GAFeatureSelectionCV
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Evolutionary optimization for feature selection. |
Call decision_function on the estimator with the best found features. |
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Main method of GAFeatureSelectionCV, starts the optimization procedure with to find the best features set |
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Get parameters for this estimator. |
Reverse the transformation operation. |
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Call predict on the estimator with the best found features. |
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Call predict_proba on the estimator with the best found features. |
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Return the score on the given data, if the estimator has been refit. |
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Set the parameters of this estimator. |
Reduce X to the selected features. |
- class sklearn_genetic.GAFeatureSelectionCV(estimator, cv=3, scoring=None, population_size=50, generations=80, crossover_probability=0.2, mutation_probability=0.8, tournament_size=3, elitism=True, max_features=None, verbose=True, keep_top_k=1, criteria='max', algorithm='eaMuPlusLambda', refit=True, n_jobs=1, pre_dispatch='2*n_jobs', error_score=nan, return_train_score=False, log_config=None)[source]
Evolutionary optimization for feature selection.
GAFeatureSelectionCV implements a “fit” and a “score” method. It also implements “predict”, “predict_proba”, “decision_function”, “predict_log_proba” if they are implemented in the estimator used. The features (variables) used by the estimator are found by optimizing the cv-scores and by minimizing the number of features
- Parameters:
- estimatorestimator object, default=None
estimator object implementing ‘fit’ The object to use to fit the data.
- cvint, cross-validation generator or an iterable, default=None
Determines the cross-validation splitting strategy. Possible inputs for cv are: - None, to use the default 5-fold cross validation, - int, to specify the number of folds in a (Stratified)KFold, - CV splitter, - An iterable yielding (train, test) splits as arrays of indices. For int/None inputs, if the estimator is a classifier and
y
is either binary or multiclass,StratifiedKFold
is used. In all other cases,KFold
is used. These splitters are instantiated with shuffle=False so the splits will be the same across calls.- population_sizeint, default=10
Size of the initial population to sample randomly generated individuals.
- generationsint, default=40
Number of generations or iterations to run the evolutionary algorithm.
- crossover_probabilityfloat or a Scheduler, default=0.2
Probability of crossover operation between two individuals.
- mutation_probabilityfloat or a Scheduler, default=0.8
Probability of child mutation.
- tournament_sizeint, default=3
Number of individuals to perform tournament selection.
- elitismbool, default=True
If True takes the tournament_size best solution to the next generation.
- max_featuresint, default=None
The upper bound number of features to be selected.
- scoringstr, callable, list, tuple or dict, default=None
Strategy to evaluate the performance of the cross-validated model on the test set. If scoring represents a single score, one can use:
a single string;
a callable that returns a single value.
If scoring represents multiple scores, one can use:
a list or tuple of unique strings;
a callable returning a dictionary where the keys are the metric names and the values are the metric scores;
a dictionary with metric names as keys and callables a values.
- n_jobsint, default=None
Number of jobs to run in parallel. Training the estimator and computing the score are parallelized over the cross-validation splits.
None
means 1 unless in ajoblib.parallel_backend
context.-1
means using all processors.- verbosebool, default=True
If
True
, shows the metrics on the optimization routine.- keep_top_kint, default=1
Number of best solutions to keep in the hof object. If a callback stops the algorithm before k iterations, it will return only one set of parameters per iteration.
- criteria{‘max’, ‘min’} , default=’max’
max
if a higher scoring metric is better,min
otherwise.- algorithm{‘eaMuPlusLambda’, ‘eaMuCommaLambda’, ‘eaSimple’}, default=’eaMuPlusLambda’
Evolutionary algorithm to use. See more details in the deap algorithms documentation.
