"""sklearn-compatible pipelines for AFQ data."""
import inspect
from string import Template
import groupyr as gpr
from sklearn.base import (
BaseEstimator,
MetaEstimatorMixin,
TransformerMixin,
is_classifier,
is_regressor,
)
from sklearn.compose import TransformedTargetRegressor
from sklearn.ensemble import (
AdaBoostClassifier,
AdaBoostRegressor,
BaggingClassifier,
BaggingRegressor,
)
from sklearn.impute import KNNImputer, SimpleImputer
from sklearn.pipeline import Pipeline
from sklearn.preprocessing import (
MaxAbsScaler,
MinMaxScaler,
PowerTransformer,
RobustScaler,
StandardScaler,
)
from ._serial_bagging import SerialBaggingClassifier, SerialBaggingRegressor
__all__ = ["make_afq_classifier_pipeline", "make_afq_regressor_pipeline"]
def make_base_afq_pipeline(
imputer="simple",
scaler="standard",
feature_transformer=False,
estimator=None,
ensemble_meta_estimator=None,
imputer_kwargs=None,
scaler_kwargs=None,
feature_transformer_kwargs=None,
estimator_kwargs=None,
ensemble_meta_estimator_kwargs=None,
memory=None,
verbose=False,
target_transformer=None,
target_transform_func=None,
target_transform_inverse_func=None,
target_transform_check_inverse=True,
):
"""Return a base AFQ-specific modeling pipeline.
This function returns a :ref:`Pipeline <sklearn:pipeline>` instance with the
following steps::
[imputer, scaler, feature_transformer, estimator]
where ``imputer`` imputes missing data due to individual subjects missing
metrics along an entire bundle; ``scaler`` is optional and scales the
features of the feature matrix; ``feature_transformer`` is optional and
applies a transform featurewise to make data more Gaussian-like;
and ``estimator`` is a scikit-learn compatible estimator. The estimator
may optionally be wrapped in an ensemble meta-estimator specified by
``ensemble_meta_estimator`` and given the keyword arguments in
``ensemble_meta_estimator_kwargs``. Additionally, the estimator may
optionally be wrapped in
``sklearn:sklearn.compose.TransformedTargetRegressor``, such that the
computation during ``fit`` is::
estimator.fit(X, target_transform_func(y))
or::
estimator.fit(X, target_transformer.transform(y))
The computation during ``predict`` is::
target_transform_inverse_func(estimator.predict(X))
or::
target_transformer.inverse_transform(estimator.predict(X))
This is a base function on which more specific classifier and regressor
pipelines will be built.
Parameters
----------
imputer : "simple", "knn", or sklearn-compatible transformer,
default="simple"
The imputer for missing data. String arguments result in the use of
specific imputers/transformers:
"simple" yields :class:`sklearn:sklearn.impute.SimpleImputer`;
"knn" yields :class:`sklearn:sklearn.impute.KNNImputer`.
Custom transformers are
allowed as long as they inherit from
:class:`sklearn:sklearn.base.TransformerMixin`.
scaler : "standard", "minmax", "maxabs", "robust", or sklearn-compatible
transformer, default="standard"
The scaler to use for the feature matrix. String arguments result in
the use of specific transformers: "standard" yields the
:class:`sklearn:sklearn.preprocessing.StandardScalar`; "minmax"
yields the :class:`sklearn:sklearn.preprocessing.MinMaxScaler`;
"maxabs" yields the
:class:`sklearn:sklearn.preprocessing.MaxAbsScaler`; "robust" yields
the :class:`sklearn:sklearn.preprocessing.RobustScaler`. Custom
transformers are allowed as long as they inherit from
:class:`sklearn:sklearn.base.TransformerMixin`.
feature_transformer : bool or sklearn-compatible transformer, default=False
An optional feature transformer for use on the feature matrix. If True,
use :class:`sklearn:sklearn.preprocessing.PowerTransformer`. If
False, skip this step. Custom transformers are allowed as long as
they inherit from :class:`sklearn:sklearn.base.TransformerMixin`.
