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'tests/tests.csv',
sep=',',
dtype=np.float64,
)
pd_features = input_data.drop('class', axis=1)
pd_target = input_data['class']
# Set up the sparse matrix for testing
sparse_features = sparse.csr_matrix(training_features)
sparse_target = training_target
np.random.seed(42)
random.seed(42)
test_operator_key = 'sklearn.feature_selection.SelectPercentile'
TPOTSelectPercentile, TPOTSelectPercentile_args = TPOTOperatorClassFactory(
test_operator_key,
classifier_config_dict[test_operator_key]
)
tpot_obj = TPOTClassifier()
tpot_obj._fit_init()
def test_init_custom_parameters():
"""Assert that the TPOT instantiator stores the TPOT variables properly."""
tpot_obj = TPOTClassifier(
population_size=500,
generations=1000,
offspring_size=2000,
mutation_rate=0.05,
crossover_rate=0.9,
scoring='accuracy',
from tpot.config.classifier import classifier_config_dict
from sklearn.datasets import load_digits
from sklearn.model_selection import train_test_split
from deap import creator
from nose.tools import assert_raises, assert_equal, nottest
train_test_split = nottest(train_test_split)
test_operator_key_1 = 'sklearn.feature_selection.SelectPercentile'
test_operator_key_2 = 'sklearn.feature_selection.SelectFromModel'
TPOTSelectPercentile, TPOTSelectPercentile_args = TPOTOperatorClassFactory(
test_operator_key_1,
classifier_config_dict[test_operator_key_1]
)
TPOTSelectFromModel, TPOTSelectFromModel_args = TPOTOperatorClassFactory(
test_operator_key_2,
classifier_config_dict[test_operator_key_2]
)
digits_data = load_digits()
training_features, testing_features, training_target, testing_target = \
train_test_split(digits_data.data.astype(np.float64), digits_data.target.astype(np.float64), random_state=42)
tpot_obj = TPOTClassifier()
tpot_obj._fit_init()
tpot_obj_reg = TPOTRegressor()
tpot_obj_reg._fit_init()
def test_export_random_ind():
"""Assert that the TPOTClassifier can generate the same pipeline export with random seed of 39."""
from tpot import TPOTClassifier, TPOTRegressor
from tpot.export_utils import export_pipeline, generate_import_code, _indent, \
generate_pipeline_code, get_by_name, set_param_recursive
from tpot.operator_utils import TPOTOperatorClassFactory
from tpot.config.classifier import classifier_config_dict
from sklearn.datasets import load_digits
from sklearn.model_selection import train_test_split
from deap import creator
from nose.tools import assert_raises, assert_equal, nottest
train_test_split = nottest(train_test_split)
test_operator_key_1 = 'sklearn.feature_selection.SelectPercentile'
test_operator_key_2 = 'sklearn.feature_selection.SelectFromModel'
TPOTSelectPercentile, TPOTSelectPercentile_args = TPOTOperatorClassFactory(
test_operator_key_1,
classifier_config_dict[test_operator_key_1]
)
TPOTSelectFromModel, TPOTSelectFromModel_args = TPOTOperatorClassFactory(
test_operator_key_2,
classifier_config_dict[test_operator_key_2]
)
digits_data = load_digits()
training_features, testing_features, training_target, testing_target = \
train_test_split(digits_data.data.astype(np.float64), digits_data.target.astype(np.float64), random_state=42)
tpot_obj = TPOTClassifier()
tpot_obj._fit_init()
# coding: utf-8
from tpot.operator_utils import ARGType, TPOTOperatorClassFactory, Operator
from tpot.config_classifier import classifier_config_dict
from sklearn.base import BaseEstimator
class TPOTBase(BaseEstimator):
"""TPOT automatically creates and optimizes machine learning pipelines using genetic programming"""
operator_dict = classifier_config_dict
ops = []
arglist = []
for key in sorted(operator_dict.keys()):
print('Creating: {}'.format(key))
op_class, arg_types = TPOTOperatorClassFactory(key, operator_dict[key], classification=True)
ops.append(op_class)
arglist += arg_types
t = TPOTBase
t()
from sklearn.pipeline import make_pipeline, make_union
from sklearn.preprocessing import FunctionTransformer
from sklearn.ensemble import VotingClassifier
from sklearn.svm import LinearSVC
from sklearn.cluster import FeatureAgglomeration
from sklearn.ensemble import RandomForestClassifier
from sklearn.feature_selection import VarianceThreshold, SelectFromModel
from sklearn.preprocessing import StandardScaler, MinMaxScaler, Normalizer, MaxAbsScaler
from sklearn.naive_bayes import MultinomialNB
from sklearn.linear_model import LogisticRegression
'sklearn.linear_model.LogisticRegression': {
'penalty': ["l1", "l2"],
'C': [1e-4, 1e-3, 1e-2, 1e-1, 0.5, 1., 5., 10., 15., 20., 25.],
'dual': [True, False]
},
'sklearn.preprocessing.Binarizer': {
'threshold': np.arange(0.0, 1.01, 0.05)
}
}
tpot_operator_list = []
tpot_argument_list = []
for key in sorted(test_config_dict.keys()):
op, args = TPOTOperatorClassFactory(key, test_config_dict[key])
tpot_operator_list.append(op)
tpot_argument_list += args
assert len(tpot_operator_list) == 3
assert len(tpot_argument_list) == 9
assert tpot_operator_list[0].root is True
assert tpot_operator_list[1].root is False
assert tpot_operator_list[2].type() == "Classifier"
assert tpot_argument_list[1].values == [True, False]
# dont save periodic pipelines more often than this
self._output_best_pipeline_period_seconds = 30
# Try crossover and mutation at most this many times for
# any one given individual (or pair of individuals)
self._max_mut_loops = 50
self._setup_config(self.config_dict)
self._setup_template(self.template)
self.operators = []
self.arguments = []
for key in sorted(self._config_dict.keys()):
op_class, arg_types = TPOTOperatorClassFactory(
key,
self._config_dict[key],
BaseClass=Operator,
ArgBaseClass=ARGType,
verbose=self.verbosity
)
if op_class:
self.operators.append(op_class)
self.arguments += arg_types
if self.max_time_mins is None and self.generations is None:
raise ValueError("Either the parameter generations should bet set or a maximum evaluation time should be defined via max_time_mins")
# Schedule TPOT to run for many generations if the user specifies a
# run-time limit TPOT will automatically interrupt itself when the timer runs out
if self.max_time_mins is not None and self.generations is None :