optimizer="random_grid_search",
optimizer_params={"n_configurations": 10},
metrics=["accuracy", "precision", "recall"],
best_config_metric="recall",
outer_cv=KFold(n_splits=3),
inner_cv=KFold(n_splits=5),
verbosity=1,
output_settings=OutputSettings(project_folder="./tmp/"),
)
# ADD ELEMENTS TO YOUR PIPELINE
my_pipe += PipelineElement("StandardScaler")
my_pipe += PipelineElement(
"PCA", hyperparameters={"n_components": IntegerRange(5, 20)}, test_disabled=True
)
my_pipe += PipelineElement(
"ImbalancedDataTransformer",
hyperparameters={"method_name": Categorical(["RandomUnderSampler", "SMOTE"])},
test_disabled=True,
)
my_pipe += PipelineElement(
"SVC",
hyperparameters={"kernel": Categorical(["rbf", "linear"]), "C": FloatRange(0.5, 2)},
)
# NOW TRAIN YOUR PIPELINE
def setUp(self):
self.scaler = PipelineElement('StandardScaler', test_disabled=True)
self.pca = PipelineElement('PCA', {'n_components': IntegerRange(1, 3)})
self.svc = PipelineElement('SVC', {'C': [0.1, 1], 'kernel': ['rbf', 'sigmoid']})
self.rf = PipelineElement("RandomForestClassifier") # no hyperparameter
self.pipeline_elements = [self.scaler, self.pca, self.svc, self.rf]
verbosity=1,
output_settings=settings,
)
preprocessing = Preprocessing()
preprocessing += PipelineElement("LabelEncoder", batch_size=10)
my_pipe += preprocessing
# ADD ELEMENTS TO YOUR PIPELINE
# first normalize all features
my_pipe.add(PipelineElement("StandardScaler"))
# then do feature selection using a PCA, specify which values to try in the hyperparameter search
my_pipe += PipelineElement(
"PCA",
hyperparameters={"n_components": IntegerRange(5, 10)},
test_disabled=True)
# engage and optimize the good old SVM for Classification
my_pipe += PipelineElement(
"SVC",
hyperparameters={
"kernel": Categorical(["rbf", "linear"]),
"C": FloatRange(0.5, 1)
},
gamma="scale",
)
# NOW TRAIN YOUR PIPELINE
my_pipe.fit(X, y)
debug = True
my_pipe = Hyperpipe('feature_selection',
optimizer='grid_search',
metrics=[
'mean_squared_error', 'pearson_correlation',
'mean_absolute_error', 'explained_variance'
],
best_config_metric='mean_squared_error',
outer_cv=KFold(n_splits=3),
inner_cv=KFold(n_splits=3),
verbosity=1,
output_settings=OutputSettings(project_folder='./tmp/'))
my_pipe += PipelineElement('StandardScaler')
lasso = PipelineElement('LassoFeatureSelection',
hyperparameters={
'percentile_to_keep': [0.1, 0.2, 0.3],
'alpha': 1
})
f_regression = PipelineElement('FRegressionSelectPercentile',
hyperparameters={'percentile': [10, 20, 30]})
my_pipe += Switch('FeatureSelection', [lasso, f_regression])
my_pipe += PipelineElement(
'RandomForestRegressor',
hyperparameters={'n_estimators': IntegerRange(10, 50)})
my_pipe.fit(X, y)
outer_cv=KFold(n_splits=3),
inner_cv=KFold(n_splits=5),
verbosity=1,
output_settings=settings)
preprocessing = Preprocessing()
preprocessing += PipelineElement("LabelEncoder", batch_size=10)
my_pipe += preprocessing
# ADD ELEMENTS TO YOUR PIPELINE
# first normalize all features
my_pipe.add(PipelineElement('StandardScaler'))
# then do feature selection using a PCA, specify which values to try in the hyperparameter search
my_pipe += PipelineElement(
'PCA',
hyperparameters={'n_components': IntegerRange(5, 10)},
test_disabled=True)
# engage and optimize the good old SVM for Classification
my_pipe += PipelineElement('SVC',
hyperparameters={
