ENH: Remove **kwargs from some samplers (#190)

Author: glemaitre

imblearn/over_sampling/smote.py

@@ -68,6 +68,10 @@ class SMOTE(BaseBinarySampler):
  The type of SMOTE algorithm to use one of the following options:
  'regular', 'borderline1', 'borderline2', 'svm'.
 
+ svm_estimator : object, optional (default=SVC())
+ If `kind='svm'`, a parametrized `sklearn.svm.SVC` classifier can
+ be passed.
+
  n_jobs : int, optional (default=1)
  The number of threads to open if possible.
 
@@ -128,16 +132,16 @@ class SMOTE(BaseBinarySampler):
 
  def __init__(self, ratio='auto', random_state=None, k=None, k_neighbors=5,
  m=None, m_neighbors=10, out_step=0.5, kind='regular',
- n_jobs=1, **kwargs):
+ svm_estimator=None, n_jobs=1):
  super(SMOTE, self).__init__(ratio=ratio, random_state=random_state)
  self.kind = kind
  self.k = k
  self.k_neighbors = k_neighbors
  self.m = m
  self.m_neighbors = m_neighbors
  self.out_step = out_step
+ self.svm_estimator = svm_estimator
  self.n_jobs = n_jobs
- self.kwargs = kwargs
 
  def _in_danger_noise(self, samples, y, kind='danger'):
  """Estimate if a set of sample are in danger or noise.
@@ -316,8 +320,13 @@ def _validate_estimator(self):
  # in danger (near the boundary). The level of extrapolation is
  # controled by the out_step.
  if self.kind == 'svm':
- # Store SVM object with any parameters
- self.svm = SVC(random_state=self.random_state, **self.kwargs)
+ if self.svm_estimator is None:
+ # Store SVM object with any parameters
+ self.svm_estimator_ = SVC(random_state=self.random_state)
+ elif isinstance(self.svm_estimator, SVC):
+ self.svm_estimator_ = self.svm_estimator
+ else:
+ raise ValueError('`svm_estimator` has to be an SVC object')
 
  def fit(self, X, y):
  """Find the classes statistics before to perform sampling.
@@ -503,11 +512,11 @@ def _sample(self, X, y):
  # belonging to each class.
 
  # Fit SVM to the full data#
- self.svm.fit(X, y)
+ self.svm_estimator_.fit(X, y)
 
  # Find the support vectors and their corresponding indexes
- support_index = self.svm.support_[y[self.svm.support_] ==
-   self.min_c_]
+ support_index = self.svm_estimator_.support_[
+ y[self.svm_estimator_.support_] == self.min_c_]
  support_vector = X[support_index]
 
  # First, find the nn of all the samples to identify samples

imblearn/over_sampling/tests/test_smote.py

@@ -9,6 +9,7 @@
 from sklearn.datasets import make_classification
 from sklearn.utils.estimator_checks import check_estimator
 from sklearn.neighbors import NearestNeighbors
+from sklearn.svm import SVC
 
 from imblearn.over_sampling import SMOTE
 
@@ -446,3 +447,57 @@ def test_wrong_nn():
  k_neighbors=nn_k)
 