- refitbool, str, or callable, default=True
Refit an estimator using the best found parameters on the whole dataset. For multiple metric evaluation, this needs to be a str denoting the scorer that would be used to find the best parameters for refitting the estimator at the end. The refitted estimator is made available at the
best_estimator_
attribute and permits usingpredict
directly on thisFeatureSelectionCV
instance. Also for multiple metric evaluation, the attributesbest_index_
,best_score_
andbest_params_
will only be available ifrefit
is set and all of them will be determined w.r.t this specific scorer. Seescoring
parameter to know more about multiple metric evaluation.If
False
, it is not possible to make predictions using this GASearchCV instance after fitting.- pre_dispatchint or str, default=’2*n_jobs’
Controls the number of jobs that get dispatched during parallel execution. Reducing this number can be useful to avoid an explosion of memory consumption when more jobs get dispatched than CPUs can process. This parameter can be:
None, in which case all the jobs are immediately created and spawned. Use this for lightweight and fast-running jobs, to avoid delays due to on-demand spawning of the jobs
An int, giving the exact number of total jobs that are spawned
A str, giving an expression as a function of n_jobs, as in ‘2*n_jobs’
- error_score‘raise’ or numeric, default=np.nan
Value to assign to the score if an error occurs in estimator fitting. If set to
'raise'
, the error is raised. If a numeric value is given, FitFailedWarning is raised.- return_train_score: bool, default=False
If
False
, thecv_results_
attribute will not include training scores. Computing training scores is used to get insights on how different parameter settings impact the overfitting/underfitting trade-off. However computing the scores on the training set can be computationally expensive and is not strictly required to select the parameters that yield the best generalization performance.- log_config
MLflowConfig
, default = None Configuration to log metrics and models to mlflow, of None, no mlflow logging will be performed
- Attributes:
- logbook
DEAP.tools.Logbook
Contains the logs of every set of hyperparameters fitted with its average scoring metric.
- historydict
Dictionary of the form: {“gen”: [], “fitness”: [], “fitness_std”: [], “fitness_max”: [], “fitness_min”: []}
gen returns the index of the evaluated generations. Each entry on the others lists, represent the average metric in each generation.
- cv_results_dict of numpy (masked) ndarrays
A dict with keys as column headers and values as columns, that can be imported into a pandas
DataFrame
.- best_estimator_estimator
Estimator that was chosen by the search, i.e. estimator which gave highest score on the left out data. Not available if
refit=False
.- best_features_list
List of bool, each index represents one feature in the same order the data was fed. 1 means the feature was selected, 0 means the features was discarded.
- support_list
The mask of selected features.
- scorer_function or a dict
Scorer function used on the held out data to choose the best parameters for the model.
- n_splits_int
The number of cross-validation splits (folds/iterations).
n_features_in_
intNumber of features seen during fit.
- refit_time_float
Seconds used for refitting the best model on the whole dataset. This is present only if
refit
is not False.
- logbook
- decision_function(X)[source]
Call decision_function on the estimator with the best found features. Only available if
refit=True
and the underlying estimator supportsdecision_function
.- Parameters:
- Xindexable, length n_samples
Must fulfill the input assumptions of the underlying estimator.
- Returns:
- y_scorendarray of shape (n_samples,) or (n_samples, n_classes) or (n_samples, n_classes * (n_classes-1) / 2)
Result of the decision function for X based on the estimator with the best found parameters.
- fit(X, y, callbacks=None)[source]
Main method of GAFeatureSelectionCV, starts the optimization procedure with to find the best features set
- Parameters:
- Xarray-like of shape (n_samples, n_features)
The data to fit. Can be for example a list, or an array.
- yarray-like of shape (n_samples,) or (n_samples, n_outputs), default=None
The target variable to try to predict in the case of supervised learning.
- callbacks: list or callable
One or a list of the callbacks methods available in
callbacks
. The callback is evaluated after fitting the estimators from the generation 1.
- fit_transform(X, y=None, **fit_params)
Fit to data, then transform it.
Fits transformer to X and y with optional parameters fit_params and returns a transformed version of X.
- Parameters:
- Xarray-like of shape (n_samples, n_features)
Input samples.
- yarray-like of shape (n_samples,) or (n_samples, n_outputs), default=None
Target values (None for unsupervised transformations).
- **fit_paramsdict
Additional fit parameters.
- Returns:
- X_newndarray array of shape (n_samples, n_features_new)
Transformed array.