'kernel': Categorical(['rbf', 'linear']),
'C': FloatRange(0.5, 1)
},
gamma='scale')
# NOW TRAIN YOUR PIPELINE
my_pipe.fit(X, y)
debug = True
my_pipe += PipelineElement('SimpleImputer')
my_pipe += PipelineElement('StandardScaler', {}, with_mean=True)
# Use only "mean" features: [mean_radius, mean_texture, mean_perimeter, mean_area, mean_smoothness, mean_compactness,
# mean_concavity, mean_concave_points, mean_symmetry, mean_fractal_dimension
mean_branch = Branch('MeanFeature')
mean_branch += DataFilter(indices=np.arange(10))
mean_branch += PipelineElement('SVC', {'C': FloatRange(0.1, 10)},
kernel='linear')
# Use only "error" features
error_branch = Branch('ErrorFeature')
error_branch += DataFilter(indices=np.arange(10, 20))
error_branch += PipelineElement('SVC', {'C': Categorical([100, 1000, 1000])},
kernel='linear')
# use only "worst" features: [worst_radius, worst_texture, ..., worst_fractal_dimension]
worst_branch = Branch('WorstFeature')
worst_branch += DataFilter(indices=np.arange(20, 30))
worst_branch += PipelineElement('SVC')
my_pipe += Stack('SourceStack', [mean_branch, error_branch, worst_branch])
my_pipe += Switch('EstimatorSwitch', [
PipelineElement('RandomForestClassifier',
{'n_estimators': IntegerRange(2, 5)}),
PipelineElement('SVC')
])
my_pipe.fit(X, y)
def test_regression_4(self):
for original_hyperpipe in self.hyperpipes:
pipe = original_hyperpipe.copy_me()
# Transformer Switch
my_switch = Switch('trans_switch')
my_switch += PipelineElement('PCA')
my_switch += PipelineElement('FRegressionSelectPercentile', hyperparameters={'percentile': IntegerRange(start=5, step=20, stop=66, range_type='range')}, test_disabled=True)
pipe += my_switch
pipe += PipelineElement('RandomForestRegressor')
self.run_hyperpipe(pipe, self.regression)
def test_against_smac(self):
# PHOTON implementation
self.pipe.add(PipelineElement('StandardScaler'))
# then do feature selection using a PCA, specify which values to try in the hyperparameter search
self.pipe += PipelineElement(
'PCA', hyperparameters={'n_components': IntegerRange(5, 30)})
# engage and optimize the good old SVM for Classification
self.pipe += PipelineElement(
'SVC',
hyperparameters={
'kernel': Categorical(["linear", "rbf", 'poly', 'sigmoid']),
'C': FloatRange(0.5, 200)
},
gamma='auto')
self.X, self.y = self.simple_classification()
self.pipe.fit(self.X, self.y)
# AUTO ML direct
# Build Configuration Space which defines all parameters and their ranges
cs = ConfigurationSpace()
# We define a few possible types of SVM-kernels and add them as "kernel" to our cs
n_components = UniformIntegerHyperparameter("PCA__n_components", 5,
30) # , default_value=5)
cs.add_hyperparameter(n_components)
kernel = CategoricalHyperparameter(
"SVC__kernel",
["linear", "rbf", 'poly', 'sigmoid']) #, default_value="linear")
cs.add_hyperparameter(kernel)
c = UniformFloatHyperparameter("SVC__C", 0.5, 200) #, default_value=1)
cs.add_hyperparameter(c)
# Scenario object
scenario = Scenario({
"run_obj":
"quality", # we optimize quality (alternatively runtime)
"runcount-limit": 800, # maximum function evaluations
"cs": cs, # configuration space
"deterministic": "true",
"shared_model": "false", # !!!!
"wallclock_limit": self.time_limit
})
# Optimize, using a SMAC-object
print(
"Optimizing! Depending on your machine, this might take a few minutes."
