Version 0.20 (under development)¶
This release packs in a mountain of bug fixes, features and enhancements for the Scikit-learn library, and improvements to the documentation and examples. Thanks to our many contributors!
Highlights¶
We have tried to improve our support for common data-science use-cases including missing values, categorical variables, heterogeneous data, and features/targets with unusual distributions.
Missing values in features, represented by NaNs, are now accepted in
column-wise preprocessing such as scalers. Each feature is fitted disregarding
NaNs, and data containing NaNs can be transformed. The new impute
module provides estimators for learning despite missing data.
ColumnTransformer handles the case where different features
or columns of a pandas.DataFrame need different preprocessing.
String or pandas Categorical columns can now be encoded with
OneHotEncoder or
OrdinalEncoder.
TransformedTargetRegressor helps when the regression target
needs to be transformed to be modeled. PowerTransformer
and KBinsDiscretizer join
QuantileTransformer as non-linear transformations.
Beyond this, we have added sample_weight support to several estimators
(including KMeans, BayesianRidge and
KernelDensity) and improved stopping criteria in others
(including MLPRegressor,
GradientBoostingRegressor and
SGDRegressor).
This release is also the first to be accompanied by a Glossary of Common Terms and API Elements developed by Joel Nothman. The glossary is a reference resource to help users and contributors become familiar with the terminology and conventions used in Scikit-learn.
Changed models¶
The following estimators and functions, when fit with the same data and parameters, may produce different models from the previous version. This often occurs due to changes in the modelling logic (bug fixes or enhancements), or in random sampling procedures.
decomposition.IncrementalPCAin Python 2 (bug fix)isotonic.IsotonicRegression(bug fix)linear_model.ARDRegression(bug fix)linear_model.OrthogonalMatchingPursuit(bug fix)metrics.roc_auc_score(bug fix)metrics.roc_curve(bug fix)neural_network.MLPRegressor(bug fix)neural_network.MLPClassifier(bug fix)neural_network.BaseMultilayerPerceptron(bug fix)linear_model.SGDClassifier(bug fix)linear_model.SGDRegressor(bug fix)linear_model.PassiveAggressiveClassifier(bug fix)linear_model.PassiveAggressiveRegressor(bug fix)linear_model.Perceptron(bug fix)ensemble.gradient_boosting.GradientBoostingClassifier(bug fix affecting feature importances)- The v0.19.0 release notes failed to mention a backwards incompatibility with
model_selection.StratifiedKFoldwhenshuffle=Truedue to #7823.
Details are listed in the changelog below.
(While we are trying to better inform users by providing this information, we cannot assure that this list is complete.)
Changelog¶
Support for Python 3.3 has been officially dropped.
New features¶
Classifiers and regressors
ensemble.GradientBoostingClassifierandensemble.GradientBoostingRegressornow support early stopping vian_iter_no_change,validation_fractionandtol. #7071 by Raghav RVdummy.DummyRegressornow has areturn_stdoption in itspredictmethod. The returned standard deviations will be zeros.- Added
multioutput.RegressorChainfor multi-target regression. #9257 by Kumar Ashutosh. - Added
naive_bayes.ComplementNB, which implements the Complement Naive Bayes classifier described in Rennie et al. (2003). #8190 by Michael A. Alcorn. ensemble.BaggingRegressorandensemble.BaggingClassifiercan now be fit with missing/non-finite values in X and/or multi-output Y to support wrapping pipelines that perform their own imputation. #9707 by Jimmy Wan.