estimator : sklearn-compatible estimator or None, default=None
The estimator to use as the last step of the pipeline. If provided,
it must inherit from :class:`sklearn:sklearn.base.BaseEstimator`
ensemble_meta_estimator : "bagging", "adaboost", "serial-bagging", or None
An optional ensemble meta-estimator to combine the predictions of
several base estimators. "Adaboost" will result in the use of
:class:`sklearn:sklearn.ensemble.AdaBoostClassifier` for classifier
base estimators or
:class:`sklearn.sklearn.ensemble.AdaBoostRegressor` for regressor
base estimators. "Bagging" will result in the use of
:class:`sklearn.sklearn.ensemble.BaggingClassifier` for classifier
base estimators or :class:`sklearn.sklearn.ensemble.BaggingRegressor`
for regressor base estimators.
imputer_kwargs : dict, default=None,
Key-word arguments for the imputer.
scaler_kwargs : dict, default=None,
Key-word arguments for the scaler.
feature_transformer_kwargs : dict, default=None,
Key-word arguments for the feature_transformer.
estimator_kwargs : dict, default=None,
Key-word arguments for the estimator.
ensemble_meta_estimator_kwargs : dict, default=None,
Key-word arguments for the ensemble meta-estimator.
memory : str or object with the joblib.Memory interface, default=None
Used to cache the fitted transformers of the pipeline. By default,
no caching is performed. If a string is given, it is the path to
the caching directory. Enabling caching triggers a clone of
the transformers before fitting. Therefore, the transformer
instance given to the pipeline cannot be inspected
directly. Use the attribute ``named_steps`` or ``steps`` to
inspect estimators within the pipeline. Caching the
transformers is advantageous when fitting is time consuming.
verbose : bool, default=False
If True, the time elapsed while fitting each step will be printed as it
is completed.
target_transformer : object, default=None
Estimator object such as derived from
:class:`sklearn.base.TransformerMixin`. Cannot be set at the same
time as ``func`` and ``inverse_func``. If ``transformer`` is ``None``
as well as ``func`` and ``inverse_func``, the transformer will be an
identity transformer. Note that the transformer will be cloned during
fitting. Also, the transformer is restricting ``y`` to be a numpy
array.
target_transform_func : function, default=None
Function to apply to ``y`` before passing to ``fit``. Cannot be set at
the same time as ``transformer``. The function needs to return a
2-dimensional array. If ``func`` is ``None``, the function used will be
the identity function.
target_transform_inverse_func : function, default=None
Function to apply to the prediction of the regressor. Cannot be set at
the same time as ``transformer`` as well. The function needs to return
a 2-dimensional array. The inverse function is used to return
predictions to the same space of the original training labels.
target_transform_check_inverse : bool, default=True
Whether to check that ``transform`` followed by ``inverse_transform``
or ``func`` followed by ``inverse_func`` leads to the original targets.
Returns
-------
pipeline : :ref:`Pipeline <sklearn:pipeline>` instance
"""
base_msg = Template(
"${kw} must be one of ${allowed} or a class that inherits "
"from {base_class}; got ${input} instead."