)
smac = SMAC4BO(scenario=scenario,
rng=np.random.RandomState(42),
tae_runner=self.objective_function)
self.traurig = smac
incumbent = smac.optimize()
inc_value = self.objective_function(incumbent)
print(incumbent)
print(inc_value)
runhistory_photon = self.smac_helper["data"].solver.runhistory
runhistory_original = smac.solver.runhistory
x_ax = range(
1,
min(len(runhistory_original.cost_per_config.keys()),
len(runhistory_photon.cost_per_config.keys())) + 1)
y_ax_original = [
runhistory_original.cost_per_config[tmp] for tmp in x_ax
]
y_ax_photon = [runhistory_photon.cost_per_config[tmp] for tmp in x_ax]
y_ax_original_inc = [min(y_ax_original[:tmp + 1]) for tmp in x_ax]
y_ax_photon_inc = [min(y_ax_photon[:tmp + 1]) for tmp in x_ax]
plt.figure(figsize=(10, 7))
plt.plot(x_ax, y_ax_original, 'g', label='Original')
plt.plot(x_ax, y_ax_photon, 'b', label='PHOTON')
plt.plot(x_ax, y_ax_photon_inc, 'r', label='PHOTON Incumbent')
plt.plot(x_ax, y_ax_original_inc, 'k', label='Original Incumbent')
plt.title('Photon Prove')
plt.xlabel('X')
plt.ylabel('Y')
plt.legend(loc='best')
plt.show()
def neighbours(items, fill=None):
before = itertools.chain([fill], items)
after = itertools.chain(
items,
[fill]) # You could use itertools.zip_longest() later instead.
next(after)
for a, b, c in zip(before, items, after):
yield [value for value in (a, b, c) if value is not fill]
print("---------------")
original_pairing = [
sum(values) / len(values) for values in neighbours(y_ax_original)
]
bias_term = np.mean([
abs(y_ax_original_inc[t] - y_ax_photon_inc[t])
for t in range(len(y_ax_photon_inc))
])
photon_pairing = [
sum(values) / len(values) - bias_term
for values in neighbours(y_ax_photon)
]
counter = 0
for i, x in enumerate(x_ax):
if abs(original_pairing[i] - photon_pairing[i]) > 0.05:
counter += 1
self.assertLessEqual(counter / len(x_ax), 0.15)
from photonai.optimization import FloatRange, IntegerRange
X, y = load_breast_cancer(True)
my_pipe = Hyperpipe('basic_stack_pipe',
optimizer='sk_opt',
optimizer_params={'n_configurations': 5},
metrics=['accuracy', 'precision', 'recall'],
best_config_metric='accuracy',
outer_cv=KFold(n_splits=3),
inner_cv=KFold(n_splits=3),
verbosity=1,
output_settings=OutputSettings(project_folder='./tmp/'))
my_pipe += PipelineElement('StandardScaler')
tree = PipelineElement('DecisionTreeClassifier',
hyperparameters={
'criterion': ['gini'],
'min_samples_split': IntegerRange(2, 4)
})
svc = PipelineElement('LinearSVC', hyperparameters={'C': FloatRange(0.5, 25)})
# for a stack that includes estimators you can choose whether predict or predict_proba is called for all estimators
# in case only some implement predict_proba, predict is called for the remaining estimators
my_pipe += Stack('final_stack', [tree, svc], use_probabilities=True)
my_pipe += PipelineElement('LinearSVC')
my_pipe.fit(X, y)
# Use only "mean" features: [mean_radius, mean_texture, mean_perimeter, mean_area, mean_smoothness, mean_compactness,
# mean_concavity, mean_concave_points, mean_symmetry, mean_fractal_dimension
mean_branch = Branch("MeanFeature")
mean_branch += DataFilter(indices=np.arange(10))
mean_branch += PipelineElement("SVC", {"C": FloatRange(0.1, 10)}, kernel="linear")
# Use only "error" features
error_branch = Branch("ErrorFeature")
error_branch += DataFilter(indices=np.arange(10, 20))
error_branch += PipelineElement(
"SVC", {"C": Categorical([100, 1000, 1000])}, kernel="linear"
)
# use only "worst" features: [worst_radius, worst_texture, ..., worst_fractal_dimension]
worst_branch = Branch("WorstFeature")
worst_branch += DataFilter(indices=np.arange(20, 30))
worst_branch += PipelineElement("SVC")
my_pipe += Stack("SourceStack", [mean_branch, error_branch, worst_branch])
