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Persisting a fitted estimator for production inference (joblib, skops.io, or ONNX export)
Do not use this skill when
The task is deep learning — neural nets on images/text/audio → use pytorch
The task is transformer or LLM fine-tuning → use the transformers cascade, not sklearn's MLPClassifier
The workload needs GPU compute for tensor math → use cuda-python
You need distributed training across nodes — sklearn is single-machine; use PyTorch DDP or Ray
More from this repository
You need gradient boosting at very large scale — XGBoost / LightGBM / CatBoost have a sklearn-compatible API but live outside this skill
The user is loading or wrangling tabular data — that is upstream (use the dataframe library directly); this skill begins once you have an X, y ready
Purpose
scikit-learn is the default first reach for any tabular machine learning task in Python — supervised (classification/regression) or unsupervised (clustering, decomposition). Before going to deep learning, you should almost always try a sklearn baseline: a Pipeline wrapping a ColumnTransformer for preprocessing and a HistGradientBoostingClassifier/Regressor as the model, evaluated with cross-validation. For most rows-and-columns problems this baseline is within 1–3% of the state of the art and is one to two orders of magnitude cheaper to train and serve.
The library is held together by one idea — the estimator API: every model, transformer, and meta-estimator shares the same fit(X, y) / predict(X) / transform(X) / score(X, y) surface, so they compose into Pipeline and ColumnTransformer objects that prevent the most common ML bug (train/test leakage). 1.8 adds free-threaded CPython 3.14 wheels, broad Array API support, a 10–100× speedup for DecisionTreeRegressor(criterion="absolute_error"), gap-safe screening for Lasso/ElasticNet on regularization paths, temperature scaling for CalibratedClassifierCV, and continues to mature set_output(transform="pandas"|"polars") plus metadata routing (set_fit_request, set_score_request).
Capabilities
Estimator API and custom estimators
Every sklearn object implements a small fixed surface: fit, predict, transform, fit_transform, score, get_params, set_params. Custom estimators subclass BaseEstimator plus a mixin (ClassifierMixin, RegressorMixin, TransformerMixin, ClusterMixin) and pass check_estimator for the contract test. set_output(transform="pandas"|"polars") switches transformer output containers without rewriting the pipeline. Metadata routing (set_fit_request, set_score_request) lets sample_weight, groups, and arbitrary keys flow correctly through meta-estimators when sklearn.set_config(enable_metadata_routing=True) is on. See references/estimator-api.md.
Pipelines and ColumnTransformer
A Pipeline([("prep", ...), ("model", ...)]) makes preprocessing part of the estimator, so fit only sees train data and predict reuses the same fitted transforms. ColumnTransformer applies different transformers to different column subsets in parallel (numeric → scaler, categorical → encoder) and combines the results. make_pipeline / make_column_transformer skip naming; remainder="passthrough" keeps unselected columns; verbose_feature_names_out=False keeps original feature names when there's no collision. Caching via Pipeline(memory=...) skips re-fitting expensive transformers during hyperparameter search. See references/pipelines.md.
Data preparation and preprocessing
Numeric: StandardScaler, MinMaxScaler, RobustScaler, MaxAbsScaler (1.8 adds clip=True for out-of-range), PowerTransformer, QuantileTransformer, KBinsDiscretizer. Categorical: OneHotEncoder (with handle_unknown="ignore", min_frequency, max_categories), OrdinalEncoder, TargetEncoder (cross-fitted, leak-safe). Missing values: SimpleImputer, IterativeImputer, KNNImputer. Splitting: train_test_split(..., stratify=y) for classification — never split without stratify on imbalanced labels. See references/data-prep.md.
Model selection — splitters, CV, hyperparameter search
Splitters: KFold, StratifiedKFold (default for classification), GroupKFold and StratifiedGroupKFold (no entity leakage across folds), TimeSeriesSplit (forward-only chronological). Scoring loops: cross_val_score, cross_validate (multi-metric, returns timings), cross_val_predict (only for stacking, never for performance reporting). Search: GridSearchCV (exhaustive), RandomizedSearchCV (budget-bounded), HalvingGridSearchCV / HalvingRandomSearchCV (successive halving, 5–10× faster on the same budget). Diagnostics: learning_curve, validation_curve. See references/model-selection.md.
