ShapeletTransformClassifier

class ShapeletTransformClassifier(n_shapelet_samples=10000, max_shapelets=None, max_shapelet_length=None, estimator=None, transform_limit_in_minutes=0, time_limit_in_minutes=0, contract_max_n_shapelet_samples=inf, save_transformed_data=False, n_jobs=1, batch_size=100, random_state=None)

A shapelet transform classifier (STC).

Implementation of the binary shapelet transform classifier pipeline along the lines of [1][2] but with random shapelet sampling. Transforms the data using the configurable RandomShapeletTransform and then builds a RotationForest classifier.

As some implementations and applications contract the transformation solely, contracting is available for the transform only and both classifier and transform.

Parameters

n_shapelet_samplesint, default=10000

The number of candidate shapelets to be considered for the final transform. Filtered down to <= max_shapelets, keeping the shapelets with the most information gain.

max_shapeletsint or None, default=None

Max number of shapelets to keep for the final transform. Each class value will have its own max, set to n_classes_ / max_shapelets. If None, uses the minimum between 10 * n_instances_ and 1000.

max_shapelet_lengthint or None, default=None

Lower bound on candidate shapelet lengths for the transform. If None, no max length is used

estimatorBaseEstimator or None, default=None

Base estimator for the ensemble, can be supplied a sklearn BaseEstimator. If None a default RotationForest classifier is used.

transform_limit_in_minutesint, default=0

Time contract to limit transform time in minutes for the shapelet transform, overriding n_shapelet_samples. A value of 0 means n_shapelet_samples is used.

time_limit_in_minutesint, default=0

Time contract to limit build time in minutes, overriding n_shapelet_samples and transform_limit_in_minutes. The estimator will only be contracted if a time_limit_in_minutes parameter is present. Default of 0 means n_shapelet_samples or transform_limit_in_minutes is used.

contract_max_n_shapelet_samplesint, default=np.inf

Max number of shapelets to extract when contracting the transform with transform_limit_in_minutes or time_limit_in_minutes.

save_transformed_databool, default=False

Save the data transformed in fit in transformed_data_ for use in _get_train_probs.

n_jobsint, default=1

The number of jobs to run in parallel for both fit and predict. -1 means using all processors.

batch_sizeint or None, default=100

Number of shapelet candidates processed before being merged into the set of best shapelets in the transform.

random_stateint, RandomState instance or None, default=None

If int, random_state is the seed used by the random number generator; If RandomState instance, random_state is the random number generator; If None, the random number generator is the RandomState instance used by np.random.

Attributes

classes_list

The unique class labels in the training set.

n_classes_int

The number of unique classes in the training set.

fit_time_int

The time (in milliseconds) for fit to run.

n_instances_int

The number of train cases in the training set.

n_dims_int

The number of dimensions per case in the training set.

series_length_int

The length of each series in the training set.

transformed_data_list of shape (n_estimators) of ndarray

The transformed training dataset for all classifiers. Only saved when save_transformed_data is True.

See also

RandomShapeletTransform

The randomly sampled shapelet transform.

RotationForest

The default rotation forest classifier used.

Notes

For the Java version, see tsml.

References

1

Jon Hills et al., “Classification of time series by shapelet transformation”, Data Mining and Knowledge Discovery, 28(4), 851–881, 2014.

2

A. Bostrom and A. Bagnall, “Binary Shapelet Transform for Multiclass Time Series Classification”, Transactions on Large-Scale Data and Knowledge Centered Systems, 32, 2017.