- get_feature_names_out(input_features=None)
Mask feature names according to selected features.
- Parameters:
- input_featuresarray-like of str or None, default=None
Input features.
If input_features is None, then feature_names_in_ is used as feature names in. If feature_names_in_ is not defined, then the following input feature names are generated: [“x0”, “x1”, …, “x(n_features_in_ - 1)”].
If input_features is an array-like, then input_features must match feature_names_in_ if feature_names_in_ is defined.
- Returns:
- feature_names_outndarray of str objects
Transformed feature names.
- 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_support(indices=False)
Get a mask, or integer index, of the features selected.
- Parameters:
- indicesbool, default=False
If True, the return value will be an array of integers, rather than a boolean mask.
- Returns:
- supportarray
An index that selects the retained features from a feature vector. If indices is False, this is a boolean array of shape [# input features], in which an element is True iff its corresponding feature is selected for retention. If indices is True, this is an integer array of shape [# output features] whose values are indices into the input feature vector.
- inverse_transform(X)
Reverse the transformation operation.
- Parameters:
- Xarray of shape [n_samples, n_selected_features]
The input samples.
- Returns:
- X_rarray of shape [n_samples, n_original_features]
X with columns of zeros inserted where features would have been removed by
transform()
.
- predict(X)[source]
Call predict on the estimator with the best found features. Only available if
refit=True
and the underlying estimator supportspredict
.- Parameters:
- Xindexable, length n_samples
Must fulfill the input assumptions of the underlying estimator.
- Returns:
- y_predndarray of shape (n_samples,)
The predicted labels or values for X based on the estimator with the best found parameters.
- predict_log_proba(X)[source]
Call predict_log_proba on the estimator with the best found features. Only available if
refit=True
and the underlying estimator supportspredict_log_proba
.- Parameters:
- Xindexable, length n_samples
Must fulfill the input assumptions of the underlying estimator.
- Returns:
- y_predndarray of shape (n_samples,) or (n_samples, n_classes)
Predicted class log-probabilities for X based on the estimator with the best found parameters. The order of the classes corresponds to that in the fitted attribute classes_.
- predict_proba(X)[source]
Call predict_proba on the estimator with the best found features. Only available if
refit=True
and the underlying estimator supportspredict_proba
.- Parameters:
- Xindexable, length n_samples
Must fulfill the input assumptions of the underlying estimator.
- Returns:
- y_predndarray of shape (n_samples,) or (n_samples, n_classes)
Predicted class probabilities for X based on the estimator with the best found parameters. The order of the classes corresponds to that in the fitted attribute classes_.
- score(X, y)[source]
Return the score on the given data, if the estimator has been refit. This uses the score defined by
scoring
where provided, and thebest_estimator_.score
method otherwise.- Parameters:
- Xarray-like of shape (n_samples, n_features)
Input data, where n_samples is the number of samples and n_features is the number of features.
- yarray-like of shape (n_samples, n_output) or (n_samples,), default=None
Target relative to X for classification or regression; None for unsupervised learning.
- Returns:
- scorefloat
The score defined by
scoring
if provided, and thebest_estimator_.score
method otherwise.
- set_output(*, transform=None)
Set output container.
See sphx_glr_auto_examples_miscellaneous_plot_set_output.py for an example on how to use the API.
- Parameters:
- transform{“default”, “pandas”}, default=None
Configure output of transform and fit_transform.
“default”: Default output format of a transformer
“pandas”: DataFrame output
None: Transform configuration is unchanged
- Returns:
- selfestimator instance
Estimator instance.
- set_params(**params)
Set the parameters of this estimator.
The method works on simple estimators as well as on nested objects (such as
Pipeline
). The latter have parameters of the form<component>__<parameter>
so that it’s possible to update each component of a nested object.- Parameters:
- **paramsdict
Estimator parameters.
- Returns:
- selfestimator instance
Estimator instance.
- transform(X)
Reduce X to the selected features.
- Parameters:
- Xarray of shape [n_samples, n_features]
The input samples.
- Returns:
- X_rarray of shape [n_samples, n_selected_features]
The input samples with only the selected features.