Classification, regression, clustering
Tabular baseline: HistGradientBoostingClassifier / HistGradientBoostingRegressor — native missing-value handling, categorical support via categorical_features=, built-in early_stopping. Linear: LogisticRegression, Ridge, Lasso, ElasticNet (gap-safe screening in 1.8). Tree ensembles: RandomForestClassifier/Regressor, ExtraTreesClassifier/Regressor. Margin: SVC, SVR (scale features first). Neighbors: KNeighborsClassifier/Regressor. Probabilistic: CalibratedClassifierCV(method="temperature") for production probability calibration. Clustering: KMeans (use n_init="auto"), DBSCAN, HDBSCAN, AgglomerativeClustering, GaussianMixture. See references/classification.md, references/regression.md, and references/clustering.md.
Metrics, feature selection, and inspection
Use make_scorer to convert any metric into a scoring object for CV. Classification: accuracy_score (only on balanced), balanced_accuracy_score, roc_auc_score(average="macro"|"weighted"), log_loss, f1_score(average=...), classification_report, confusion_matrix. Regression: mean_squared_error, root_mean_squared_error, mean_absolute_error, mean_absolute_percentage_error, r2_score. Feature selection: SelectKBest, RFECV, SelectFromModel, mutual_info_classif/regression. Inspection: prefer permutation_importance over .feature_importances_ (the latter is biased toward high-cardinality features). See references/metrics.md and references/feature-selection.md.
Model persistence
Choose by trust boundary: ONNX if the consumer is non-Python or you want long-term forward compatibility; skops.io if you control the consumer but the model file may travel across an untrusted boundary (no arbitrary code execution on load); joblib (or pickle) when both producer and consumer are trusted Python with pinned versions. Always pin scikit-learn version + Python version + NumPy version in the deployment manifest — fitted estimators are not forward-compatible across majors. See references/model-persistence.md.
Behavioral Traits
Wraps every preprocessing step inside Pipeline / ColumnTransformer — never fit_transforms before splitting
Uses train_test_split(..., stratify=y, random_state=...) for every classification problem
Sets random_state= on every estimator, splitter, and search that supports it — reproducibility is non-negotiable
Defaults to HistGradientBoostingClassifier / HistGradientBoostingRegressor as the strong tabular baseline before reaching for anything fancier
Defaults to StratifiedKFold(n_splits=5, shuffle=True, random_state=...) for classification CV; KFold for regression; GroupKFold whenever rows share a meaningful group key
Uses permutation_importance for feature importance (model-agnostic, unbiased), not .feature_importances_
Reports multiple metrics from cross_validate(..., scoring=[...]) rather than a single number
Calls RandomizedSearchCV or HalvingRandomSearchCV before GridSearchCV — the search space is almost never small enough for exhaustive
Uses Pipeline(memory=...) when CV-tuning a model with an expensive transformer (e.g., IterativeImputer)
NEVER fit a transformer on the full dataset before train_test_split — that's textbook target leakage; the transformer goes inside the Pipeline
NEVER mix train + test data inside cross-validation — every fold's preprocessing must be fit only on that fold's training rows (Pipeline enforces this; manual loops typically do not)
NEVER report accuracy_score on imbalanced classification — use balanced_accuracy_score, roc_auc_score, average_precision_score, or per-class f1_score instead
NEVER call .predict / .transform before .fit — sklearn raises NotFittedError; catch this in tests, not in production
NEVER pickle or joblib.dump a model without recording sklearn.__version__, numpy.__version__, and Python version — fitted estimators are not version-portable
NEVER load an .skops / pickle / joblib file from an untrusted source without inspection — pickle-based formats allow arbitrary code execution; skops.io requires explicit trusted= whitelisting
NEVER use cross_val_predict results to report model performance — its design is for stacking; use cross_validate for performance estimates
ALWAYS stratify the train/test split for classification; ALWAYS stratify the CV splitter for classification; ALWAYS set random_state for any reproducible result
Related Skills
Language and data
python — Python 3.14 foundation (type hints, packaging, asyncio); sklearn runs on top of this
pandas — primary dataframe library for feature engineering before X, y = df[features], df[target]