  assert_raises(ValueError, smote.fit_sample, X, Y)
+
+
+def test_sample_regular_with_nn_svm():
+ """Test sample function with regular SMOTE with a NN object."""
+
+ # Create the object
+ kind = 'svm'
+ nn_k = NearestNeighbors(n_neighbors=6)
+ svm = SVC(random_state=RND_SEED)
+ smote = SMOTE(random_state=RND_SEED, kind=kind,
+ k_neighbors=nn_k, svm_estimator=svm)
+
+ X_resampled, y_resampled = smote.fit_sample(X, Y)
+
+ X_gt = np.array([[0.11622591, -0.0317206],
+ [0.77481731, 0.60935141],
+ [1.25192108, -0.22367336],
+ [0.53366841, -0.30312976],
+ [1.52091956, -0.49283504],
+ [-0.28162401, -2.10400981],
+ [0.83680821, 1.72827342],
+ [0.3084254, 0.33299982],
+ [0.70472253, -0.73309052],
+ [0.28893132, -0.38761769],
+ [1.15514042, 0.0129463],
+ [0.88407872, 0.35454207],
+ [1.31301027, -0.92648734],
+ [-1.11515198, -0.93689695],
+ [-0.18410027, -0.45194484],
+ [0.9281014, 0.53085498],
+ [-0.14374509, 0.27370049],
+ [-0.41635887, -0.38299653],
+ [0.08711622, 0.93259929],
+ [1.70580611, -0.11219234],
+ [0.47436888, -0.2645749],
+ [1.07844561, -0.19435291],
+ [1.44015515, -1.30621303]])
+ y_gt = np.array([0, 1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1,
+ 0, 0, 0, 0])
+ assert_array_almost_equal(X_resampled, X_gt)
+ assert_array_equal(y_resampled, y_gt)
+
+
+def test_sample_regular_wrong_svm():
+ """Test sample function with regular SMOTE with a NN object."""
+
+ # Create the object
+ kind = 'svm'
+ nn_k = NearestNeighbors(n_neighbors=6)
+ svm = 'rnd'
+ smote = SMOTE(random_state=RND_SEED, kind=kind,
+ k_neighbors=nn_k, svm_estimator=svm)
+
+ assert_raises(ValueError, smote.fit_sample, X, Y)

imblearn/pipeline.py

@@ -101,7 +101,7 @@ class Pipeline(pipeline.Pipeline):
  >>> X_train, X_test, y_train, y_test = tts(X, y, random_state=42)
  >>> pipeline.fit(X_train, y_train)
  Pipeline(steps=[('smt', SMOTE(k=None, k_neighbors=5, kind='regular', m=None, m_neighbors=10, n_jobs=1,
- out_step=0.5, random_state=42, ratio='auto')), ('pca', PCA(copy=True, n_components=None, whiten=False)), ('knn', KNeighborsClassifier(algorithm='auto', leaf_size=30, metric='minkowski',
+ out_step=0.5, random_state=42, ratio='auto', svm_estimator=None)), ('pca', PCA(copy=True, n_components=None, whiten=False)), ('knn', KNeighborsClassifier(algorithm='auto', leaf_size=30, metric='minkowski',
  metric_params=None, n_jobs=1, n_neighbors=5, p=2,
  weights='uniform'))])
  >>> y_hat = pipeline.predict(X_test)

imblearn/under_sampling/cluster_centroids.py

@@ -35,12 +35,12 @@ class ClusterCentroids(BaseMulticlassSampler):
  If None, the random number generator is the RandomState instance used
  by np.random.
 
+ estimator : object, optional(default=KMeans())
+ Pass a `sklearn.cluster.KMeans` estimator.
+
  n_jobs : int, optional (default=1)
  The number of threads to open if possible.
 
- **kwargs : keywords
- Parameter to use for the KMeans object.
-
  Attributes
  ----------
  min_c_ : str or int
@@ -79,11 +79,47 @@ class ClusterCentroids(BaseMulticlassSampler):
 
  """
 
- def __init__(self, ratio='auto', random_state=None, n_jobs=1, **kwargs):
+ def __init__(self, ratio='auto', random_state=None, estimator=None,
+ n_jobs=1):
  super(ClusterCentroids, self).__init__(ratio=ratio,
  random_state=random_state)
+ self.estimator = estimator
  self.n_jobs = n_jobs
- self.kwargs = kwargs
+
+ def _validate_estimator(self):
+ """Private function to create the NN estimator"""
+
+ if self.estimator is None:
+ self.estimator_ = KMeans(random_state=self.random_state,
+ n_jobs=self.n_jobs)
+ elif isinstance(self.estimator, KMeans):
+ self.estimator_ = self.estimator
+ else:
+ raise ValueError('`estimator` has to be a KMeans clustering.')
+
+ def fit(self, X, y):
+ """Find the classes statistics before to perform sampling.
+
+ Parameters
+ ----------
+ X : ndarray, shape (n_samples, n_features)
+ Matrix containing the data which have to be sampled.
+
+ y : ndarray, shape (n_samples, )
+ Corresponding label for each sample in X.
+
+ Returns
+ -------
+ self : object,
+ Return self.
+
+ """
+
+ super(ClusterCentroids, self).fit(X, y)
+
+ self._validate_estimator()
+
+ return self
 
  def _sample(self, X, y):
  """Resample the dataset.
@@ -105,17 +141,15 @@ def _sample(self, X, y):
  The corresponding label of `X_resampled`
 
