[MRG] ROSE

README.rst

@@ -155,6 +155,7 @@ Below is a list of the methods currently implemented in this module.
     5. SVM SMOTE - Support Vectors SMOTE [10]_
     6. ADASYN - Adaptive synthetic sampling approach for imbalanced learning [15]_
     7. KMeans-SMOTE [17]_
+    8. ROSE - Random OverSampling Examples [19]_
 
 * Over-sampling followed by under-sampling
     1. SMOTE + Tomek links [12]_
@@ -210,4 +211,6 @@ References:
 
 .. [17] : Felix Last, Georgios Douzas, Fernando Bacao, "Oversampling for Imbalanced Learning Based on K-Means and SMOTE"
 
-.. [18] : Seiffert, C., Khoshgoftaar, T. M., Van Hulse, J., & Napolitano, A. "RUSBoost: A hybrid approach to alleviating class imbalance." IEEE Transactions on Systems, Man, and Cybernetics-Part A: Systems and Humans 40.1 (2010): 185-197.
+.. [18] : Seiffert, C., Khoshgoftaar, T. M., Van Hulse, J., & Napolitano, A. "RUSBoost: A hybrid approach to alleviating class imbalance." IEEE Transactions on Systems, Man, and Cybernetics-Part A: Systems and Humans 40.1 (2010): 185-197.
+
+.. [19] : Menardi, G., Torelli, N.: "Training and assessing classification rules with unbalanced data", Data Mining and Knowledge Discovery,  28, (2014): 92–122

doc/api.rst

@@ -76,6 +76,7 @@ Prototype selection
    over_sampling.SMOTE
    over_sampling.SMOTENC
    over_sampling.SVMSMOTE
+   over_sampling.ROSE
 
 
 .. _combine_ref:

doc/bibtex/refs.bib

@@ -193,3 +193,18 @@ @article{smith2014instance
   year={2014},
   publisher={Springer}
 }
+
+@article{torelli2014rose,
+  author = {Menardi, Giovanna and Torelli, Nicola},
+  title={Training and assessing classification rules with imbalanced data},
+  author={Menardi G and Torelli N},
+  journal={Data Mining and Knowledge Discovery},
+  volume={28},
+  pages={92-122},
+  year={2014},
+  publisher={Springer},
+  issue = {1},
+  issn = {1573-756X},
+  url = {https://doi.org/10.1007/s10618-012-0295-5},
+  doi = {10.1007/s10618-012-0295-5}
+}

doc/over_sampling.rst

@@ -198,6 +198,23 @@ Therefore, it can be seen that the samples generated in the first and last
 columns are belonging to the same categories originally presented without any
 other extra interpolation.
 
+.. _rose:
+
+ROSE (Random Over-Sampling Examples)
+------------------------------------
+
+ROSE uses smoothed bootstrapping to draw artificial samples from the 
+feature space neighborhood around selected classes, using a multivariate
+Gaussian kernel around randomly selected samples. First, random samples are 
+selected from original classes. Then the smoothing kernel distribution
+is computed around the samples: :math:`\hat f(x|y=Y_i) = \sum_i^{n_j} 
+p_i Pr(x|x_i)=\sum_i^{n_j} \frac{1}{n_j} Pr(x|x_i)=\sum_i^{n_j} 
+\frac{1}{n_j} K_{H_j}(x|x_i)`.
+
+Then new samples are drawn from the computed distribution.
+
+
+
 Mathematical formulation
 ========================
 

doc/whats_new/v0.7.rst

@@ -63,6 +63,9 @@ Enhancements
 - Lazy import `keras` module when importing `imblearn.keras`
   :pr:`719` by :user:`Guillaume Lemaitre <glemaitre>`.
 