Examples

>>> from sktime.classification.shapelet_based import ShapeletTransformClassifier
>>> from sktime.classification.sklearn import RotationForest
>>> from sktime.datasets import load_unit_test
>>> X_train, y_train = load_unit_test(split="train", return_X_y=True)
>>> X_test, y_test = load_unit_test(split="test", return_X_y=True)
>>> clf = ShapeletTransformClassifier(
...     estimator=RotationForest(n_estimators=3),
...     n_shapelet_samples=100,
...     max_shapelets=10,
...     batch_size=20,
... )
>>> clf.fit(X_train, y_train)
ShapeletTransformClassifier(...)
>>> y_pred = clf.predict(X_test)

Methods

check_is_fitted()	Check if the estimator has been fitted.
clone()	Obtain a clone of the object with same hyper-parameters.
clone_tags(estimator[, tag_names])	clone/mirror tags from another estimator as dynamic override.
create_test_instance([parameter_set])	Construct Estimator instance if possible.
create_test_instances_and_names([parameter_set])	Create list of all test instances and a list of names for them.
fit(X, y)	Fit time series classifier to training data.
fit_predict(X, y[, cv, change_state])	Fit and predict labels for sequences in X.
fit_predict_proba(X, y[, cv, change_state])	Fit and predict labels probabilities for sequences in X.
get_class_tag(tag_name[, tag_value_default])	Get tag value from estimator class (only class tags).
get_class_tags()	Get class tags from estimator class and all its parent classes.
get_fitted_params()	Get fitted parameters.
get_param_defaults()	Get parameter defaults for the object.
get_param_names()	Get parameter names for the object.
get_params([deep])	Get parameters for this estimator.
get_tag(tag_name[, tag_value_default, …])	Get tag value from estimator class and dynamic tag overrides.
get_tags()	Get tags from estimator class and dynamic tag overrides.
get_test_params([parameter_set])	Return testing parameter settings for the estimator.
is_composite()	Check if the object is composite.
load_from_path(serial)	Load object from file location.
load_from_serial(serial)	Load object from serialized memory container.
predict(X)	Predicts labels for sequences in X.
predict_proba(X)	Predicts labels probabilities for sequences in X.
reset()	Reset the object to a clean post-init state.
save([path])	Save serialized self to bytes-like object or to (.zip) file.
score(X, y)	Scores predicted labels against ground truth labels on X.
set_params(**params)	Set the parameters of this object.
set_tags(**tag_dict)	Set dynamic tags to given values.

classmethod get_test_params(parameter_set='default')

Return testing parameter settings for the estimator.

Parameters

parameter_setstr, default=”default”

Name of the set of test parameters to return, for use in tests. If no special parameters are defined for a value, will return “default” set. For classifiers, a “default” set of parameters should be provided for general testing, and a “results_comparison” set for comparing against previously recorded results if the general set does not produce suitable probabilities to compare against.

Returns

paramsdict or list of dict, default={}

Parameters to create testing instances of the class. Each dict are parameters to construct an “interesting” test instance, i.e., MyClass(**params) or MyClass(**params[i]) creates a valid test instance. create_test_instance uses the first (or only) dictionary in params.

check_is_fitted()

Check if the estimator has been fitted.

Raises

NotFittedError

If the estimator has not been fitted yet.

clone()

Obtain a clone of the object with same hyper-parameters.

A clone is a different object without shared references, in post-init state. This function is equivalent to returning sklearn.clone of self. Equal in value to type(self)(**self.get_params(deep=False)).

Returns

instance of type(self), clone of self (see above)

clone_tags(estimator, tag_names=None)

clone/mirror tags from another estimator as dynamic override.

Parameters

estimatorestimator inheriting from :class:BaseEstimator

tag_namesstr or list of str, default = None

Names of tags to clone. If None then all tags in estimator are used as tag_names.

Returns

Self

Reference to self.

Notes

Changes object state by setting tag values in tag_set from estimator as dynamic tags in self.

classmethod create_test_instance(parameter_set='default')

Construct Estimator instance if possible.

Parameters

parameter_setstr, default=”default”

Name of the set of test parameters to return, for use in tests. If no special parameters are defined for a value, will return “default” set.