)
transformer_msg = Template(
base_msg.safe_substitute(base_class="sklearn.base.TransformerMixin")
)
ensembler_msg = Template(
base_msg.safe_substitute(base_class="sklearn.base.MetaEstimatorMixin")
)
def call_with_kwargs(Transformer, kwargs):
if kwargs is None:
return Transformer()
else:
return Transformer(**kwargs)
allowed = ["simple", "knn"]
err_msg = Template(transformer_msg.safe_substitute(kw="imputer", allowed=allowed))
if isinstance(imputer, str):
if imputer.lower() == "simple":
pl_imputer = call_with_kwargs(SimpleImputer, imputer_kwargs)
elif imputer.lower() == "knn":
pl_imputer = call_with_kwargs(KNNImputer, imputer_kwargs)
else:
raise ValueError(err_msg.substitute(input=imputer))
elif inspect.isclass(imputer):
if issubclass(imputer, TransformerMixin):
pl_imputer = call_with_kwargs(imputer, imputer_kwargs)
else:
raise ValueError(err_msg.substitute(input=imputer))
else:
raise ValueError(err_msg.substitute(input=imputer))
allowed = ["standard", "minmax", "maxabs", "robust"]
err_msg = Template(transformer_msg.safe_substitute(kw="scaler", allowed=allowed))
if isinstance(scaler, str):
if scaler.lower() == "standard":
pl_scaler = call_with_kwargs(StandardScaler, scaler_kwargs)
elif scaler.lower() == "minmax":
pl_scaler = call_with_kwargs(MinMaxScaler, scaler_kwargs)
elif scaler.lower() == "maxabs":
pl_scaler = call_with_kwargs(MaxAbsScaler, scaler_kwargs)
elif scaler.lower() == "robust":
pl_scaler = call_with_kwargs(RobustScaler, scaler_kwargs)
else:
raise ValueError(err_msg.substitute(input=scaler))
elif inspect.isclass(scaler):
if issubclass(scaler, TransformerMixin):
pl_scaler = call_with_kwargs(scaler, scaler_kwargs)
else:
raise ValueError(err_msg.substitute(input=scaler))
elif scaler is None:
pl_scaler = None
else:
raise ValueError(err_msg.substitute(input=scaler))
allowed = [True, False]
err_msg = Template(
transformer_msg.safe_substitute(kw="feature_transformer", allowed=allowed)
)
if isinstance(feature_transformer, bool):
if feature_transformer:
pl_feature_transformer = call_with_kwargs(
PowerTransformer, feature_transformer_kwargs
)
else:
pl_feature_transformer = None
elif inspect.isclass(feature_transformer):
if issubclass(feature_transformer, TransformerMixin):
pl_feature_transformer = call_with_kwargs(
feature_transformer, feature_transformer_kwargs
)
else:
raise ValueError(err_msg.substitute(input=feature_transformer))
else:
raise ValueError(err_msg.substitute(input=feature_transformer))
if estimator is not None:
if inspect.isclass(estimator) and issubclass(estimator, BaseEstimator):
base_estimator = call_with_kwargs(estimator, estimator_kwargs)
if ensemble_meta_estimator is not None:
allowed = ["bagging", "adaboost", "serial-bagging"]
err_msg = Template(
ensembler_msg.safe_substitute(
kw="ensemble_meta_estimator", allowed=allowed
)
)
if ensemble_meta_estimator_kwargs is not None:
ensembler_kwargs = ensemble_meta_estimator_kwargs.copy()
else:
ensembler_kwargs = {}
ensembler_kwargs["base_estimator"] = base_estimator
if isinstance(ensemble_meta_estimator, str):
if ensemble_meta_estimator.lower() == "bagging":
if is_classifier(base_estimator):
ensembler = call_with_kwargs(
BaggingClassifier, ensembler_kwargs
)
elif is_regressor(base_estimator):
ensembler = call_with_kwargs(
BaggingRegressor, ensembler_kwargs
)
elif ensemble_meta_estimator.lower() == "serial-bagging":
if is_classifier(base_estimator):
ensembler = call_with_kwargs(
SerialBaggingClassifier, ensembler_kwargs
)
elif is_regressor(base_estimator):
ensembler = call_with_kwargs(
SerialBaggingRegressor, ensembler_kwargs
)
