DrCIF#

class DrCIF(n_estimators=200, n_intervals=None, att_subsample_size=10, min_interval=4, max_interval=None, base_estimator='CIT', time_limit_in_minutes=0.0, contract_max_n_estimators=500, save_transformed_data=False, n_jobs=1, random_state=None)[source]#

Diverse Representation Canonical Interval Forest Classifier (DrCIF).

Extension of the CIF algorithm using multple representations. Implementation of the interval based forest making use of the catch22 feature set on randomly selected intervals on the base series, periodogram representation and differences representation described in the HIVE-COTE 2.0 paper Middlehurst et al (2021). [1]

Overview: Input “n” series with “d” dimensions of length “m”. For each tree

Sample n_intervals intervals per representation of random position and length

Subsample att_subsample_size catch22 or summary statistic attributes randomly

Randomly select dimension for each interval

Calculate attributes for each interval from its representation, concatenate to form new data set

Build decision tree on new data set

Ensemble the trees with averaged probability estimates

Parameters:

n_estimatorsint, default=200: Number of estimators to build for the ensemble.
n_intervalsint, length 3 list of int or None, default=None: Number of intervals to extract per representation per tree as an int for all representations or list for individual settings, if None extracts (4 + (sqrt(representation_length) * sqrt(n_dims)) / 3) intervals.
att_subsample_sizeint, default=10: Number of catch22 or summary statistic attributes to subsample per tree.
min_intervalint or length 3 list of int, default=4: Minimum length of an interval per representation as an int for all representations or list for individual settings.
max_intervalint, length 3 list of int or None, default=None: Maximum length of an interval per representation as an int for all representations or list for individual settings, if None set to (representation_length / 2).
base_estimatorBaseEstimator or str, default=”DTC”: Base estimator for the ensemble, can be supplied a sklearn BaseEstimator or a string for suggested options. “DTC” uses the sklearn DecisionTreeClassifier using entropy as a splitting measure. “CIT” uses the aeon ContinuousIntervalTree, an implementation of the original tree used with embedded attribute processing for faster predictions.
time_limit_in_minutesint, default=0: Time contract to limit build time in minutes, overriding n_estimators. Default of 0 means n_estimators is used.
contract_max_n_estimatorsint, default=500: Max number of estimators when time_limit_in_minutes is set.
save_transformed_databool, default=False: Save the data transformed in fit 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.
random_stateint or None, default=None: Seed for random number generation.

Attributes:

n_classes_int: The number of classes.
n_instances_int: The number of train cases.
n_dims_int: The number of dimensions per case.
series_length_int: The length of each series.
classes_list: The classes labels.
total_intervals_int: Total number of intervals per tree from all representations.
estimators_list of shape (n_estimators) of BaseEstimator: The collections of estimators trained in fit.
intervals_list of shape (n_estimators) of ndarray with shape (total_intervals,2): Stores indexes of each intervals start and end points for all classifiers.
atts_list of shape (n_estimators) of array with shape (att_subsample_size): Attribute indexes of the subsampled catch22 or summary statistic for all classifiers.
dims_list of shape (n_estimators) of array with shape (total_intervals): The dimension to extract attributes from each interval for all classifiers.
transformed_data_list of shape (n_estimators) of ndarray with shape
(n_instances,total_intervals * att_subsample_size): The transformed dataset for all classifiers. Only saved when save_transformed_data is true.

See also

CanonicalIntervalForest

Notes

For the Java version, see TSML.

References

[1]

Middlehurst, Matthew, James Large, Michael Flynn, Jason Lines, Aaron Bostrom, and Anthony Bagnall. “HIVE-COTE 2.0: a new meta ensemble for time series classification.” arXiv preprint arXiv:2104.07551 (2021).

Examples

>>> from aeon.classification.interval_based import DrCIF
>>> from aeon.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 = DrCIF(n_estimators=3, n_intervals=2, att_subsample_size=2)
>>> clf.fit(X_train, y_train)
DrCIF(...)
>>> 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.
`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`([deep])	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 time series 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')[source]#

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. DrCIF provides the following special sets:

“results_comparison” - used in some classifiers to compare against
previously generated results where the default set of parameters cannot produce suitable probability estimates

“contracting” - used in classifiers that set the
“capability:contractable” tag to True to test contacting functionality

“train_estimate” - used in some classifiers that set the
“capability:train_estimate” tag to True to allow for more efficient testing when relevant parameters are available

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()[source]#

Check if the estimator has been fitted.

Raises:

NotFittedError: If the estimator has not been fitted yet.

clone()[source]#

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)[source]#

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')[source]#

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')[source]#

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)[source]#

Fit time series classifier to training data.

Parameters:

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

of shape [n_instances, n_channels, series_length]

or 2D np.array (univariate, equal length series): of shape [n_instances, series_length]

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.

classmethod get_class_tag(tag_name, tag_value_default=None)[source]#

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()[source]#

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(deep=True)[source]#

Get fitted parameters.

State required:: Requires state to be “fitted”.

Parameters:

deepbool, default=True

Whether to return fitted parameters of components.

If True, will return a dict of parameter name : value for this object, including fitted parameters of fittable components (= BaseEstimator-valued parameters).
If False, will return a dict of parameter name : value for this object, but not include fitted parameters of components.

Returns:

fitted_paramsdict with str-valued keys

Dictionary of fitted parameters, paramname : paramvalue keys-value pairs include:

always: all fitted parameters of this object, as via get_param_names values are fitted parameter value for that key, of this object
if deep=True, also contains keys/value pairs of component parameters parameters of components are indexed as [componentname]__[paramname] all parameters of componentname appear as paramname with its value
if deep=True, also contains arbitrary levels of component recursion, e.g., [componentname]__[componentcomponentname]__[paramname], etc

classmethod get_param_defaults()[source]#

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()[source]#

Get parameter names for the object.

Returns:

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

get_params(deep=True)[source]#

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)[source]#

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()[source]#

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()[source]#

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[source]#: Whether fit has been called.

classmethod load_from_path(serial)[source]#

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)[source]#

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) → ndarray[source]#

Predicts labels for time series in X.

Parameters:

X3D np.array of shape (n_instances, n_channels, series_length): or 2D np.array of shape (n_instances, series_length)

Returns:

y1D np.array of int, of shape [n_instances] - predicted class labels: indices correspond to instance indices in X

predict_proba(X) → ndarray[source]#

Predicts labels probabilities for sequences in X.

Parameters:

X3D np.array of shape (n_cases, n_channels, series_length): or 2D np.array of shape (n_cases, series_length)

Returns:

y2D array of shape (n_cases, n_classes) - predicted class probabilities: First dimension indices correspond to instance indices in X, second dimension indices correspond to class labels, (i, j)-th entry is estimated probability that i-th instance is of class j

reset()[source]#

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)[source]#

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[source]#

Scores predicted labels against ground truth labels on X.

Parameters:

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

of shape [n_instances, n_channels, series_length]

or 2D np.array (univariate, equal length series): of shape [n_instances, series_length]

y1D np.ndarray 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)[source]#

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)[source]#

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.