Preprocessing
- Expanded
preprocessing.OneHotEncoderto allow to encode categorical string features as a numeric array using a one-hot (or dummy) encoding scheme, and addedpreprocessing.OrdinalEncoderto convert to ordinal integers. Those two classes now handle encoding of all feature types (also handles string-valued features) and derives the categories based on the unique values in the features instead of the maximum value in the features. #9151 and #10521 by Vighnesh Birodkar and Joris Van den Bossche. - Added
preprocessing.KBinsDiscretizerfor turning continuous features into categorical or one-hot encoded features. #7668, #9647, #10195, #10192, #11272 and #11467. by Henry Lin, Hanmin Qin and Tom Dupre la Tour. - Added
compose.ColumnTransformer, which allows to apply different transformers to different columns of arrays or pandas DataFrames. #9012 by Andreas Müller and Joris Van den Bossche, and #11315 by Thomas Fan. - Added
preprocessing.PowerTransformer, which implements the Box-Cox power transformation, allowing users to map data from any distribution to a Gaussian distribution. This is useful as a variance-stabilizing transformation in situations where normality and homoscedasticity are desirable. #10210 by Eric Chang and Maniteja Nandana. - Added the
compose.TransformedTargetRegressorwhich transforms the target y before fitting a regression model. The predictions are mapped back to the original space via an inverse transform. #9041 by Andreas Müller and Guillaume Lemaitre. - Added
impute.ChainedImputer, which is a strategy for imputing missing values by modeling each feature with missing values as a function of other features in a round-robin fashion. #8478 by Sergey Feldman. linear_model.SGDClassifier,linear_model.SGDRegressor,linear_model.PassiveAggressiveClassifier,linear_model.PassiveAggressiveRegressorandlinear_model.Perceptronnow exposeearly_stopping,validation_fractionandn_iter_no_changeparameters, to stop optimization monitoring the score on a validation set. A new learning rate"adaptive"strategy divides the learning rate by 5 each timen_iter_no_changeconsecutive epochs fail to improve the model. #9043 by Tom Dupre la Tour.
Model evaluation
- Added the
metrics.davies_bouldin_scoremetric for unsupervised evaluation of clustering models. #10827 by Luis Osa. - Added the
metrics.balanced_accuracy_scoremetric and a corresponding'balanced_accuracy'scorer for binary classification. #8066 by @xyguo and Aman Dalmia.
Decomposition, manifold learning and clustering
cluster.AgglomerativeClusteringnow supports Single Linkage clustering vialinkage='single'. #9372 by Leland McInnes and Steve Astels.cluster.KMeansandcluster.MiniBatchKMeansnow support sample weights via new parametersample_weightinfitfunction. #10933 by Johannes Hansen.dict_learningfunctions and models now support positivity constraints. This applies to the dictionary and sparse code. #6374 by John Kirkham.
Metrics
- Partial AUC is available via
max_fprparameter inmetrics.roc_auc_score. #3273 by Alexander Niederbühl. - Added
output_dictparameter inmetrics.classification_reportto return classification statistics as dictionary. #11160 by Dan Barkhorn.
Misc
- A new configuration parameter,
working_memorywas added to control memory consumption limits in chunked operations, such as the newmetrics.pairwise_distances_chunked. See Limiting Working Memory. #10280 by Joel Nothman and Aman Dalmia. - An environment variable to use the site joblib instead of the vendored
one was added (Environment variables). The main API of joblib is now
exposed in
sklearn.utils.joblib. #11166 by Gael Varoquaux, Joel Nothman and Olivier Grisel.