Returns

instanceinstance of the class with default parameters

Notes

get_test_params can return dict or list of dict. This function takes first or single dict that get_test_params returns, and constructs the object with that.

classmethod create_test_instances_and_names(parameter_set='default')

Create list of all test instances and a list of names for them.

Parameters

parameter_setstr, default=”default”

Name of the set of test parameters to return, for use in tests. If no special parameters are defined for a value, will return “default” set.

Returns

objslist of instances of cls

i-th instance is cls(**cls.get_test_params()[i])

nameslist of str, same length as objs

i-th element is name of i-th instance of obj in tests convention is {cls.__name__}-{i} if more than one instance otherwise {cls.__name__}

parameter_setstr, default=”default”

Name of the set of test parameters to return, for use in tests. If no special parameters are defined for a value, will return “default” set.

fit(X, y)

Fit time series classifier to training data.

Parameters

X3D np.array (any number of dimensions, equal length series)

of shape [n_instances, n_dimensions, series_length]

or 2D np.array (univariate, equal length series)

of shape [n_instances, series_length]

or pd.DataFrame with each column a dimension, each cell a pd.Series

(any number of dimensions, equal or unequal length series)

or of any other supported Panel mtype

for list of mtypes, see datatypes.SCITYPE_REGISTER for specifications, see examples/AA_datatypes_and_datasets.ipynb

y1D np.array of int, of shape [n_instances] - class labels for fitting

indices correspond to instance indices in X

Returns

selfReference to self.

Notes

Changes state by creating a fitted model that updates attributes ending in “_” and sets is_fitted flag to True.

fit_predict(X, y, cv=None, change_state=True) → numpy.ndarray

Fit and predict labels for sequences in X.

Convenience method to produce in-sample predictions and cross-validated out-of-sample predictions.

Writes to self, if change_state=True:

Sets self.is_fitted to True. Sets fitted model attributes ending in “_”.

Does not update state if change_state=False.

Parameters

X3D np.array (any number of dimensions, equal length series)

of shape [n_instances, n_dimensions, series_length]

or 2D np.array (univariate, equal length series)

of shape [n_instances, series_length]

or pd.DataFrame with each column a dimension, each cell a pd.Series

(any number of dimensions, equal or unequal length series)

or of any other supported Panel mtype

for list of mtypes, see datatypes.SCITYPE_REGISTER for specifications, see examples/AA_datatypes_and_datasets.ipynb

y1D np.array of int, of shape [n_instances] - class labels for fitting

indices correspond to instance indices in X

cvNone, int, or sklearn cross-validation object, optional, default=None

None : predictions are in-sample, equivalent to fit(X, y).predict(X) cv : predictions are equivalent to fit(X_train, y_train).predict(X_test)

where multiple X_train, y_train, X_test are obtained from cv folds returned y is union over all test fold predictions cv test folds must be non-intersecting

intequivalent to cv=KFold(cv, shuffle=True, random_state=x),

i.e., k-fold cross-validation predictions out-of-sample random_state x is taken from self if exists, otherwise x=None

change_statebool, optional (default=True)

if False, will not change the state of the classifier,

i.e., fit/predict sequence is run with a copy, self does not change

if True, will fit self to the full X and y,

end state will be equivalent to running fit(X, y)

Returns

y1D np.array of int, of shape [n_instances] - predicted class labels

indices correspond to instance indices in X if cv is passed, -1 indicates entries not seen in union of test sets

fit_predict_proba(X, y, cv=None, change_state=True) → numpy.ndarray

Fit and predict labels probabilities for sequences in X.

Convenience method to produce in-sample predictions and cross-validated out-of-sample predictions.

