writer.writerow(['cost', 'time', 'status', 'budget', 'seed', 'config_id'])
configs_writer.writerow(['CONFIG_ID', 'random_parameter_1', 'random_parameter_2', 'random_parameter_3'])
for idx, run in enumerate(runhistory):
rh_writer.writerow(run[:5] + [idx])
configs_writer.writerow([idx] + run[5:])
for path in [ALLINONE, SEPARATE]:
with open(os.path.join(path, 'configspace.json'), 'w') as f:
f.write(pcs_json.write(config_space))
with open(os.path.join(path, 'trajectory.csv'), 'w', newline='') as f:
writer = csv.writer(f, delimiter=',')
writer.writerow(['cpu_time', 'wallclock_time', 'evaluations', 'cost', 'random_parameter_1', 'random_parameter_2',
'random_parameter_3'])
for t in trajectory:
writer.writerow(t)
with open(os.path.join(path, 'scenario.txt'), 'w' ) as f:
f.write('paramfile = {}\nrun_obj = quality'.format(os.path.join(os.path.basename(path.rstrip('/')),
'configspace.json')))
def read(pcs_string, debug=False):
configuration_space = ConfigurationSpace()
conditions = []
forbidden = []
# some statistics
ct = 0
cont_ct = 0
cat_ct = 0
ord_ct = 0
line_ct = 0
for line in pcs_string:
line_ct += 1
if "#" in line:
# It contains a comment
pos = line.find("#")
line = line[:pos]
# Remove quotes and whitespaces at beginning and end
line = line.replace('"', "").replace("'", "")
line = line.strip()
if "|" in line:
# It's a condition
try:
c = pp_condition.parseString(line)
conditions.append(c)
except pyparsing.ParseException:
raise NotImplementedError("Could not parse condition: %s" % line)
continue
if "}" not in line and "]" not in line:
continue
if line.startswith("{") and line.endswith("}"):
forbidden.append(line)
continue
if len(line.strip()) == 0:
continue
ct += 1
param = None
create = {"int": UniformIntegerHyperparameter,
"float": UniformFloatHyperparameter,
"categorical": CategoricalHyperparameter,
"ordinal": OrdinalHyperparameter
}
try:
param_list = pp_cont_param.parseString(line)
name = param_list[0]
if param_list[1] == 'integer':
paramtype = 'int'
elif param_list[1] == 'real':
paramtype = 'float'
else:
paramtype = None
if paramtype in ['int', 'float']:
log = param_list[10:]
param_list = param_list[:10]
if len(log) > 0:
log = log[0]
lower = float(param_list[3])
upper = float(param_list[5])
log_on = True if "log" in log else False
default = float(param_list[8])
param = create[paramtype](name=name, lower=lower, upper=upper,
q=None, log=log_on, default=default)
cont_ct += 1
except pyparsing.ParseException:
pass
try:
if "categorical" in line:
param_list = pp_cat_param.parseString(line)
name = param_list[0]
choices = [choice for choice in param_list[3:-4:2]]
default = param_list[-2]
param = create["categorical"](name=name, choices=choices, default=default)
cat_ct += 1
elif "ordinal" in line:
param_list = pp_ord_param.parseString(line)
name = param_list[0]
sequence = [seq for seq in param_list[3:-4:2]]
default = param_list[-2]
param = create["ordinal"](name=name, sequence=sequence, default=default)
ord_ct += 1
except pyparsing.ParseException:
pass
if param is None:
raise NotImplementedError("Could not parse: %s" % line)
configuration_space.add_hyperparameter(param)
for clause in forbidden:
param_list = pp_forbidden_clause.parseString(clause)
tmp_list = []
clause_list = []
for value in param_list[1:]:
if len(tmp_list) < 3:
tmp_list.append(value)
else:
# So far, only equals is supported by SMAC
if tmp_list[1] == '=':
# TODO maybe add a check if the hyperparameter is
# actually in the configuration space
clause_list.append(ForbiddenEqualsClause(
configuration_space.get_hyperparameter(tmp_list[0]),
tmp_list[2]))
else:
raise NotImplementedError()
tmp_list = []
configuration_space.add_forbidden_clause(ForbiddenAndConjunction(
*clause_list))
conditions_per_child = OrderedDict()
for condition in conditions:
child_name = condition[0]
if child_name not in conditions_per_child:
conditions_per_child[child_name] = list()
conditions_per_child[child_name].append(condition)
for child_name in conditions_per_child:
for condition in conditions_per_child[child_name]:
condition = condition[2:]
condition = ' '.join(condition)
if '||' in str(condition):
ors = []
# 1st case we have a mixture of || and &&
if '&&' in str(condition):
ors_combis = []
for cond_parts in str(condition).split('||'):
condition = str(cond_parts).split('&&')
# if length is 1 it must be or
if len(condition) == 1:
element_list = condition[0].split()
ors_combis.append(condition_specification(child_name, element_list, configuration_space))