Enhancements¶
Classifiers and regressors
- In
gaussian_process.GaussianProcessRegressor, methodpredictis faster when usingreturn_std=Truein particular more when called several times in a row. #9234 by andrewww and Minghui Liu. - Add named_estimators_ parameter in
ensemble.VotingClassifierto access fitted estimators. #9157 by Herilalaina Rakotoarison. - Add var_smoothing parameter in
naive_bayes.GaussianNBto give a precise control over variances calculation. #9681 by Dmitry Mottl. - Add n_iter_no_change parameter in
neural_network.BaseMultilayerPerceptron,neural_network.MLPRegressor, andneural_network.MLPClassifierto give control over maximum number of epochs to not meettolimprovement. #9456 by Nicholas Nadeau. - A parameter
check_inversewas added topreprocessing.FunctionTransformerto ensure thatfuncandinverse_funcare the inverse of each other. #9399 by Guillaume Lemaitre. - Add sample_weight parameter to the fit method of
linear_model.BayesianRidgefor weighted linear regression. #10111 by Peter St. John. dummy.DummyClassifieranddummy.DummyRegressornow only require X to be an object with finite length or shape. #9832 by Vrishank Bhardwaj.- Add sample_weight parameter to the fit method of
neighbors.KernelDensityto enables weighting in kernel density estimation. #4394 by Samuel O. Ronsin. neighbors.RadiusNeighborsRegressorandneighbors.RadiusNeighborsClassifierare now parallelized according ton_jobsregardless ofalgorithm. #8003 by Joël Billaud.- Memory usage improvement for
_class_meansand_class_covindiscriminant_analysis. #10898 by Nanxin Chen.` manifold.t_sne.trustworthinessaccepts metrics other than Euclidean. #9775 by William de Vazelhes.Nearest neighborsquery methods are now more memory efficient whenalgorithm='brute'. #11136 by Joel Nothman and Aman Dalmia.
Cluster
cluster.KMeans,cluster.MiniBatchKMeansandcluster.k_meanspassed withalgorithm='full'now enforces row-major ordering, improving runtime. #10471 by Gaurav Dhingra.cluster.DBSCANnow is parallelized according ton_jobsregardless ofalgorithm. #8003 by Joël Billaud.
Datasets
- In
datasets.make_blobs, one can now pass a list to the n_samples parameter to indicate the number of samples to generate per cluster. #8617 by Maskani Filali Mohamed and Konstantinos Katrioplas.
Preprocessing
preprocessing.PolynomialFeaturesnow supports sparse input. #10452 by Aman Dalmia and Joel Nothman.- Enable the call to
get_feature_namesin unfittedfeature_extraction.text.CountVectorizerinitialized with a vocabulary. #10908 by Mohamed Maskani. - The
transformmethod ofsklearn.preprocessing.MultiLabelBinarizernow ignores any unknown classes. A warning is raised stating the unknown classes classes found which are ignored. #10913 by Rodrigo Agundez. - NaN values are ignored and handled in the following preprocessing methods:
preprocessing.MaxAbsScaler,preprocessing.MinMaxScaler,preprocessing.RobustScaler,preprocessing.StandardScaler,preprocessing.PowerTransformer,preprocessing.QuantileTransformerclasses andpreprocessing.maxabs_scale,preprocessing.minmax_scale,preprocessing.robust_scale,preprocessing.scale,preprocessing.power_transform,preprocessing.quantile_transformfunctions respectively addressed in issues #11011, #11005, #11308, #11206, #11306, and #10437. By Lucija Gregov and Guillaume Lemaitre. preprocessing.RobustScalerandpreprocessing.robust_scalecan be fitted using sparse matrices. #11308 by Guillaume Lemaitre.
Model evaluation and meta-estimators
- A scorer based on
metrics.brier_score_lossis also available. #9521 by Hanmin Qin. - The default of
iidparameter ofmodel_selection.GridSearchCVandmodel_selection.RandomizedSearchCVwill change fromTruetoFalsein version 0.22 to correspond to the standard definition of cross-validation, and the parameter will be removed in version 0.24 altogether. This parameter is of greatest practical significance where the sizes of different test sets in cross-validation were very unequal, i.e. in group-based CV strategies. #9085 by Laurent Direr and Andreas Müller. - The
predictmethod ofpipeline.Pipelinenow passes keyword arguments on to the pipeline’s last estimator, enabling the use of parameters such asreturn_stdin a pipeline with caution. #9304 by Breno Freitas. - Add return_estimator parameter in
model_selection.cross_validateto return estimators fitted on each split. #9686 by Aurélien Bellet. - New
refit_time_attribute will be stored inmodel_selection.GridSearchCVandmodel_selection.RandomizedSearchCVifrefitis set toTrue. This will allow measuring the complete time it takes to perform hyperparameter optimization and refitting the best model on the whole dataset. #11310 by Matthias Feurer.