elif ensemble_meta_estimator.lower() == "adaboost":
if is_classifier(base_estimator):
ensembler = call_with_kwargs(
AdaBoostClassifier, ensembler_kwargs
)
elif is_regressor(base_estimator):
ensembler = call_with_kwargs(
AdaBoostRegressor, ensembler_kwargs
)
else:
raise ValueError(
err_msg.substitute(input=ensemble_meta_estimator)
)
elif inspect.isclass(ensemble_meta_estimator):
if issubclass(ensemble_meta_estimator, MetaEstimatorMixin):
ensembler = call_with_kwargs(
ensemble_meta_estimator, ensembler_kwargs
)
else:
raise ValueError(
err_msg.substitute(input=ensemble_meta_estimator)
)
else:
raise ValueError(err_msg.substitute(input=ensemble_meta_estimator))
base_estimator = ensembler
if any(
[
target_transformer,
target_transform_func,
target_transform_inverse_func,
]
):
pl_estimator = TransformedTargetRegressor(
base_estimator,
transformer=target_transformer,
func=target_transform_func,
inverse_func=target_transform_inverse_func,
check_inverse=target_transform_check_inverse,
)
else:
pl_estimator = base_estimator
else:
raise ValueError(
"If provided, estimator must inherit from sklearn.base.BaseEstimator; "
"got {0} instead.".format(estimator)
)
else:
pl_estimator = None
# Build the pipeline steps. We will always start with the imputer and end
# with the estimator. The scaler and feature_transform steps are optional.
pl = [
("impute", pl_imputer),
("scale", pl_scaler),
("feature_transform", pl_feature_transformer),
("estimate", pl_estimator),
]
return Pipeline(steps=pl, memory=memory, verbose=verbose)
[docs]
def make_afq_classifier_pipeline(
imputer="simple",
scaler="standard",
feature_transformer=False,
ensemble_meta_estimator=None,
imputer_kwargs=None,
scaler_kwargs=None,
feature_transformer_kwargs=None,
ensemble_meta_estimator_kwargs=None,
use_cv_estimator=True,
memory=None,
pipeline_verbosity=False,
target_transformer=None,
target_transform_func=None,
target_transform_inverse_func=None,
target_transform_check_inverse=True,
**estimator_kwargs,
):
"""Return the recommended AFQ-specific classification pipeline.
This function returns a :ref:`Pipeline <sklearn:pipeline>` instance with the
following steps::
[imputer, scaler, feature_transformer, estimator]
where ``imputer`` imputes missing data due to individual subjects missing
metrics along an entire bundle; ``scaler`` is optional and scales the
features of the feature matrix; ``feature_transformer`` is optional and
applies a transform featurewise to make data more Gaussian-like;
and ``estimator`` is an instance of
:class:`groupyr:groupyr.LogisticSGLCV` if ``use_cv_estimator=True`` or
:class:`groupyr:groupyr.LogisticSGL` if ``use_cv_estimator=False``. The
estimator may optionally be wrapped in an ensemble meta-estimator
specified by ``ensemble_meta_estimator`` and given the keyword arguments
in ``ensemble_meta_estimator_kwargs``. Additionally, the estimator may
optionally be wrapped in
``sklearn:sklearn.compose.TransformedTargetRegressor``, such that the
computation during ``fit`` is::
estimator.fit(X, target_transform_func(y))
or::
estimator.fit(X, target_transformer.transform(y))
The computation during ``predict`` is::
target_transform_inverse_func(estimator.predict(X))
or::
target_transformer.inverse_transform(estimator.predict(X))
Parameters
----------
imputer : "simple", "knn", or sklearn-compatible transformer, default="simple"
The imputer for missing data. String arguments result in the use of
specific imputers/transformers:
"simple" yields :class:`sklearn:sklearn.impute.SimpleImputer`;
"knn" yields :class:`sklearn:sklearn.impute.KNNImputer`.