my_pipe += Switch(
"EstimatorSwitch",
[
PipelineElement("RandomForestClassifier", {"n_estimators": IntegerRange(2, 5)}),
PipelineElement("SVC"),
],
)
my_pipe.fit(X, y)
from photonai.base import Hyperpipe, PipelineElement, OutputSettings
from photonai.optimization import IntegerRange
# WE USE THE BREAST CANCER SET FROM SKLEARN
X, y = load_breast_cancer(True)
# DESIGN YOUR PIPELINE
my_pipe = Hyperpipe('basic_svm_pipe',
optimizer='sk_opt',
optimizer_params={'n_configurations': 10},
metrics=['accuracy', 'precision', 'recall', 'balanced_accuracy'],
best_config_metric='accuracy',
outer_cv=KFold(n_splits=3),
inner_cv=KFold(n_splits=3),
verbosity=1,
output_settings=OutputSettings(project_folder='./tmp/'))
# ADD ELEMENTS TO YOUR PIPELINE
my_pipe.add(PipelineElement('StandardScaler'))
my_pipe += PipelineElement('PhotonMLPClassifier', hyperparameters={'layer_1': IntegerRange(0, 5),
'layer_2': IntegerRange(0, 5),
'layer_3': IntegerRange(0, 5)})
# NOW TRAIN YOUR PIPELINE
my_pipe.fit(X, y)
def test_save_optimum_pipe(self):
# todo: test .save() of custom model
tmp_path = os.path.join(self.tmp_folder_path, 'optimum_pipypipe')
settings = OutputSettings(project_folder=tmp_path,
overwrite_results=True)
my_pipe = Hyperpipe('hyperpipe',
optimizer='random_grid_search',
optimizer_params={'n_configurations': 3},
metrics=['accuracy', 'precision', 'recall'],
best_config_metric='f1_score',
outer_cv=KFold(n_splits=2),
inner_cv=KFold(n_splits=2),
verbosity=1,
output_settings=settings)
preproc = Preprocessing()
preproc += PipelineElement('StandardScaler')
# BRANCH WITH QUANTILTRANSFORMER AND DECISIONTREECLASSIFIER
tree_qua_branch = Branch('tree_branch')
tree_qua_branch += PipelineElement('QuantileTransformer')
tree_qua_branch += PipelineElement(
'DecisionTreeClassifier',
{'min_samples_split': IntegerRange(2, 4)},
criterion='gini')
# BRANCH WITH MinMaxScaler AND DecisionTreeClassifier
svm_mima_branch = Branch('svm_branch')
svm_mima_branch += PipelineElement('MinMaxScaler')
svm_mima_branch += PipelineElement(
'SVC', {
'kernel': Categorical(['rbf', 'linear']),
'C': 2.0
},
gamma='auto')
# BRANCH WITH StandardScaler AND KNeighborsClassifier
knn_sta_branch = Branch('neighbour_branch')
knn_sta_branch += PipelineElement.create("dummy", DummyTransformer(),
{})
knn_sta_branch += PipelineElement('KNeighborsClassifier')
my_pipe += preproc
# voting = True to mean the result of every branch
my_pipe += Stack('final_stack',
[tree_qua_branch, svm_mima_branch, knn_sta_branch])
my_pipe += PipelineElement('LogisticRegression', solver='lbfgs')
my_pipe.fit(self.__X, self.__y)
model_path = os.path.join(my_pipe.output_settings.results_folder,
'photon_best_model.photon')
self.assertTrue(os.path.exists(model_path))
# now move optimum pipe to new folder
test_folder = os.path.join(my_pipe.output_settings.results_folder,
'new_test_folder')
new_model_path = os.path.join(test_folder, 'photon_best_model.photon')
os.makedirs(test_folder)
shutil.copyfile(model_path, new_model_path)
# check if load_optimum_pipe also works
# check if we have the meta information recovered
loaded_optimum_pipe = Hyperpipe.load_optimum_pipe(new_model_path)
self.assertIsNotNone(loaded_optimum_pipe._meta_information)
self.assertIsNotNone(
loaded_optimum_pipe._meta_information['photon_version'])
# check if predictions stay realiably the same
y_pred_loaded = loaded_optimum_pipe.predict(self.__X)
y_pred = my_pipe.optimum_pipe.predict(self.__X)
np.testing.assert_array_equal(y_pred_loaded, y_pred)
metrics=["accuracy"],
best_config_metric="accuracy",
inner_cv=KFold(n_splits=3),
cache_folder=cache_grid_folder_path,
verbosity=0,
)
pipeline_elements = []