Decomposition and manifold learning
- Speed improvements for both ‘exact’ and ‘barnes_hut’ methods in
manifold.TSNE. #10593 and #10610 by Tom Dupre la Tour. - Support sparse input in
manifold.Isomap.fit. #8554 by Leland McInnes.
Metrics
metrics.roc_auc_scorenow supports binaryy_trueother than{0, 1}or{-1, 1}. #9828 by Hanmin Qin.metrics.label_ranking_average_precision_scorenow supports vectorsample_weight. #10845 by Jose Perez-Parras Toledano.- Add
dense_outputparameter tometrics.pairwise.linear_kernel. When False and both inputs are sparse, will return a sparse matrix. #10999 by Taylor G Smith. metrics.cluster.silhouette_scoreandmetrics.cluster.silhouette_samplesare more memory efficient and run faster. This avoids some reported freezes and MemoryErrors. #11135 by Joel Nothman.
Linear, kernelized and related models
- Deprecate
random_stateparameter insvm.OneClassSVMas the underlying implementation is not random. #9497 by Albert Thomas.
Decomposition, manifold learning and clustering
- Deprecate
precomputedparameter in functionmanifold.t_sne.trustworthiness. Instead, the new parametermetricshould be used with any compatible metric including ‘precomputed’, in which case the input matrixXshould be a matrix of pairwise distances or squared distances. #9775 by William de Vazelhes.
Utils
- Avoid copying the data in
utils.check_arraywhen the input data is a memmap (andcopy=False). #10663 by Arthur Mensch and Loïc Estève.
Miscellaneous
- Add
filenameattribute to datasets that have a CSV file. #9101 by alex-33 and Maskani Filali Mohamed.
Bug fixes¶
Classifiers and regressors
- Fixed a bug in
isotonic.IsotonicRegressionwhich incorrectly combined weights when fitting a model to data involving points with identical X values. #9432 by Dallas Card - Fixed a bug in
neural_network.BaseMultilayerPerceptron,neural_network.MLPRegressor, andneural_network.MLPClassifierwith newn_iter_no_changeparameter now at 10 from previously hardcoded 2. #9456 by Nicholas Nadeau. - Fixed a bug in
neural_network.MLPRegressorwhere fitting quit unexpectedly early due to local minima or fluctuations. #9456 by Nicholas Nadeau - Fixed a bug in
naive_bayes.GaussianNBwhich incorrectly raised error for prior list which summed to 1. #10005 by Gaurav Dhingra. - Fixed a bug in
linear_model.LogisticRegressionwhere when using the parametermulti_class='multinomial', thepredict_probamethod was returning incorrect probabilities in the case of binary outcomes. #9939 by Roger Westover. - Fixed a bug in
linear_model.LogisticRegressionCVwhere thescoremethod always computes accuracy, not the metric given by thescoringparameter. #10998 by Thomas Fan. - Fixed a bug in
linear_model.OrthogonalMatchingPursuitthat was broken when settingnormalize=False. #10071 by Alexandre Gramfort. - Fixed a bug in
linear_model.ARDRegressionwhich caused incorrectly updated estimates for the standard deviation and the coefficients. #10153 by Jörg Döpfert. - Fixed a bug when fitting
ensemble.GradientBoostingClassifierorensemble.GradientBoostingRegressorwithwarm_start=Truewhich previously raised a segmentation fault due to a non-conversion of CSC matrix into CSR format expected bydecision_function. Similarly, Fortran-ordered arrays are converted to C-ordered arrays in the dense case. #9991 by Guillaume Lemaitre. - Fixed a bug in
neighbors.NearestNeighborswhere fitting a NearestNeighbors model fails when a) the distance metric used is a callable and b) the input to the NearestNeighbors model is sparse. #9579 by Thomas Kober. - Fixed a bug in
linear_model.RidgeClassifierCVwhere the parameterstore_cv_valueswas not implemented though it was documented incv_valuesas a way to set up the storage of cross-validation values for different alphas. #10297 by Mabel Villalba-Jiménez. - Fixed a bug in