+- Added Random Over-Sampling Examples (ROSE) class.
+  :pr:`754` by :user:`Andrea Lorenzon <andrealorenzon>`.
+
 Deprecation
 ...........
 

imblearn/over_sampling/__init__.py

@@ -10,6 +10,7 @@
 from ._smote import KMeansSMOTE
 from ._smote import SVMSMOTE
 from ._smote import SMOTENC
+from ._rose import ROSE
 
 __all__ = [
     "ADASYN",
@@ -19,4 +20,5 @@
     "BorderlineSMOTE",
     "SVMSMOTE",
     "SMOTENC",
+    "ROSE"
 ]

imblearn/over_sampling/_rose.py

@@ -0,0 +1,202 @@
+"""Class to perform over-sampling using ROSE."""
+
+import numpy as np
+from scipy import sparse
+from sklearn.utils import check_random_state
+from .base import BaseOverSampler
+from ..utils._validation import _deprecate_positional_args
+
+
+class ROSE(BaseOverSampler):
+    """Random Over-Sampling Examples (ROSE).
+
+    This object is the implementation of ROSE algorithm.
+    It generates new samples by a smoothed bootstrap approach,
+    taking a random subsample of original data and adding a
+    multivariate kernel density estimate :math:`f(x|Y_i)` around
+    them with a smoothing matrix :math:`H_j`, and finally sampling
+    from this distribution. A shrinking matrix can be provided, to
+    set the bandwidth of the gaussian kernel.
+
+    Read more in the :ref:`User Guide <rose>`.
+
+    Parameters
+    ----------
+    sampling_strategy : float, str, dict or callable, default='auto'
+        Sampling information to resample the data set.
+
+        - When ``float``, it corresponds to the desired ratio of the number of
+          samples in the minority class over the number of samples in the
+          majority class after resampling. Therefore, the ratio is expressed as
+          :math:`\\alpha_{os} = N_{rm} / N_{M}` where :math:`N_{rm}` is the
+          number of samples in the minority class after resampling and
+          :math:`N_{M}` is the number of samples in the majority class.
+
+            .. warning::
+               ``float`` is only available for **binary** classification. An
+               error is raised for multi-class classification.
+
+        - When ``str``, specify the class targeted by the resampling. The
+          number of samples in the different classes will be equalized.
+          Possible choices are:
+
+            ``'minority'``: resample only the minority class;
+
+            ``'not minority'``: resample all classes but the minority class;
+
+            ``'not majority'``: resample all classes but the majority class;
+
+            ``'all'``: resample all classes;
+
+            ``'auto'``: equivalent to ``'not majority'``.
+
+        - When ``dict``, the keys correspond to the targeted classes. The
+          values correspond to the desired number of samples for each targeted
+          class.
+
+        - When callable, function taking ``y`` and returns a ``dict``. The keys
+          correspond to the targeted classes. The values correspond to the
+          desired number of samples for each class.
+
+    shrink_factors : dict, default= 1 for every class
+        Dict of {classes: shrinkfactors} items, applied to
+        the gaussian kernels. It can be used to compress/dilate the kernel.
+
+    random_state : int, RandomState instance, default=None
+        Control the randomization of the algorithm.
+
+        - If int, ``random_state`` is the seed used by the random number
+          generator;
+        - If ``RandomState`` instance, random_state is the random number
+          generator;
+        - If ``None``, the random number generator is the ``RandomState``
+          instance used by ``np.random``.
+
+    n_jobs : int, default=None
+        Number of CPU cores used during the cross-validation loop.
+        ``None`` means 1 unless in a :obj:`joblib.parallel_backend` context.
+        ``-1`` means using all processors. See
+        `Glossary <https://scikit-learn.org/stable/glossary.html#term-n-jobs>`_
+        for more details.
+
+    See Also
+    --------
+    SMOTE : Over-sample using SMOTE.
+
+    Notes
+    -----
+
+    References
+    ----------
+    .. [1] N. Lunardon, G. Menardi, N.Torelli, "ROSE: A Package for Binary
+       Imbalanced Learning," R Journal, 6(1), 2014.
+
+    .. [2] G Menardi, N. Torelli, "Training and assessing classification
+       rules with imbalanced data," Data Mining and Knowledge