# scaling
pipeline_elements.append(PipelineElement("StandardScaler", test_disabled=True))
pipeline_elements.append(PipelineElement("Normalizer", test_disabled=True))
prepro_switch = Switch("PreprocSwitch")
prepro_switch += PipelineElement(
"PCA", hyperparameters={"n_components": IntegerRange(5, 30)})
prepro_switch += PipelineElement(
"RandomTreesEmbedding",
hyperparameters={
"n_estimators": IntegerRange(10, 30),
"max_depth": IntegerRange(3, 6),
},
)
prepro_switch += PipelineElement(
"SelectPercentile", hyperparameters={"percentile": IntegerRange(5, 15)})
# prepro_switch += PipelineElement('FastICA', hyperparameters={'algorithm': Categorical(['parallel', 'deflation'])})
estimator_switch = Switch("EstimatorSwitch")
estimator_switch += PipelineElement(
"SVC",
hyperparameters={
# DESIGN YOUR PIPELINE
settings = OutputSettings(project_folder="./tmp/")
my_pipe = Hyperpipe('batching',
optimizer='sk_opt',
# optimizer_params={'n_configurations': 25},
metrics=['accuracy', 'precision', 'recall', 'balanced_accuracy'],
# forced to 0th element in metrics
best_config_metric='accuracy',
outer_cv=KFold(n_splits=2),
inner_cv=KFold(n_splits=2),
verbosity=1,
output_settings=settings)
# ADD ELEMENTS TO YOUR PIPELINE
my_pipe += PipelineElement("StandardScaler")
my_pipe += PipelineElement('RandomForestClassifier', hyperparameters={
'n_estimators': IntegerRange(2, 1999),
},random_state=777)
# NOW TRAIN YOUR PIPELINE
my_pipe.fit(X, y)
debug = True
#### # ====================== Data ===========================
# self.data = Hyperpipe.Data()
# self.results = None
#self.best_config = None
inner_cv=KFold(n_splits=10),
outer_cv=KFold(n_splits=5),
metrics=['balanced_accuracy', 'precision'],
best_config_metric='balanced_accuracy',
output_settings=OutputSettings(project_folder='./tmp'))
my_pipe += PipelineElement("SimpleImputer")
switch = Switch("my_copy_switch")
switch += PipelineElement("StandardScaler")
switch += PipelineElement("RobustScaler", test_disabled=True)
my_pipe += switch
stack = Stack("EstimatorStack")
branch1 = Branch("SVMBranch")
branch1 += PipelineElement("PCA", hyperparameters={'n_components': IntegerRange(5, 10)})
branch1 += PipelineElement("SVC")
branch2 = Branch('TreeBranch')
branch2 += PipelineElement("PCA", hyperparameters={'n_components': IntegerRange(5, 10)})
branch2 += PipelineElement("DecisionTreeClassifier")
stack += branch1
stack += branch2
my_pipe += stack
my_pipe += PipelineElement("PhotonVotingClassifier")
my_pipe.fit(X, y)
def test_photon_implementation_switch(self):
# PHOTON implementation
self.pipe.add(PipelineElement('StandardScaler'))
self.pipe += PipelineElement(
'PCA', hyperparameters={'n_components': IntegerRange(5, 30)})
estimator_siwtch = Switch("Estimator")
estimator_siwtch += PipelineElement('SVC',
hyperparameters={
'kernel':
Categorical(
["rbf", 'poly']),
'C':
FloatRange(0.5, 200)
},
gamma='auto')
estimator_siwtch += PipelineElement('RandomForestClassifier',
hyperparameters={
'criterion':
Categorical(
['gini', 'entropy']),
'min_samples_split':
IntegerRange(2, 4)
})
self.pipe += estimator_siwtch
self.X, self.y = self.simple_classification()
self.pipe.fit(self.X, self.y)
# direct AUTO ML implementation
# Build Configuration Space which defines all parameters and their ranges
cs = ConfigurationSpace()
n_components = UniformIntegerHyperparameter(
"PCA__n_components", 5, 30)
cs.add_hyperparameter(n_components)
switch = CategoricalHyperparameter("Estimator_switch",
['svc', 'rf'])
cs.add_hyperparameter(switch)
kernel = CategoricalHyperparameter("SVC__kernel", ["rbf", 'poly'])
cs.add_hyperparameter(kernel)
c = UniformFloatHyperparameter("SVC__C", 0.5, 200)
cs.add_hyperparameter(c)
use_svc_c = InCondition(child=kernel,
parent=switch,
values=["svc"])
