def test_feature_detection(self):
"""Test automatic dectection of metafeature extraction method."""
name, mtd, groups = _internal.process_features(
features="all",
groups=tuple(),
suppress_warnings=True,
custom_class_=MFETestClass)
assert len(name) == 3 and len(mtd) == 3 and len(groups) == 1
def test_feature_warning2(self):
"""Test memory error handling of feature extraction."""
name, mtd, groups = map(
np.asarray,
_internal.process_features(
features="memory_error",
groups=tuple(),
suppress_warnings=True,
custom_class_=MFETestClass,
),
)
with pytest.warns(RuntimeWarning):
_internal.get_feat_value(
mtd_name=name[0],
mtd_args={
"X": np.array([]),
"y": np.ndarray([]),
"raise_mem_err": True,
},
mtd_callable=mtd[0][1],
suppress_warnings=False,
)
def __init__(self,
groups: t.Union[str, t.Iterable[str]] = "all",
features: t.Union[str, t.Iterable[str]] = "all",
summary: t.Union[str, t.Iterable[str]] = ("mean", "sd"),
measure_time: t.Optional[str] = None,
wildcard: str = "all",
score="accuracy",
folds=10,
sample_size=1.0,
suppress_warnings: bool = False,
random_state: t.Optional[int] = None) -> None:
"""This class provides easy access for metafeature extraction from
datasets.
It expected that user first calls ``fit`` method after instantiation
and then ``extract`` for effectively extract the selected metafeatures.
Check reference [1]_ for more information.
Parameters
----------
groups : :obj:`Iterable` of :obj:`str` or :obj:`str`
A collection or a single metafeature group name representing the
desired group of metafeatures for extraction. The supported groups
are:
1. ``general``: general/simples metafeatures.
2. ``statistical``: statistical metafeatures.
3. ``info-theory``: information-theoretic type of metafeature.
4. ``model-based``: metafeatures based on machine learning
model characteristics.
5. ``landmarking``: metafeatures representing performance
metrics from simple machine learning models or machine
learning models induced with sampled data.
The value provided by the argument ``wildcard`` can be used to
select all metafeature groups rapidly.
features : :obj:`Iterable` of :obj:`str` or :obj:`str`, optional
A collection or a single metafeature name desired for extraction.
Keep in mind that the extraction only gathers features also in the
selected ``groups``. Check this class ``feature`` attribute to get
a list of available metafeatures from selected groups.
The value provided by the argument ``wildcard`` can be used to
select all features from all selected groups rapidly.
summary : :obj:`Iterable` of :obj:`str` or :obj:`str`, optional
A collection or a single summary function to summarize a group of
metafeature measures into a fixed-length group of value, typically
a single value. The values must be one of the following:
1. ``mean``: Average of the values.
2. ``sd``: Standard deviation of the values.
3. ``count``: Computes the cardinality of the measure. Suitable
for variable cardinality.
4. ``histogram``: Describes the distribution of the measured
values. Suitable for high cardinality.
5. ``iq_range``: Computes the interquartile range of the
measured values.
6. ``kurtosis``: Describes the shape of the measures values
distribution.
7. ``max``: Results in the maximum value of the measure.
8. ``median``: Results in the central value of the measure.
9. ``min``: Results in the minimum value of the measure.
10. ``quantiles``: Results in the minimum, first quartile,
median, third quartile and maximum of the measured values.
11. ``range``: Computes the range of the measured values.
12. ``skewness``: Describes the shape of the measure values
distribution in terms of symmetry.
If more than one summary function is selected, then all multivalued
extracted metafeatures are summarized with each summary function.
The particular value provided by the argument ``wildcard`` can be
used to select all summary functions rapidly.
measure_time : :obj:`str`, optional
Options for measuring the time elapsed during metafeature
extraction. If this argument value is :obj:`NoneType`, no time
elapsed is measured. Otherwise, this argument must be a :obj:`str`
valued as one of the options below:
1. ``avg``: average time for each metafeature (total time
divided by the feature cardinality, i.e., number of features
extracted by a single feature-extraction related method),
without summarization time.
2. ``avg_summ``: average time for each metafeature (total time
of extraction divided by feature cardinality) including
required time for summarization.
3. ``total``: total time for each metafeature, without
summarization time.
4. ``total_summ``: total time for each metafeature including
the required time for summarization.
The ``cardinality`` of the feature is the number of values
extracted by a single calculation method.
For example, ``mean`` feature has cardinality equal to the number
of numeric features in the dataset, where ``cor`` (from
``correlation``) has cardinality equals to (N - 1)/2, where N is
the number of numeric features in the dataset.