Custom transformers are
allowed as long as they inherit from
:class:`sklearn:sklearn.base.TransformerMixin`.
scaler : "standard", "minmax", "maxabs", "robust", or
sklearn-compatible transformer, default="standard"
The scaler to use for the feature matrix. String arguments result in
the use of specific transformers: "standard" yields the
:class:`sklearn:sklearn.preprocessing.StandardScalar`; "minmax"
yields the :class:`sklearn:sklearn.preprocessing.MinMaxScaler`;
"maxabs" yields the
:class:`sklearn:sklearn.preprocessing.MaxAbsScaler`; "robust" yields
the :class:`sklearn:sklearn.preprocessing.RobustScaler`. Custom
transformers are allowed as long as they inherit from
:class:`sklearn:sklearn.base.TransformerMixin`.
feature_transformer : bool or sklearn-compatible transformer, default=False
An optional transformer for use on the feature matrix. If True,
use :class:`sklearn:sklearn.preprocessing.PowerTransformer`. If
False, skip this step. Custom transformers are allowed as long as
they inherit from :class:`sklearn:sklearn.base.TransformerMixin`.
ensemble_meta_estimator : "bagging", "adaboost", or None
An optional ensemble meta-estimator to combine the predictions of
several base estimators. "Adaboost" will result in the use of
:class:`sklearn:sklearn.ensemble.AdaBoostClassifier` and "bagging"
will result in the use of
:class:`sklearn.sklearn.ensemble.BaggingClassifier`.
imputer_kwargs : dict, default=None,
Key-word arguments for the imputer.
scaler_kwargs : dict, default=None,
Key-word arguments for the scaler.
feature_transformer_kwargs : dict, default=None,
Key-word arguments for the feature_transformer.
ensemble_meta_estimator_kwargs : dict, default=None,
Key-word arguments for the ensemble meta-estimator.
use_cv_estimator : bool, default=True,
If True, use :class:`groupyr:groupyr.LogisticSGLCV` as the final
estimator. Otherwise, use :class:`groupyr:groupyr.LogisticSGL`.
memory : str or object with the joblib.Memory interface, default=None
Used to cache the fitted transformers of the pipeline. By default,
no caching is performed. If a string is given, it is the path to
the caching directory. Enabling caching triggers a clone of
the transformers before fitting. Therefore, the transformer
instance given to the pipeline cannot be inspected
directly. Use the attribute ``named_steps`` or ``steps`` to
inspect estimators within the pipeline. Caching the
transformers is advantageous when fitting is time consuming.
pipeline_verbosity : bool, default=False
If True, the time elapsed while fitting each step will be printed as it
is completed.
target_transformer : object, default=None
Estimator object such as derived from
:class:`sklearn.base.TransformerMixin`. Cannot be set at the same
time as ``func`` and ``inverse_func``. If ``transformer`` is ``None``
as well as ``func`` and ``inverse_func``, the transformer will be an
identity transformer. Note that the transformer will be cloned during
fitting. Also, the transformer is restricting ``y`` to be a numpy
array.
target_transform_func : function, default=None
Function to apply to ``y`` before passing to ``fit``. Cannot be set at
the same time as ``transformer``. The function needs to return a
2-dimensional array. If ``func`` is ``None``, the function used will be
the identity function.
target_transform_inverse_func : function, default=None
Function to apply to the prediction of the regressor. Cannot be set at
the same time as ``transformer`` as well. The function needs to return
a 2-dimensional array. The inverse function is used to return
predictions to the same space of the original training labels.
target_transform_check_inverse : bool, default=True
Whether to check that ``transform`` followed by ``inverse_transform``
or ``func`` followed by ``inverse_func`` leads to the original targets.
**estimator_kwargs : kwargs
Keyword arguments passed to :class:`groupyr:groupyr.LogisticSGLCV` if
``use_cv_estimator=True`` or :class:`groupyr:groupyr.LogisticSGL` if
``use_cv_estimator=False``.