Parameters

X3D np.array (any number of dimensions, equal length series)

of shape [n_instances, n_dimensions, series_length]

or 2D np.array (univariate, equal length series)

of shape [n_instances, series_length]

or pd.DataFrame with each column a dimension, each cell a pd.Series

(any number of dimensions, equal or unequal length series)

or of any other supported Panel mtype

for list of mtypes, see datatypes.SCITYPE_REGISTER for specifications, see examples/AA_datatypes_and_datasets.ipynb

y1D np.array of int, of shape [n_instances] - class labels for fitting

indices correspond to instance indices in X

cvNone, int, or sklearn cross-validation object, optional, default=None

None : predictions are in-sample, equivalent to fit(X, y).predict(X) cv : predictions are equivalent to fit(X_train, y_train).predict(X_test)

where multiple X_train, y_train, X_test are obtained from cv folds returned y is union over all test fold predictions cv test folds must be non-intersecting

int : equivalent to cv=Kfold(int), i.e., k-fold cross-validation predictions

change_statebool, optional (default=True)

if False, will not change the state of the classifier,

i.e., fit/predict sequence is run with a copy, self does not change

if True, will fit self to the full X and y,

end state will be equivalent to running fit(X, y)

Returns

y2D array of shape [n_instances, n_classes] - predicted class probabilities

1st dimension indices correspond to instance indices in X 2nd dimension indices correspond to possible labels (integers) (i, j)-th entry is predictive probability that i-th instance is of class j

classmethod get_class_tag(tag_name, tag_value_default=None)

Get tag value from estimator class (only class tags).

Parameters

tag_namestr

Name of tag value.

tag_value_defaultany type

Default/fallback value if tag is not found.

Returns

tag_value

Value of the tag_name tag in self. If not found, returns tag_value_default.

classmethod get_class_tags()

Get class tags from estimator class and all its parent classes.

Returns

collected_tagsdict

Dictionary of tag name : tag value pairs. Collected from _tags class attribute via nested inheritance. NOT overridden by dynamic tags set by set_tags or mirror_tags.

get_fitted_params()

Get fitted parameters.

State required:

Requires state to be “fitted”.

Returns

fitted_paramsdict of fitted parameters, keys are str names of parameters

parameters of components are indexed as [componentname]__[paramname]

classmethod get_param_defaults()

Get parameter defaults for the object.

Returns

default_dict: dict with str keys

keys are all parameters of cls that have a default defined in __init__ values are the defaults, as defined in __init__

classmethod get_param_names()

Get parameter names for the object.

Returns

param_names: list of str, alphabetically sorted list of parameter names of cls

get_params(deep=True)

Get parameters for this estimator.

Parameters

deepbool, default=True

If True, will return the parameters for this estimator and contained subobjects that are estimators.

Returns

paramsdict

Parameter names mapped to their values.

get_tag(tag_name, tag_value_default=None, raise_error=True)

Get tag value from estimator class and dynamic tag overrides.

Parameters

tag_namestr

Name of tag to be retrieved

tag_value_defaultany type, optional; default=None

Default/fallback value if tag is not found

raise_errorbool

whether a ValueError is raised when the tag is not found

Returns

tag_value

Value of the tag_name tag in self. If not found, returns an error if raise_error is True, otherwise it returns tag_value_default.

Raises

ValueError if raise_error is True i.e. if tag_name is not in self.get_tags(

).keys()

get_tags()

Get tags from estimator class and dynamic tag overrides.

Returns

collected_tagsdict

Dictionary of tag name : tag value pairs. Collected from _tags class attribute via nested inheritance and then any overrides and new tags from _tags_dynamic object attribute.

is_composite()

Check if the object is composite.

A composite object is an object which contains objects, as parameters. Called on an instance, since this may differ by instance.

Returns

composite: bool, whether self contains a parameter which is BaseObject

property is_fitted

Whether fit has been called.

classmethod load_from_path(serial)

Load object from file location.

Parameters

serialresult of ZipFile(path).open(“object)

Returns

deserialized self resulting in output at path, of cls.save(path)

classmethod load_from_serial(serial)

Load object from serialized memory container.

Parameters

serial1st element of output of cls.save(None)

Returns

deserialized self resulting in output serial, of cls.save(None)

predict(X) → numpy.ndarray

Predicts labels for sequences in X.