else:
# now taking care of ands
ands = []
for and_part in condition:
element_list = [element for part in condition for element in and_part.split()]
ands.append(condition_specification(child_name, element_list, configuration_space))
ors_combis.append(AndConjunction(*ands))
mixed_conjunction = OrConjunction(*ors_combis)
configuration_space.add_condition(mixed_conjunction)
else:
# 2nd case: we only have ors
for cond_parts in str(condition).split('||'):
element_list = [element for element in cond_parts.split()]
ors.append(condition_specification(child_name, element_list, configuration_space))
or_conjunction = OrConjunction(*ors)
configuration_space.add_condition(or_conjunction)
else:
# 3rd case: we only have ands
if '&&' in str(condition):
ands = []
for cond_parts in str(condition).split('&&'):
element_list = [element for element in cond_parts.split()]
ands.append(condition_specification(child_name, element_list, configuration_space))
and_conjunction = AndConjunction(*ands)
configuration_space.add_condition(and_conjunction)
else:
# 4th case: we have a normal condition
element_list = [element for element in condition.split()]
normal_condition = condition_specification(child_name, element_list, configuration_space)
configuration_space.add_condition(normal_condition)
return configuration_space
def read(pcs_string, debug=False):
configuration_space = ConfigurationSpace()
conditions = []
forbidden = []
# some statistics
ct = 0
cont_ct = 0
cat_ct = 0
line_ct = 0
for line in pcs_string:
line_ct += 1
if "#" in line:
# It contains a comment
pos = line.find("#")
line = line[:pos]
# Remove quotes and whitespaces at beginning and end
line = line.replace('"', "").replace("'", "")
line = line.strip()
if "|" in line:
# It's a condition
try:
c = pp_condition.parseString(line)
conditions.append(c)
except pyparsing.ParseException:
raise NotImplementedError("Could not parse condition: %s" %
line)
continue
if "}" not in line and "]" not in line:
continue
if line.startswith("{") and line.endswith("}"):
forbidden.append(line)
continue
if len(line.strip()) == 0:
continue
ct += 1
param = None
create = {
"int": UniformIntegerHyperparameter,
"float": UniformFloatHyperparameter,
"categorical": CategoricalHyperparameter
}
try:
param_list = pp_cont_param.parseString(line)
il = param_list[9:]
if len(il) > 0:
il = il[0]
param_list = param_list[:9]
name = param_list[0]
lower = float(param_list[2])
upper = float(param_list[4])
paramtype = "int" if "i" in il else "float"
log = True if "l" in il else False
default = float(param_list[7])
param = create[paramtype](name=name,
lower=lower,
upper=upper,
q=None,
log=log,
default=default)
cont_ct += 1
except pyparsing.ParseException:
pass
try:
param_list = pp_cat_param.parseString(line)
name = param_list[0]
choices = [c for c in param_list[2:-4:2]]
default = param_list[-2]
param = create["categorical"](name=name,
choices=choices,
default=default)
cat_ct += 1
except pyparsing.ParseException:
pass
if param is None:
raise NotImplementedError("Could not parse: %s" % line)
configuration_space.add_hyperparameter(param)
for clause in forbidden:
# TODO test this properly!
# TODO Add a try/catch here!
# noinspection PyUnusedLocal
param_list = pp_forbidden_clause.parseString(clause)
tmp_list = []
clause_list = []
for value in param_list[1:]:
if len(tmp_list) < 3:
tmp_list.append(value)
else:
# So far, only equals is supported by SMAC
if tmp_list[1] == '=':
# TODO maybe add a check if the hyperparameter is
# actually in the configuration space
clause_list.append(
ForbiddenEqualsClause(
configuration_space.get_hyperparameter(
tmp_list[0]), tmp_list[2]))
else:
raise NotImplementedError()
tmp_list = []
configuration_space.add_forbidden_clause(
ForbiddenAndConjunction(*clause_list))
#Now handle conditions
# If there are two conditions for one child, these two conditions are an
# AND-conjunction of conditions, thus we have to connect them
conditions_per_child = OrderedDict()
for condition in conditions:
child_name = condition[0]
if child_name not in conditions_per_child:
conditions_per_child[child_name] = list()
conditions_per_child[child_name].append(condition)
for child_name in conditions_per_child:
condition_objects = []
for condition in conditions_per_child[child_name]:
child = configuration_space.get_hyperparameter(child_name)
parent_name = condition[2]
parent = configuration_space.get_hyperparameter(parent_name)
restrictions = condition[5:-1:2]
