scikit-learn RandomForestClassifier probabilistic prediction vs majority vote

Question

In the documentation of scikit-learn in section 1.9.2.1 (excerpt is posted below), why does the implementation of random forest differ from the original paper by Breiman? As far as I'm aware, Breiman opted for a majority vote (mode) for classification and an average for regression (paper written by Liaw and Wiener, the maintainers of the original R code with citation below) when aggregating the ensembles of classifiers.

Why does scikit-learn use probabilistic prediction instead of a majority vote?
Is there any advantage in using probabilistic prediction?

The section in question:

In contrast to the original publication [B2001], the scikit-learn implementation combines classifiers by averaging their probabilistic prediction, instead of letting each classifier vote for a single class.

Source: Liaw, A., & Wiener, M. (2002). Classification and Regression by randomForest. R news, 2(3), 18-22.

AN6U5 AN6U5 · Accepted Answer · 2015-04-30T01:19:44

This question has now been answered on Cross Validated. Included here for reference:

Such questions are always best answered by looking at the code, if you're fluent in Python.

RandomForestClassifier.predict, at least in the current version 0.16.1, predicts the class with highest probability estimate, as given by predict_proba. (this line)

The documentation for predict_proba says:

The predicted class probabilities of an input sample is computed as the mean predicted class probabilities of the trees in the forest. The class probability of a single tree is the fraction of samples of the same class in a leaf.

The difference from the original method is probably just so that predict gives predictions consistent with predict_proba. The result is sometimes called "soft voting", rather than the "hard" majority vote used in the original Breiman paper. I couldn't in quick searching find an appropriate comparison of the performance of the two methods, but they both seem fairly reasonable in this situation.

The predict documentation is at best quite misleading; I've submitted a pull request to fix it.

If you want to do majority vote prediction instead, here's a function to do it. Call it like predict_majvote(clf, X) rather than clf.predict(X). (Based on predict_proba; only lightly tested, but I think it should work.)
from scipy.stats import mode
from sklearn.ensemble.forest import _partition_estimators, _parallel_helper
from sklearn.tree._tree import DTYPE
from sklearn.externals.joblib import Parallel, delayed
from sklearn.utils import check_array
from sklearn.utils.validation import check_is_fitted

def predict_majvote(forest, X):
    """Predict class for X.

    Uses majority voting, rather than the soft voting scheme
    used by RandomForestClassifier.predict.

    Parameters
    ----------
    X : array-like or sparse matrix of shape = [n_samples, n_features]
        The input samples. Internally, it will be converted to
        ``dtype=np.float32`` and if a sparse matrix is provided
        to a sparse ``csr_matrix``.
    Returns
    -------
    y : array of shape = [n_samples] or [n_samples, n_outputs]
        The predicted classes.
    """
    check_is_fitted(forest, 'n_outputs_')

    # Check data
    X = check_array(X, dtype=DTYPE, accept_sparse="csr")

    # Assign chunk of trees to jobs
    n_jobs, n_trees, starts = _partition_estimators(forest.n_estimators,
                                                    forest.n_jobs)

    # Parallel loop
    all_preds = Parallel(n_jobs=n_jobs, verbose=forest.verbose,
                         backend="threading")(
        delayed(_parallel_helper)(e, 'predict', X, check_input=False)
        for e in forest.estimators_)

    # Reduce
    modes, counts = mode(all_preds, axis=0)

    if forest.n_outputs_ == 1:
        return forest.classes_.take(modes[0], axis=0)
    else:
        n_samples = all_preds[0].shape[0]
        preds = np.zeros((n_samples, forest.n_outputs_),
                         dtype=forest.classes_.dtype)
        for k in range(forest.n_outputs_):
            preds[:, k] = forest.classes_[k].take(modes[:, k], axis=0)
        return preds
On the dumb synthetic case I tried, predictions agreed with the predict method every time.

scikit-learn RandomForestClassifier probabilistic prediction vs majority vote

2 Answers