+       Discovery, 28(1), pp.92-122, 2014.
+
+    Examples
+    --------
+
+    >>> from imblearn.over_sampling import ROSE
+    >>> from sklearn.datasets import make_classification
+    >>> from collections import Counter
+    >>> r = ROSE(shrink_factors={0:1, 1:0.5, 2:0.7})
+    >>> X, y = make_classification(n_classes=3, class_sep=2,
+    ... weights=[0.1, 0.7, 0.2], n_informative=3, n_redundant=1, flip_y=0,
+    ... n_features=20, n_clusters_per_class=1, n_samples=2000, random_state=10)
+    >>> print('Original dataset shape %s' % Counter(y))
+    Original dataset shape Counter({1: 1400, 2: 400, 0: 200})
+    >>> X_res, y_res = r.fit_resample(X, y)
+    >>> print('Resampled dataset shape %s' % Counter(y_res))
+    Resampled dataset shape Counter({2: 1400, 1: 1400, 0: 1400})
+    """
+
+    @_deprecate_positional_args
+    def __init__(self, *, sampling_strategy="auto", shrink_factors=None,
+                 random_state=None, n_jobs=None):
+        super().__init__(sampling_strategy=sampling_strategy)
+        self.random_state = random_state
+        self.shrink_factors = shrink_factors
+        self.n_jobs = n_jobs
+
+    def _make_samples(self,
+                      X,
+                      class_indices,
+                      n_class_samples,
+                      h_shrink):
+        """ A support function that returns artificial samples constructed
+        from a random subsample of the data, by adding a multiviariate
+        gaussian kernel and sampling from this distribution. An optional
+        shrink factor can be included, to compress/dilate the kernel.
+
+        Parameters
+        ----------
+        X : {array-like, sparse matrix}, shape (n_samples, n_features)
+            Observations from which the samples will be created.
+
+        class_indices : ndarray, shape (n_class_samples,)
+            The target class indices
+
+        n_class_samples : int
+            The total number of samples per class to generate
+
+        h_shrink : int
+            the shrink factor
+
+        Returns
+        -------
+        X_new : {ndarray, sparse matrix}, shape (n_samples, n_features)
+            Synthetically generated samples.
+
+        y_new : ndarray, shape (n_samples,)
+            Target values for synthetic samples.
+
+        """
+
+        number_of_features = X.shape[1]
+        random_state = check_random_state(self.random_state)
+        samples_indices = random_state.choice(
+            class_indices, size=n_class_samples, replace=True)
+        minimize_amise = (4 / ((number_of_features + 2) * len(
+            class_indices))) ** (1 / (number_of_features + 4))
+        if sparse.issparse(X):
+            variances = np.diagflat(
+                np.std(X[class_indices, :].toarray(), axis=0, ddof=1))
+        else:
+            variances = np.diagflat(
+                np.std(X[class_indices, :], axis=0, ddof=1))
+        h_opt = h_shrink * minimize_amise * variances
+        randoms = random_state.standard_normal(size=(n_class_samples,
+                                                     number_of_features))
+        Xrose = np.matmul(randoms, h_opt) + X[samples_indices, :]
+        if sparse.issparse(X):
+            return sparse.csr_matrix(Xrose)
+        return Xrose
+
+    def _fit_resample(self, X, y):
+
+        X_resampled = X.copy()
+        y_resampled = y.copy()
+
+        if self.shrink_factors is None:
+            self.shrink_factors = {
+                key: 1 for key in self.sampling_strategy_.keys()}
+
+        for class_sample, n_samples in self.sampling_strategy_.items():
+            class_indices = np.flatnonzero(y == class_sample)
+            n_class_samples = n_samples
+            X_new = self._make_samples(X,
+                                       class_indices,
+                                       n_samples,
+                                       self.shrink_factors[class_sample])
+            y_new = np.array([class_sample] * n_class_samples)
+
+            if sparse.issparse(X_new):
+                X_resampled = sparse.vstack([X_resampled, X_new])
+            else:
+                X_resampled = np.concatenate((X_resampled, X_new))
+
+            y_resampled = np.hstack((y_resampled, y_new))
+
+        return X_resampled.astype(X.dtype), y_resampled.astype(y.dtype)