# TODO: cast the type of the restriction!
if len(restrictions) == 1:
condition = EqualsCondition(child, parent, restrictions[0])
else:
condition = InCondition(child, parent, values=restrictions)
condition_objects.append(condition)
# Now we have all condition objects for this child, so we can build a
# giant AND-conjunction of them (if number of conditions >= 2)!
if len(condition_objects) > 1:
and_conjunction = AndConjunction(*condition_objects)
configuration_space.add_condition(and_conjunction)
else:
configuration_space.add_condition(condition_objects[0])
return configuration_space
def add_params(cs: ConfigurationSpace):
'''
adds parameters to ConfigurationSpace
'''
try:
classifier = cs.get_hyperparameter("classifier")
classifier.choices.append("RandomForest")
except KeyError:
classifier = CategoricalHyperparameter("classifier",
choices=["RandomForest"],
default="RandomForest")
cs.add_hyperparameter(classifier)
n_estimators = UniformIntegerHyperparameter(name="rf:n_estimators",
lower=10,
upper=100,
default=10,
log=True)
cs.add_hyperparameter(n_estimators)
criterion = CategoricalHyperparameter(name="rf:criterion",
choices=["gini", "entropy"],
default="gini")
cs.add_hyperparameter(criterion)
max_features = CategoricalHyperparameter(
name="rf:max_features",
choices=["sqrt", "log2", None],
default="sqrt")
cs.add_hyperparameter(max_features)
max_depth = UniformIntegerHyperparameter(name="rf:max_depth",
lower=10,
upper=2**31,
default=2**31,
log=True)
cs.add_hyperparameter(max_depth)
min_samples_split = UniformIntegerHyperparameter(
name="rf:min_samples_split",
lower=2,
upper=100,
default=2,
log=True)
cs.add_hyperparameter(min_samples_split)
min_samples_leaf = UniformIntegerHyperparameter(
name="rf:min_samples_leaf",
lower=2,
upper=100,
default=10,
log=True)
cs.add_hyperparameter(min_samples_leaf)
bootstrap = CategoricalHyperparameter(name="rf:bootstrap",
choices=[True, False],
default=True)
cs.add_hyperparameter(bootstrap)
cond = InCondition(child=n_estimators,
parent=classifier,
values=["RandomForest"])
cs.add_condition(cond)
cond = InCondition(child=criterion,
parent=classifier,
values=["RandomForest"])
cs.add_condition(cond)
cond = InCondition(child=max_features,
parent=classifier,
values=["RandomForest"])
cs.add_condition(cond)
cond = InCondition(child=max_depth,
parent=classifier,
values=["RandomForest"])
cs.add_condition(cond)
cond = InCondition(child=min_samples_split,
parent=classifier,
values=["RandomForest"])
cs.add_condition(cond)
cond = InCondition(child=min_samples_leaf,
parent=classifier,
values=["RandomForest"])
cs.add_condition(cond)
cond = InCondition(child=bootstrap,
parent=classifier,
values=["RandomForest"])
cs.add_condition(cond)
def _get_hyperparameter_search_space(
self,
dataset_properties: Dict[str, BaseDatasetPropertiesType],
include: Optional[Dict[str, Any]] = None,
exclude: Optional[Dict[str, Any]] = None,
) -> ConfigurationSpace:
"""Create the hyperparameter configuration space.
For the given steps, and the Choices within that steps,
this procedure returns a configuration space object to
explore.
Args:
include (Optional[Dict[str, Any]]):
What hyper-parameter configurations
to honor when creating the configuration space
exclude (Optional[Dict[str, Any]]):
What hyper-parameter configurations
to remove from the configuration space
dataset_properties (Optional[Dict[str, BaseDatasetPropertiesType]]):
Characteristics of the dataset to guide the pipeline
choices of components
Returns:
cs (ConfigurationSpace):
The configuration space describing
the TabularClassificationPipeline.
"""
cs = ConfigurationSpace()
if not isinstance(dataset_properties, dict):
warnings.warn(
'The given dataset_properties argument contains an illegal value.'