use_svc_kernel = InCondition(child=c,
parent=switch,
values=["svc"])
criterion = CategoricalHyperparameter(
"RandomForestClassifier__criterion", ['gini', 'entropy'])
cs.add_hyperparameter(criterion)
minsplit = UniformIntegerHyperparameter(
"RandomForestClassifier__min_samples_split", 2, 4)
cs.add_hyperparameter(minsplit)
use_rf_crit = InCondition(child=criterion,
parent=switch,
values=["rf"])
use_rf_minsplit = InCondition(child=minsplit,
parent=switch,
values=["rf"])
cs.add_conditions(
[use_svc_c, use_svc_kernel, use_rf_crit, use_rf_minsplit])
# Scenario object
scenario = Scenario({
"run_obj": "quality",
"cs": cs,
"deterministic": "true",
"wallclock_limit": self.time_limit,
"limit_resources": False,
'abort_on_first_run_crash': False
})
# Optimize, using a SMAC directly
smac = SMAC4HPO(scenario=scenario,
rng=42,
tae_runner=self.objective_function_switch)
_ = smac.optimize()
runhistory_photon = self.smac_helper["data"].solver.runhistory
runhistory_original = smac.solver.runhistory
x_ax = range(
1,
min(len(runhistory_original._cost_per_config.keys()),
len(runhistory_photon._cost_per_config.keys())) + 1)
y_ax_original = [
runhistory_original._cost_per_config[tmp] for tmp in x_ax
]
y_ax_photon = [
runhistory_photon._cost_per_config[tmp] for tmp in x_ax
]
min_len = min(len(y_ax_original), len(y_ax_photon))
self.assertLessEqual(
np.max(
np.abs(
np.array(y_ax_original[:min_len]) -
np.array(y_ax_photon[:min_len]))), 0.01)
def test_NumberRange(self):
"""
Test for class IntegerRange and FloatRange.
"""
dtypes = {int: np.int32, float: np.float32}
expected_linspace = [1, 2, 3, 4, 5, 6, 7, 8, 9]
number_range_linspace = IntegerRange(start=1, stop=9, num=9, range_type="linspace")
number_range_linspace.transform()
self.assertListEqual(expected_linspace, number_range_linspace.values)
expected_geomspace = [1, 10, 100, 1000, 10000]
number_range_geomspace = IntegerRange(1, 10000, num=5, range_type="geomspace")
number_range_geomspace.transform()
self.assertListEqual(expected_geomspace, number_range_geomspace.values)
number_range_range = IntegerRange(self.start, self.end, step=2, range_type="range")
number_range_range.transform()
self.assertListEqual(number_range_range.values, list(np.arange(self.start, self.end, 2)))
number_range_logspace = FloatRange(-1, 1, num=50, range_type='logspace')
number_range_logspace.transform()
np.testing.assert_array_almost_equal(number_range_logspace.values, np.logspace(-1, 1, num=50).tolist())
# error tests
with self.assertRaises(ValueError):
number_range = IntegerRange(start=0, stop=self.end, range_type="geomspace")
number_range.transform()
with self.assertRaises(ValueError):
number_range = IntegerRange(start=1, stop=15, range_type="logspace")
number_range.transform()
with self.assertRaises(ValueError):
IntegerRange(start=self.start, stop=self.end, range_type="ownspace")
def test_photon_implementation_simple(self):
# PHOTON implementation
self.pipe.add(PipelineElement('StandardScaler'))
self.pipe += PipelineElement(
'PCA', hyperparameters={'n_components': IntegerRange(5, 30)})
self.pipe += PipelineElement('SVC',
hyperparameters={
'kernel':
Categorical(["rbf", 'poly']),
'C': FloatRange(0.5, 200)
},
gamma='auto')
self.X, self.y = self.simple_classification()
self.pipe.fit(self.X, self.y)
# direct AUTO ML implementation
# Build Configuration Space which defines all parameters and their ranges
cs = ConfigurationSpace()
n_components = UniformIntegerHyperparameter(
"PCA__n_components", 5, 30)
cs.add_hyperparameter(n_components)
kernel = CategoricalHyperparameter("SVC__kernel", ["rbf", 'poly'])
cs.add_hyperparameter(kernel)
c = UniformFloatHyperparameter("SVC__C", 0.5, 200)
cs.add_hyperparameter(c)