The cardinality is used to divide the total execution time of that
method if an option starting with ``avg`` is selected.
If a summary method has cardinality higher than one (more than one
value returned after summarization and, thus, creating more than
one entry in the result lists) like, for example, ``histogram``
summary method, then the corresponding time of this summary will be
inserted only in the first correspondent element of the time list.
The remaining entries are all filled with 0 value, to keep
consistency between the size of all lists returned and index
correspondence between they.
wildcard : :obj:`str`, optional
Value used as ``select all`` for ``groups``, ``features`` and
``summary`` arguments.
score : :obj:`str`, optional
Score metric used to extract ``landmarking`` metafeatures.
folds : :obj:`int`, optional
Number of folds to create a Stratified K-Fold cross validation
to produce the ``landmarking`` metafeatures.
sample_size : :obj:`float`, optional
Sample proportion used to produce the ``landmarking`` metafeatures.
This argument must be in 0.5 and 1.0 (both inclusive) interval.
suppress_warnings : :obj:`bool`, optional
If True, then ignore all warnings invoked at the instantiation
time.
Notes
-----
.. [1] Rivolli et al. "Towards Reproducible Empirical
Research in Meta-Learning,".
Rivolli et al. URL: https://arxiv.org/abs/1808.10406
Examples
--------
Load a dataset
>>> from sklearn.datasets import load_iris
>>> from pymfe.mfe import MFE
>>> data = load_iris()
>>> y = data.target
>>> X = data.data
Extract all measures
>>> mfe = MFE()
>>> mfe.fit(X, y)
>>> ft = mfe.extract()
>>> print(ft)
Extract general, statistical and information-theoretic measures
>>> mfe = MFE(groups=["general", "statistical", "info-theory"])
>>> mfe.fit(X, y)
>>> ft = mfe.extract()
>>> print(ft)
"""
self.groups = _internal.process_generic_set(
values=groups, group_name="groups") # type: t.Tuple[str, ...]
self.groups, self.inserted_group_dep = (
_internal.solve_group_dependencies(
groups=self.groups))
proc_feat = _internal.process_features(
features=features,
groups=self.groups,
suppress_warnings=suppress_warnings,
wildcard=wildcard,
) # type: t.Tuple[t.Tuple[str, ...], _TypeSeqExt, t.Tuple[str, ...]]
self.features, self._metadata_mtd_ft, self.groups = proc_feat
del proc_feat
self.summary, self._metadata_mtd_sm = _internal.process_summary(
summary) # type: t.Tuple[t.Tuple[str, ...], _TypeSeqExt]
self.timeopt = _internal.process_generic_option(
value=measure_time, group_name="timeopt",
allow_none=True) # type: t.Optional[str]
self.X = None # type: t.Optional[np.ndarray]
self.y = None # type: t.Optional[np.ndarray]
self._custom_args_ft = None # type: t.Optional[t.Dict[str, t.Any]]
"""User-independent arguments for ft. methods (e.g. ``X`` and ``y``)"""
self._custom_args_sum = None # type: t.Optional[t.Dict[str, t.Any]]
"""User-independent arguments for summary functions methods."""
self._attr_indexes_num = None # type: t.Optional[t.Tuple[int, ...]]
"""Numeric column indexes from ``X`` (independent attributes)."""
self._attr_indexes_cat = None # type: t.Optional[t.Tuple[int, ...]]
"""Categoric column indexes from ``X`` (independent attributes)."""
self._precomp_args_ft = None # type: t.Optional[t.Dict[str, t.Any]]
"""Precomputed common feature-extraction method arguments."""
self._postprocess_args_ft = {} # type: t.Dict[str, t.Any]
"""User-independent arguments for post-processing methods."""
if random_state is None or isinstance(random_state, int):
self.random_state = random_state
np.random.seed(random_state)
else:
raise ValueError(
'Invalid "random_state" argument ({0}). '
'Expecting None or an integer.'.format(random_state))
if isinstance(folds, int):
self.folds = folds
else:
raise ValueError('Invalid "folds" argument ({0}). '
'Expecting an integer.'.format(random_state))
if isinstance(sample_size, int):
sample_size = float(sample_size)
if isinstance(sample_size, float)\
and 0.5 <= sample_size <= 1.0:
self.sample_size = sample_size
else:
raise ValueError('Invalid "sample_size" argument ({0}). '
'Expecting an float [0.5, 1].'
.format(random_state))
self.score = _internal.check_score(score, self.groups)
