.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "auto_examples/ensemble/plot_gradient_boosting_oob.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code or to run this example in your browser via JupyterLite or Binder .. rst-class:: sphx-glr-example-title .. _sphx_glr_auto_examples_ensemble_plot_gradient_boosting_oob.py: ====================================== Gradient Boosting Out-of-Bag estimates ====================================== Out-of-bag (OOB) estimates can be a useful heuristic to estimate the "optimal" number of boosting iterations. OOB estimates are almost identical to cross-validation estimates but they can be computed on-the-fly without the need for repeated model fitting. OOB estimates are only available for Stochastic Gradient Boosting (i.e. ``subsample < 1.0``), the estimates are derived from the improvement in loss based on the examples not included in the bootstrap sample (the so-called out-of-bag examples). The OOB estimator is a pessimistic estimator of the true test loss, but remains a fairly good approximation for a small number of trees. The figure shows the cumulative sum of the negative OOB improvements as a function of the boosting iteration. As you can see, it tracks the test loss for the first hundred iterations but then diverges in a pessimistic way. The figure also shows the performance of 3-fold cross validation which usually gives a better estimate of the test loss but is computationally more demanding. .. GENERATED FROM PYTHON SOURCE LINES 24-145 .. image-sg:: /auto_examples/ensemble/images/sphx_glr_plot_gradient_boosting_oob_001.png :alt: plot gradient boosting oob :srcset: /auto_examples/ensemble/images/sphx_glr_plot_gradient_boosting_oob_001.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none Accuracy: 0.6860 | .. code-block:: Python # Author: Peter Prettenhofer # # License: BSD 3 clause import matplotlib.pyplot as plt import numpy as np from scipy.special import expit from sklearn import ensemble from sklearn.metrics import log_loss from sklearn.model_selection import KFold, train_test_split # Generate data (adapted from G. Ridgeway's gbm example) n_samples = 1000 random_state = np.random.RandomState(13) x1 = random_state.uniform(size=n_samples) x2 = random_state.uniform(size=n_samples) x3 = random_state.randint(0, 4, size=n_samples) p = expit(np.sin(3 * x1) - 4 * x2 + x3) y = random_state.binomial(1, p, size=n_samples) X = np.c_[x1, x2, x3] X = X.astype(np.float32) X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.5, random_state=9) # Fit classifier with out-of-bag estimates params = { "n_estimators": 1200, "max_depth": 3, "subsample": 0.5, "learning_rate": 0.01, "min_samples_leaf": 1, "random_state": 3, } clf = ensemble.GradientBoostingClassifier(**params) clf.fit(X_train, y_train) acc = clf.score(X_test, y_test) print("Accuracy: {:.4f}".format(acc)) n_estimators = params["n_estimators"] x = np.arange(n_estimators) + 1 def heldout_score(clf, X_test, y_test): """compute deviance scores on ``X_test`` and ``y_test``.""" score = np.zeros((n_estimators,), dtype=np.float64) for i, y_proba in enumerate(clf.staged_predict_proba(X_test)): score[i] = 2 * log_loss(y_test, y_proba[:, 1]) return score def cv_estimate(n_splits=None): cv = KFold(n_splits=n_splits) cv_clf = ensemble.GradientBoostingClassifier(**params) val_scores = np.zeros((n_estimators,), dtype=np.float64) for train, test in cv.split(X_train, y_train): cv_clf.fit(X_train[train], y_train[train]) val_scores += heldout_score(cv_clf, X_train[test], y_train[test]) val_scores /= n_splits return val_scores # Estimate best n_estimator using cross-validation cv_score = cv_estimate(3) # Compute best n_estimator for test data test_score = heldout_score(clf, X_test, y_test) # negative cumulative sum of oob improvements cumsum = -np.cumsum(clf.oob_improvement_) # min loss according to OOB oob_best_iter = x[np.argmin(cumsum)] # min loss according to test (normalize such that first loss is 0) test_score -= test_score[0] test_best_iter = x[np.argmin(test_score)] # min loss according to cv (normalize such that first loss is 0) cv_score -= cv_score[0] cv_best_iter = x[np.argmin(cv_score)] # color brew for the three curves oob_color = list(map(lambda x: x / 256.0, (190, 174, 212))) test_color = list(map(lambda x: x / 256.0, (127, 201, 127))) cv_color = list(map(lambda x: x / 256.0, (253, 192, 134))) # line type for the three curves oob_line = "dashed" test_line = "solid" cv_line = "dashdot" # plot curves and vertical lines for best iterations plt.figure(figsize=(8, 4.8)) plt.plot(x, cumsum, label="OOB loss", color=oob_color, linestyle=oob_line) plt.plot(x, test_score, label="Test loss", color=test_color, linestyle=test_line) plt.plot(x, cv_score, label="CV loss", color=cv_color, linestyle=cv_line) plt.axvline(x=oob_best_iter, color=oob_color, linestyle=oob_line) plt.axvline(x=test_best_iter, color=test_color, linestyle=test_line) plt.axvline(x=cv_best_iter, color=cv_color, linestyle=cv_line) # add three vertical lines to xticks xticks = plt.xticks() xticks_pos = np.array( xticks[0].tolist() + [oob_best_iter, cv_best_iter, test_best_iter] ) xticks_label = np.array(list(map(lambda t: int(t), xticks[0])) + ["OOB", "CV", "Test"]) ind = np.argsort(xticks_pos) xticks_pos = xticks_pos[ind] xticks_label = xticks_label[ind] plt.xticks(xticks_pos, xticks_label, rotation=90) plt.legend(loc="upper center") plt.ylabel("normalized loss") plt.xlabel("number of iterations") plt.show() .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 8.934 seconds) .. _sphx_glr_download_auto_examples_ensemble_plot_gradient_boosting_oob.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: binder-badge .. image:: images/binder_badge_logo.svg :target: https://mybinder.org/v2/gh/scikit-learn/scikit-learn/main?urlpath=lab/tree/notebooks/auto_examples/ensemble/plot_gradient_boosting_oob.ipynb :alt: Launch binder :width: 150 px .. container:: lite-badge .. image:: images/jupyterlite_badge_logo.svg :target: ../../lite/lab/?path=auto_examples/ensemble/plot_gradient_boosting_oob.ipynb :alt: Launch JupyterLite :width: 150 px .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_gradient_boosting_oob.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_gradient_boosting_oob.py ` .. include:: plot_gradient_boosting_oob.recommendations .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_