naive_bayes.MultinomialNBwhich did not accept vector valued pseudocounts (alpha). #10346 by Tobias Madsen - Fixed a bug in
svm.SVCwhere when the argumentkernelis unicode in Python2, thepredict_probamethod was raising an unexpected TypeError given dense inputs. #10412 by Jiongyan Zhang. - Fixed a bug in
tree.BaseDecisionTreewith splitter=”best” where split threshold could become infinite when values in X were near infinite. #10536 by Jonathan Ohayon. - Fixed a bug in
linear_model.ElasticNetwhich caused the input to be overridden when using parametercopy_X=Trueandcheck_input=False. #10581 by Yacine Mazari. - Fixed a bug in
sklearn.linear_model.Lassowhere the coefficient had wrong shape whenfit_intercept=False. #10687 by Martin Hahn. - Fixed a bug in
sklearn.linear_model.LogisticRegressionwhere the multi_class=’multinomial’ with binary output with warm_start = True #10836 by Aishwarya Srinivasan. - Fixed a bug in
linear_model.RidgeCVwhere using integeralphasraised an error. #10393 by Mabel Villalba-Jiménez. - Fixed condition triggering gap computation in
linear_model.Lassoandlinear_model.ElasticNetwhen working with sparse matrices. #10992 by Alexandre Gramfort. - Fixed a bug in
linear_model.SGDClassifier,linear_model.SGDRegressor,linear_model.PassiveAggressiveClassifier,linear_model.PassiveAggressiveRegressorandlinear_model.Perceptron, where the stopping criterion was stopping the algorithm before convergence. A parameter n_iter_no_change was added and set by default to 5. Previous behavior is equivalent to setting the parameter to 1. #9043 by Tom Dupre la Tour. - Fixed a bug where liblinear and libsvm-based estimators would segfault if passed a scipy.sparse matrix with 64-bit indices. They now raise a ValueError. #11327 by Karan Dhingra and Joel Nothman.
- Fixed a bug in
ensemble.gradient_boosting.GradientBoostingRegressorandensemble.gradient_boosting.GradientBoostingClassifierto have feature importances summed and then normalized, rather than normalizing on a per-tree basis. The previous behavior over-weighted the Gini importance of features that appear in later stages. This issue only affected feature importances. #11176 by Gil Forsyth.
Decomposition, manifold learning and clustering
- Fix for uninformative error in
decomposition.IncrementalPCA: now an error is raised if the number of components is larger than the chosen batch size. Then_components=Nonecase was adapted accordingly. #6452. By Wally Gauze. - Fixed a bug where the
partial_fitmethod ofdecomposition.IncrementalPCAused integer division instead of float division on Python 2 versions. #9492 by James Bourbeau. - Fixed a bug where the
fitmethod ofcluster.AffinityPropagationstored cluster centers as 3d array instead of 2d array in case of non-convergence. For the same class, fixed undefined and arbitrary behavior in case of training data where all samples had equal similarity. #9612. By Jonatan Samoocha. - In
decomposition.PCAselecting a n_components parameter greater than the number of samples now raises an error. Similarly, then_components=Nonecase now selects the minimum of n_samples and n_features. #8484. By Wally Gauze. - Fixed a bug in
datasets.fetch_kddcup99, where data were not properly shuffled. #9731 by Nicolas Goix. - Fixed a bug in
decomposition.PCAwhere users will get unexpected error with large datasets whenn_components='mle'on Python 3 versions. #9886 by Hanmin Qin. - Fixed a bug when setting parameters on meta-estimator, involving both a wrapped estimator and its parameter. #9999 by Marcus Voss and Joel Nothman.