# Scenario object
scenario = Scenario({
"run_obj": "quality",
"cs": cs,
"deterministic": "true",
"wallclock_limit": self.time_limit,
"limit_resources": False,
'abort_on_first_run_crash': False
})
# Optimize, using a SMAC directly
smac = SMAC4HPO(scenario=scenario,
rng=42,
tae_runner=self.objective_function_simple)
_ = smac.optimize()
runhistory_photon = self.smac_helper["data"].solver.runhistory
runhistory_original = smac.solver.runhistory
x_ax = range(
1,
min(len(runhistory_original._cost_per_config.keys()),
len(runhistory_photon._cost_per_config.keys())) + 1)
y_ax_original = [
runhistory_original._cost_per_config[tmp] for tmp in x_ax
]
y_ax_photon = [
runhistory_photon._cost_per_config[tmp] for tmp in x_ax
]
y_ax_original_inc = [min(y_ax_original[:tmp + 1]) for tmp in x_ax]
y_ax_photon_inc = [min(y_ax_photon[:tmp + 1]) for tmp in x_ax]
plot = False
if plot:
plt.figure(figsize=(10, 7))
plt.plot(x_ax, y_ax_original, 'g', label='Original')
plt.plot(x_ax, y_ax_photon, 'b', label='PHOTON')
plt.plot(x_ax, y_ax_photon_inc, 'r', label='PHOTON Incumbent')
plt.plot(x_ax,
y_ax_original_inc,
'k',
label='Original Incumbent')
plt.title('Photon Prove')
plt.xlabel('X')
plt.ylabel('Y')
plt.legend(loc='best')
plt.savefig("smac.png")
min_len = min(len(y_ax_original), len(y_ax_photon))
self.assertLessEqual(
np.max(
np.abs(
np.array(y_ax_original[:min_len]) -
np.array(y_ax_photon[:min_len]))), 0.01)
# DESIGN YOUR PIPELINE
my_pipe = Hyperpipe('custom_estimator_pipe',
optimizer='random_grid_search',
optimizer_params={'n_configurations': 2},
metrics=['accuracy', 'precision', 'recall', 'balanced_accuracy'],
best_config_metric='accuracy',
outer_cv=KFold(n_splits=3),
inner_cv=KFold(n_splits=3),
verbosity=1,
output_settings=settings)
# SHOW WHAT IS POSSIBLE IN THE CONSOLE
registry.list_available_elements()
# NOW FIND OUT MORE ABOUT A SPECIFIC ELEMENT
registry.info('MyCustomEstimator')
registry.info('MyCustomTransformer')
my_pipe.add(PipelineElement('StandardScaler'))
my_pipe += PipelineElement('PCA', hyperparameters={'n_components': IntegerRange(5, 20)}, test_disabled=True)
my_pipe += PipelineElement('MyCustomEstimator')
# NOW TRAIN YOUR PIPELINE
my_pipe.fit(X, y)
optimizer_params={'n_configurations': 300, 'acq_func': 'LCB', 'acq_func_kwargs': {'kappa': 1.96}},
metrics=['accuracy'],
best_config_metric='accuracy',
inner_cv=KFold(n_splits=5),
cache_folder=cache_skopt_folder_path,
verbosity=0,
output_settings=settings)
pipeline_elements = []
# scaling
pipeline_elements.append(PipelineElement('StandardScaler', test_disabled=True))
pipeline_elements.append(PipelineElement('Normalizer', test_disabled=True))
prepro_switch = Switch("PreprocSwitch")
prepro_switch += PipelineElement('PCA', hyperparameters={'n_components': IntegerRange(2, 30)})
prepro_switch += PipelineElement('RandomTreesEmbedding',
hyperparameters={'n_estimators': IntegerRange(1,50),
'max_depth':IntegerRange(1,6)})
prepro_switch += PipelineElement('SelectPercentile', hyperparameters={'percentile': IntegerRange(5,15)}, test_disabled=True)
#prepro_switch += PipelineElement('FastICA', hyperparameters={'algorithm': Categorical(['parallel', 'deflation'])})
estimator_switch = Switch("EstimatorSwitch")
estimator_switch += PipelineElement('SVC', hyperparameters={'kernel': Categorical(["linear", "rbf", 'poly', 'sigmoid']),
'C': FloatRange(0.5, 200),
'decision_function_shape': Categorical(['ovo', 'ovr']),
'degree': IntegerRange(2,5)})
estimator_switch += PipelineElement("RandomForestClassifier", hyperparameters={'n_estimators': IntegerRange(10, 200),
"min_samples_split": IntegerRange(2, 6)})
estimator_switch += PipelineElement("ExtraTreesClassifier", hyperparameters={'n_estimators':IntegerRange(5,500)})