'Proceeding with the default value')
dataset_properties = dict()
if 'target_type' not in dataset_properties:
dataset_properties['target_type'] = 'tabular_classification'
if dataset_properties['target_type'] != 'tabular_classification':
warnings.warn(
'Tabular classification is being used, however the target_type'
'is not given as "tabular_classification". Overriding it.')
dataset_properties['target_type'] = 'tabular_classification'
# get the base search space given this
# dataset properties. Then overwrite with custom
# classification requirements
cs = self._get_base_search_space(cs=cs,
dataset_properties=dataset_properties,
exclude=exclude,
include=include,
pipeline=self.steps)
# Here we add custom code, that is used to ensure valid configurations, For example
# Learned Entity Embedding is only valid when encoder is one hot encoder
if 'network_embedding' in self.named_steps.keys(
) and 'encoder' in self.named_steps.keys():
embeddings = cs.get_hyperparameter(
'network_embedding:__choice__').choices
if 'LearnedEntityEmbedding' in embeddings:
encoders = cs.get_hyperparameter('encoder:__choice__').choices
possible_default_embeddings = copy.copy(list(embeddings))
del possible_default_embeddings[
possible_default_embeddings.index(
'LearnedEntityEmbedding')]
for encoder in encoders:
if encoder == 'OneHotEncoder':
continue
while True:
try:
cs.add_forbidden_clause(
ForbiddenAndConjunction(
ForbiddenEqualsClause(
cs.get_hyperparameter(
'network_embedding:__choice__'),
'LearnedEntityEmbedding'),
ForbiddenEqualsClause(
cs.get_hyperparameter(
'encoder:__choice__'), encoder)))
break
except ValueError:
# change the default and try again
try:
default = possible_default_embeddings.pop()
except IndexError:
raise ValueError(
"Cannot find a legal default configuration"
)
cs.get_hyperparameter(
'network_embedding:__choice__'
).default_value = default
self.configuration_space = cs
self.dataset_properties = dataset_properties
return cs
def __rely_model(self, cs: ConfigurationSpace):
if not RelyModels.info:
return
all_models = list(
cs.get_hyperparameter("estimator:__choice__").choices)
rely_model_counter = Counter([x[0] for x in RelyModels.info])
# 依赖模式->所有相应模型
relied2AllModels = {}
# 依赖模式->无交集相应模型
relied2models = {}
for rely_model in rely_model_counter.keys():
_, hit = self.get_forbid_hit_in_models_by_rely(
all_models, rely_model)
relied2AllModels[rely_model] = hit
# 如果某依赖模式不对应任何模型，删除
for k, v in list(relied2AllModels.items()):
if not v:
relied2AllModels.pop(k)
rely_model_counter.pop(k)
has_any_hit = any(relied2AllModels.values())
if not has_any_hit:
return
# 按照规则计算 relied2models ： 无交集相应模型
relied_cnts_tuples = [(k, v) for k, v in rely_model_counter.items()]
relied_cnts_tuples.sort(key=lambda x: x[-1])
visited = set()
for rely_model, _ in relied_cnts_tuples:
models = relied2AllModels[rely_model]
for other in set(rely_model_counter.keys()) - {rely_model}:
if (rely_model, other) in visited:
continue
other_models = relied2AllModels[other]
if len(other_models) <= len(models):
models = list(set(models) - set(other_models))
visited.add((rely_model, other))
visited.add((other, rely_model))
relied2models[rely_model] = models
# 键的顺序遵循rely_model_counter.keys()
def objective(relyModel2prob, debug=False):
# relyModel2prob = {rely_model: prob for rely_model, prob in zip(list(rely_model_counter.keys()), args)}
cur_cs = deepcopy(cs)
self.set_probabilities_in_cs(cur_cs, relied2models,
relied2AllModels, all_models,
**relyModel2prob)
cur_cs.seed(42)
try:
counter = Counter([
_hp.get("estimator:__choice__")
for _hp in cur_cs.sample_configuration(
len(all_models) * 15)
])
if debug:
print(counter)
except Exception:
return np.inf
vl = list(counter.values())
return np.var(vl) + 100 * (len(models) - len(vl))
space = {}
eps = 0.001
N_rely_model = len(rely_model_counter.keys())
for rely_model in rely_model_counter.keys():
space[rely_model] = hp.uniform(rely_model, eps,
(1 / N_rely_model) - eps)
best = fmin(
fn=objective,
space=space,
algo=tpe.suggest,
max_evals=100,
rstate=np.random.RandomState(42),
show_progressbar=False,
)
print("best =", best)
objective(best, debug=True)
self.set_probabilities_in_cs(cs, relied2models, relied2AllModels,
all_models, **best)