k_meansnow gives a warning, if the number of distinct clusters found is smaller thann_clusters. This may occur when the number of distinct points in the data set is actually smaller than the number of cluster one is looking for. #10059 by Christian Braune.- Fixed a bug in
datasets.make_circles, where no odd number of data points could be generated. #10037 by Christian Braune. - Fixed a bug in
cluster.spectral_clusteringwhere the normalization of the spectrum was using a division instead of a multiplication. #8129 by Jan Margeta, Guillaume Lemaitre, and Devansh D.. - Fixed a bug in
mixture.BaseMixturewhere the reported n_iter_ was missing an iteration. It affectedmixture.GaussianMixtureandmixture.BayesianGaussianMixture. #10740 by Erich Schubert and Guillaume Lemaitre. - Fixed a bug in
decomposition.SparseCoderwhen running OMP sparse coding in parallel using readonly memory mapped datastructures. #5956 by Vighnesh Birodkar and Olivier Grisel. - Fixed a bug in
cluster.k_means_elkanwhere the returned iteration was 1 less than the correct value. Also added the missing n_iter_ attribute in the docstring ofcluster.KMeans. #11353 by Jeremie du Boisberranger.
Metrics
- Fixed a bug in
metrics.precision_recall_fscore_supportwhen truncated range(n_labels) is passed as value for labels. #10377 by Gaurav Dhingra. - Fixed a bug due to floating point error in
metrics.roc_auc_scorewith non-integer sample weights. #9786 by Hanmin Qin. - Fixed a bug where
metrics.roc_curvesometimes starts on y-axis instead of (0, 0), which is inconsistent with the document and other implementations. Note that this will not influence the result frommetrics.roc_auc_score#10093 by alexryndin and Hanmin Qin. - Fixed a bug to avoid integer overflow. Casted product to 64 bits integer in
metrics.mutual_info_score. #9772 by Kumar Ashutosh. - Fixed a bug in
metrics.fowlkes_mallows_scoreto avoid integer overflow. Casted return value of contingency_matrix to int64 and computed product of square roots rather than square root of product. #9515 by Alan Liddell and Manh Dao.
Neighbors
- Fixed a bug so
predictinneighbors.RadiusNeighborsRegressorcan handle empty neighbor set when using non uniform weights. Also raises a new warning when no neighbors are found for samples. #9655 by Andreas Bjerre-Nielsen.
Feature Extraction
- Fixed a bug in
feature_extraction.image.extract_patches_2dwhich would throw an exception ifmax_patcheswas greater than or equal to the number of all possible patches rather than simply returning the number of possible patches. #10100 by Varun Agrawal - Fixed a bug in
feature_extraction.text.CountVectorizer,feature_extraction.text.TfidfVectorizer,feature_extraction.text.HashingVectorizerto support 64 bit sparse array indexing necessary to process large datasets with more than 2·10⁹ tokens (words or n-grams). #9147 by Claes-Fredrik Mannby and Roman Yurchak. - Fixed bug in
feature_extraction.text.TFIDFVectorizerwhich was ignoring the parameterdtype. In addition,feature_extraction.text.TFIDFTransformerwill preservedtypefor floating and raise a warning ifdtyperequested is integer. #10441 by Mayur Kulkarni and Guillaume Lemaitre.
Utils
utils.check_arrayyield aFutureWarningindicating that arrays of bytes/strings will be interpreted as decimal numbers beginning in version 0.22. #10229 by Ryan Lee
Preprocessing
- Fixed bugs in
preprocessing.LabelEncoderwhich would sometimes throw errors whentransformorinverse_transformwas called with empty arrays. #10458 by Mayur Kulkarni. - Fix ValueError in
preprocessing.LabelEncoderwhen usinginverse_transformon unseen labels. #9816 by Charlie Newey. - Fix bug in
preprocessing.OneHotEncoderwhich discarded thedtypewhen returning a sparse matrix output. #11042 by Daniel Morales. - Fix
fitandpartial_fitinpreprocessing.StandardScalerin the rare case when with_mean=False and with_std=False which was crashing by callingfitmore than once and giving inconsistent results formean_whether the input was a sparse or a dense matrix.mean_will be set toNonewith both sparse and dense inputs.n_samples_seen_will be also reported for both input types. #11235 by Guillaume Lemaitre.