Parameters

X3D np.array (any number of dimensions, equal length series)

of shape [n_instances, n_dimensions, series_length]

or 2D np.array (univariate, equal length series)

of shape [n_instances, series_length]

or pd.DataFrame with each column a dimension, each cell a pd.Series

(any number of dimensions, equal or unequal length series)

or of any other supported Panel mtype

for list of mtypes, see datatypes.SCITYPE_REGISTER for specifications, see examples/AA_datatypes_and_datasets.ipynb

Returns

y1D np.array of int, of shape [n_instances] - predicted class labels

indices correspond to instance indices in X

predict_proba(X) → numpy.ndarray

Predicts labels probabilities for sequences in X.

Parameters

X3D np.array (any number of dimensions, equal length series)

of shape [n_instances, n_dimensions, series_length]

or 2D np.array (univariate, equal length series)

of shape [n_instances, series_length]

or pd.DataFrame with each column a dimension, each cell a pd.Series

(any number of dimensions, equal or unequal length series)

or of any other supported Panel mtype

for list of mtypes, see datatypes.SCITYPE_REGISTER for specifications, see examples/AA_datatypes_and_datasets.ipynb

Returns

y2D array of shape [n_instances, n_classes] - predicted class probabilities

1st dimension indices correspond to instance indices in X 2nd dimension indices correspond to possible labels (integers) (i, j)-th entry is predictive probability that i-th instance is of class j

reset()

Reset the object to a clean post-init state.

Equivalent to sklearn.clone but overwrites self. After self.reset() call, self is equal in value to type(self)(**self.get_params(deep=False))

Detail behaviour: removes any object attributes, except:

hyper-parameters = arguments of __init__ object attributes containing double-underscores, i.e., the string “__”

runs __init__ with current values of hyper-parameters (result of get_params)

Not affected by the reset are: object attributes containing double-underscores class and object methods, class attributes

save(path=None)

Save serialized self to bytes-like object or to (.zip) file.

Behaviour: if path is None, returns an in-memory serialized self if path is a file location, stores self at that location as a zip file

saved files are zip files with following contents: _metadata - contains class of self, i.e., type(self) _obj - serialized self. This class uses the default serialization (pickle).

Parameters

pathNone or file location (str or Path)

if None, self is saved to an in-memory object if file location, self is saved to that file location. If:

path=”estimator” then a zip file estimator.zip will be made at cwd. path=”/home/stored/estimator” then a zip file estimator.zip will be stored in /home/stored/.

Returns

if path is None - in-memory serialized self

if path is file location - ZipFile with reference to the file

score(X, y) → float

Scores predicted labels against ground truth labels on X.

Parameters

X3D np.array (any number of dimensions, equal length series)

of shape [n_instances, n_dimensions, series_length]

or 2D np.array (univariate, equal length series)

of shape [n_instances, series_length]

or pd.DataFrame with each column a dimension, each cell a pd.Series

(any number of dimensions, equal or unequal length series)

or of any other supported Panel mtype

for list of mtypes, see datatypes.SCITYPE_REGISTER for specifications, see examples/AA_datatypes_and_datasets.ipynb

y1D np.ndarray of int, of shape [n_instances] - class labels (ground truth)

indices correspond to instance indices in X

Returns

float, accuracy score of predict(X) vs y

set_params(**params)

Set the parameters of this object.

The method works on simple estimators as well as on nested objects. The latter have parameters of the form <component>__<parameter> so that it’s possible to update each component of a nested object.

Parameters

**paramsdict

BaseObject parameters

Returns

selfreference to self (after parameters have been set)

set_tags(**tag_dict)

Set dynamic tags to given values.

Parameters

tag_dictdict

Dictionary of tag name : tag value pairs.

Returns

Self

Reference to self.

Notes

Changes object state by settting tag values in tag_dict as dynamic tags in self.