Returns
-------
pipeline : :ref:`Pipeline <sklearn:pipeline>` instance
"""
return make_base_afq_pipeline(
imputer=imputer,
scaler=scaler,
feature_transformer=feature_transformer,
estimator=gpr.LogisticSGLCV if use_cv_estimator else gpr.LogisticSGL,
ensemble_meta_estimator=ensemble_meta_estimator,
imputer_kwargs=imputer_kwargs,
scaler_kwargs=scaler_kwargs,
feature_transformer_kwargs=feature_transformer_kwargs,
ensemble_meta_estimator_kwargs=ensemble_meta_estimator_kwargs,
estimator_kwargs=estimator_kwargs,
memory=memory,
verbose=pipeline_verbosity,
target_transformer=target_transformer,
target_transform_func=target_transform_func,
target_transform_inverse_func=target_transform_inverse_func,
target_transform_check_inverse=target_transform_check_inverse,
)
[docs]
def make_afq_regressor_pipeline(
imputer="simple",
scaler="standard",
feature_transformer=False,
ensemble_meta_estimator=None,
imputer_kwargs=None,
scaler_kwargs=None,
feature_transformer_kwargs=None,
ensemble_meta_estimator_kwargs=None,
use_cv_estimator=True,
memory=None,
pipeline_verbosity=False,
target_transformer=None,
target_transform_func=None,
target_transform_inverse_func=None,
target_transform_check_inverse=True,
**estimator_kwargs,
):
"""Return the recommended AFQ-specific regression pipeline.
This function returns a :ref:`Pipeline <sklearn:pipeline>` instance with the
following steps::
[imputer, scaler, feature_transformer, estimator]
where ``imputer`` imputes missing data due to individual subjects missing
metrics along an entire bundle; ``scaler`` is optional and scales the
features of the feature matrix; ``feature_transformer`` is optional and
applies a transform featurewise to make data more Gaussian-like;
and ``estimator`` is an instance of :class:`groupyr:groupyr.SGLCV` if
``use_cv_estimator=True`` or :class:`groupyr:groupyr.SGL` if
``use_cv_estimator=False``. The estimator may optionally be wrapped in an
ensemble meta-estimator specified by ``ensemble_meta_estimator`` and
given the keyword arguments in ``ensemble_meta_estimator_kwargs``.
Additionally, the estimator may optionally be wrapped in
``sklearn:sklearn.compose.TransformedTargetRegressor``, such that the
computation during ``fit`` is::
estimator.fit(X, target_transform_func(y))
or::
estimator.fit(X, target_transformer.transform(y))
The computation during ``predict`` is::
target_transform_inverse_func(estimator.predict(X))
or::
target_transformer.inverse_transform(estimator.predict(X))
Parameters
----------
imputer : "simple", "knn", or sklearn-compatible transformer, default="simple"
The imputer for missing data. String arguments result in the use of
specific imputers/transformers:
"simple" yields :class:`sklearn:sklearn.impute.SimpleImputer`;
"knn" yields :class:`sklearn:sklearn.impute.KNNImputer`.
Custom transformers are
allowed as long as they inherit from
:class:`sklearn:sklearn.base.TransformerMixin`.
scaler : "standard", "minmax", "maxabs", "robust", or
sklearn-compatible transformer, default="standard"
The scaler to use for the feature matrix. String arguments result in
the use of specific transformers: "standard" yields the
:class:`sklearn:sklearn.preprocessing.StandardScalar`; "minmax"
yields the :class:`sklearn:sklearn.preprocessing.MinMaxScaler`;
"maxabs" yields the
:class:`sklearn:sklearn.preprocessing.MaxAbsScaler`; "robust" yields
the :class:`sklearn:sklearn.preprocessing.RobustScaler`. Custom
transformers are allowed as long as they inherit from
:class:`sklearn:sklearn.base.TransformerMixin`.
feature_transformer : bool or sklearn-compatible transformer, default=False
An optional transformer for use on the feature matrix. If True,
use :class:`sklearn:sklearn.preprocessing.PowerTransformer`. If
False, skip this step. Custom transformers are allowed as long as
they inherit from :class:`sklearn:sklearn.base.TransformerMixin`.