Feature selection
- Fixed computation of
n_features_to_computefor edge case with tied CV scores infeature_selection.RFECV. #9222 by Nick Hoh <nickypie>.
Model evaluation and meta-estimators
- Add improved error message in
model_selection.cross_val_scorewhen multiple metrics are passed inscoringkeyword. #11006 by Ming Li.
Datasets
- Fixed a bug in
datasets.load_bostonwhich had a wrong data point. #10801 by Takeshi Yoshizawa. - Fixed a bug in
datasets.load_iriswhich had two wrong data points. #11082 by Sadhana Srinivasan and Hanmin Qin.
API changes summary¶
Linear, kernelized and related models
- Deprecate
random_stateparameter insvm.OneClassSVMas the underlying implementation is not random. #9497 by Albert Thomas. - Deprecate
positive=Trueoption inlinear_model.Larsas the underlying implementation is broken. Uselinear_model.Lassoinstead. #9837 by Alexandre Gramfort. n_iter_may vary from previous releases inlinear_model.LogisticRegressionwithsolver='lbfgs'andlinear_model.HuberRegressor. For Scipy <= 1.0.0, the optimizer could perform more than the requested maximum number of iterations. Now both estimators will report at mostmax_iteriterations even if more were performed. #10723 by Joel Nothman.- The default value of
gammaparameter ofsvm.SVC,NuSVC,SVR,NuSVR,OneClassSVMwill change from'auto'to'scale'in version 0.22 to account better for unscaled features. #8361 by Gaurav Dhingra and Ting Neo. - Added convergence warning to
svm.LinearSVCandlinear_model.LogisticRegressionwhenverboseis set to 0. #10881 by Alexandre Sevin.
Preprocessing
- Deprecate
n_valuesandcategorical_featuresparameters andactive_features_,feature_indices_andn_values_attributes ofpreprocessing.OneHotEncoder. Then_valuesparameter can be replaced with the newcategoriesparameter, and the attributes with the newcategories_attribute. Selecting the categorical features with thecategorical_featuresparameter is now better supported using thecompose.ColumnTransformer. #10521 by Joris Van den Bossche.
Decomposition, manifold learning and clustering
- Deprecate
precomputedparameter in functionmanifold.t_sne.trustworthiness. Instead, the new parametermetricshould be used with any compatible metric including ‘precomputed’, in which case the input matrixXshould be a matrix of pairwise distances or squared distances. #9775 by William de Vazelhes. - Added function
fit_predicttomixture.GaussianMixtureandmixture.GaussianMixture, which is essentially equivalent to callingfitandpredict. #10336 by Shu Haoran and Andrew Peng.
Metrics
- Deprecate
reorderparameter inmetrics.aucas it’s no longer required formetrics.roc_auc_score. Moreover usingreorder=Truecan hide bugs due to floating point error in the input. #9851 by Hanmin Qin. - The
batch_sizeparameter tometrics.pairwise_distances_argmin_minandmetrics.pairwise_distances_argminis deprecated to be removed in v0.22. It no longer has any effect, as batch size is determined by globalworking_memoryconfig. See Limiting Working Memory. #10280 by Joel Nothman and Aman Dalmia.
Cluster
- Deprecate
pooling_funcunused parameter incluster.AgglomerativeClustering. #9875 by Kumar Ashutosh.
Imputer
- Deprecate
preprocessing.Imputerand move the corresponding module toimpute.SimpleImputer. #9726 by Kumar Ashutosh. - The
axisparameter that was inpreprocessing.Imputeris no longer present inimpute.SimpleImputer. The behavior is equivalent toaxis=0(impute along columns). Row-wise imputation can be performed with FunctionTransformer (e.g.,FunctionTransformer(lambda X: SimpleImputer().fit_transform(X.T).T)). #10829 by Guillaume Lemaitre and Gilberto Olimpio. - The
impute.SimpleImputerhas a new strategy,'constant', to complete missing values with a fixed one, given by thefill_valueparameter. This strategy supports numeric and non-numeric data, and so does the'most_frequent'strategy now. #11211 by Jeremie du Boisberranger. - The NaN marker for the missing values has been changed between the
preprocessing.Imputerand theimpute.SimpleImputer.missing_values='NaN'should now bemissing_values=np.nan. #11211 by Jeremie du Boisberranger.
Outlier Detection models
- More consistent outlier detection API:
Add a
score_samplesmethod insvm.OneClassSVM,ensemble.IsolationForest,neighbors.LocalOutlierFactor,covariance.EllipticEnvelope. It allows to access raw score functions from original papers. A newoffset_parameter allows to linkscore_samplesanddecision_functionmethods. Thecontaminationparameter ofensemble.IsolationForestandneighbors.LocalOutlierFactordecision_functionmethods is used to define thisoffset_such that outliers (resp. inliers) have negative (resp. positive)decision_functionvalues. By default,contaminationis kept unchanged to 0.1 for a deprecation period. In 0.22, it will be set to “auto”, thus using method-specific score offsets. Incovariance.EllipticEnvelopedecision_functionmethod, theraw_valuesparameter is deprecated as the shifted Mahalanobis distance will be always returned in 0.22. #9015 by Nicolas Goix.
Covariance
- The
covariance.graph_lasso,covariance.GraphLassoandcovariance.GraphLassoCVhave been renamed tocovariance.graphical_lasso,covariance.GraphicalLassoandcovariance.GraphicalLassoCVrespectively and will be removed in version 0.22. #9993 by Artiem Krinitsyn
Misc
- Changed warning type from
UserWarningtoexceptions.ConvergenceWarningfor failing convergence inlinear_model.logistic_regression_path,linear_model.RANSACRegressor,linear_model.ridge_regression,gaussian_process.GaussianProcessRegressor,gaussian_process.GaussianProcessClassifier,decomposition.fastica,cross_decomposition.PLSCanonical,cluster.AffinityPropagation, andcluster.Birch. ##10306 by Jonathan Siebert. - Changed ValueError exception raised in
model_selection.ParameterSamplerto a UserWarning for case where the class is instantiated with a greater value ofn_iterthan the total space of parameters in the parameter grid.n_iternow acts as an upper bound on iterations. ##10982 by Juliet Lawton - Invalid input for
model_selection.ParameterGridnow raises TypeError. #10928 by Solutus Immensus utils.check_arrayandutils.check_X_ynow haveaccept_large_sparseto control whether scipy.sparse matrices with 64-bit indices should be rejected. #11327 by Karan Dhingra and Joel Nothman.
Preprocessing
- In
preprocessing.FunctionTransformer, the default ofvalidatewill be fromTruetoFalsein 0.22. #10655 by Guillaume Lemaitre.
Changes to estimator checks¶
These changes mostly affect library developers.
- Allow tests in
utils.estimator_checks.check_estimatorto test functions that accept pairwise data. #9701 by Kyle Johnson - Allow
check_estimatorto check that there is no private settings apart from parameters during estimator initialization. #9378 by Herilalaina Rakotoarison - Add
check_methods_subset_invariancetocheck_estimator, which checks that estimator methods are invariant if applied to a data subset. #10420 by Jonathan Ohayon - Add tests in
utils.estimator_checks.check_estimatorto check that an estimator can handle read-only memmap input data. #10663 by Arthur Mensch and Loïc Estève. check_sample_weights_pandas_seriesnow uses 8 rather than 6 samples to accommodate for the default number of clusters incluster.KMeans. #10933 by Johannes Hansen.