ensemble_meta_estimator : "bagging", "adaboost", or None
An optional ensemble meta-estimator to combine the predictions of
several base estimators. "Adaboost" will result in the use of
:class:`sklearn:sklearn.ensemble.AdaBoostClassifier` for classifier
base estimators or
:class:`sklearn.sklearn.ensemble.AdaBoostRegressor` for regressor
base estimators. "Bagging" will result in the use of
:class:`sklearn.sklearn.ensemble.BaggingClassifier` for classifier
base estimators or :class:`sklearn.sklearn.ensemble.BaggingRegressor`
for regressor base estimators.
imputer_kwargs : dict, default=None,
Key-word arguments for the imputer.
scaler_kwargs : dict, default=None,
Key-word arguments for the scaler.
feature_transformer_kwargs : dict, default=None,
Key-word arguments for the feature_transformer.
use_cv_estimator : bool, default=True,
If True, use :class:`groupyr:groupyr.SGLCV` as the final
estimator. Otherwise, use :class:`groupyr:groupyr.SGL`.
memory : str or object with the joblib.Memory interface, default=None
Used to cache the fitted transformers of the pipeline. By default,
no caching is performed. If a string is given, it is the path to
the caching directory. Enabling caching triggers a clone of
the transformers before fitting. Therefore, the transformer
instance given to the pipeline cannot be inspected
directly. Use the attribute ``named_steps`` or ``steps`` to
inspect estimators within the pipeline. Caching the
transformers is advantageous when fitting is time consuming.
pipeline_verbosity : bool, default=False
If True, the time elapsed while fitting each step will be printed as it
is completed.
target_transformer : object, default=None
Estimator object such as derived from
:class:`sklearn.base.TransformerMixin`. Cannot be set at the same
time as ``func`` and ``inverse_func``. If ``transformer`` is ``None``
as well as ``func`` and ``inverse_func``, the transformer will be an
identity transformer. Note that the transformer will be cloned during
fitting. Also, the transformer is restricting ``y`` to be a numpy
array.
target_transform_func : function, default=None
Function to apply to ``y`` before passing to ``fit``. Cannot be set at
the same time as ``transformer``. The function needs to return a
2-dimensional array. If ``func`` is ``None``, the function used will be
the identity function.
target_transform_inverse_func : function, default=None
Function to apply to the prediction of the regressor. Cannot be set at
the same time as ``transformer`` as well. The function needs to return
a 2-dimensional array. The inverse function is used to return
predictions to the same space of the original training labels.
target_transform_check_inverse : bool, default=True
Whether to check that ``transform`` followed by ``inverse_transform``
or ``func`` followed by ``inverse_func`` leads to the original targets.
**estimator_kwargs : kwargs
Keyword arguments passed to :class:`groupyr:groupyr.SGLCV` if
``use_cv_estimator=True`` or :class:`groupyr:groupyr.SGL` if
``use_cv_estimator=False``.
Returns
-------
pipeline : :ref:`Pipeline <sklearn:pipeline>` instance
"""
return make_base_afq_pipeline(
imputer=imputer,
scaler=scaler,
feature_transformer=feature_transformer,
ensemble_meta_estimator=ensemble_meta_estimator,
estimator=gpr.SGLCV if use_cv_estimator else gpr.SGL,
imputer_kwargs=imputer_kwargs,
scaler_kwargs=scaler_kwargs,
feature_transformer_kwargs=feature_transformer_kwargs,
ensemble_meta_estimator_kwargs=ensemble_meta_estimator_kwargs,
estimator_kwargs=estimator_kwargs,
memory=memory,
verbose=pipeline_verbosity,
target_transformer=target_transformer,
target_transform_func=target_transform_func,
target_transform_inverse_func=target_transform_inverse_func,
target_transform_check_inverse=target_transform_check_inverse,
)