  """
- random_state = check_random_state(self.random_state)
 
  # Compute the number of cluster needed
  if self.ratio == 'auto':
  num_samples = self.stats_c_[self.min_c_]
  else:
  num_samples = int(self.stats_c_[self.min_c_] / self.ratio)
 
- # Create the clustering object
- kmeans = KMeans(n_clusters=num_samples, random_state=random_state)
- kmeans.set_params(**self.kwargs)
+ # Set the number of sample for the estimator
+ self.estimator_.set_params(**{'n_clusters': num_samples})
 
  # Start with the minority class
  X_min = X[y == self.min_c_]
@@ -133,8 +167,8 @@ def _sample(self, X, y):
  continue
 
  # Find the centroids via k-means
- kmeans.fit(X[y == key])
- centroids = kmeans.cluster_centers_
+ self.estimator_.fit(X[y == key])
+ centroids = self.estimator_.cluster_centers_
 
  # Concatenate to the minority class
  X_resampled = np.concatenate((X_resampled, centroids), axis=0)

imblearn/under_sampling/condensed_nearest_neighbour.py

@@ -36,20 +36,18 @@ class CondensedNearestNeighbour(BaseMulticlassSampler):
  NOTE: size_ngh is deprecated from 0.2 and will be replaced in 0.4
  Use ``n_neighbors`` instead.
 
- n_neighbors : int, optional (default=1)
- Size of the neighbourhood to consider to compute the average
+ n_neighbors : int or object, optional (default=KNeighborsClassifier(n_neighbors=1))
+ If int, size of the neighbourhood to consider to compute the average
  distance to the minority point samples.
+ If object, an object inherited from
+ `sklearn.neigbors.KNeighborsClassifier` should be passed.
 
  n_seeds_S : int, optional (default=1)
  Number of samples to extract in order to build the set S.
 
  n_jobs : int, optional (default=1)
  The number of threads to open if possible.
 
- **kwargs : keywords
- Parameter to use for the Neareast Neighbours object.
-
-
  Attributes
  ----------
  min_c_ : str or int
@@ -95,16 +93,55 @@ class CondensedNearestNeighbour(BaseMulticlassSampler):
  """
 
  def __init__(self, return_indices=False, random_state=None,
- size_ngh=None, n_neighbors=1, n_seeds_S=1, n_jobs=1,
- **kwargs):
+ size_ngh=None, n_neighbors=None, n_seeds_S=1, n_jobs=1):
  super(CondensedNearestNeighbour, self).__init__(
  random_state=random_state)
  self.return_indices = return_indices
  self.size_ngh = size_ngh
  self.n_neighbors = n_neighbors
  self.n_seeds_S = n_seeds_S
  self.n_jobs = n_jobs
- self.kwargs = kwargs
+
+ def _validate_estimator(self):
+ """Private function to create the NN estimator"""
+
+ if self.n_neighbors is None:
+ self.estimator_ = KNeighborsClassifier(
+ n_neighbors=1,
+ n_jobs=self.n_jobs)
+ elif isinstance(self.n_neighbors, int):
+ self.estimator_ = KNeighborsClassifier(
+ n_neighbors=self.n_neighbors,
+ n_jobs=self.n_jobs)
+ elif isinstance(self.n_neighbors, KNeighborsClassifier):
+ self.estimator_ = self.n_neighbors
+ else:
+ raise ValueError('`n_neighbors` has to be a in or an object'
+ ' inhereited from KNeighborsClassifier.')
+
+ def fit(self, X, y):
+ """Find the classes statistics before to perform sampling.
+
+ Parameters
+ ----------
+ X : ndarray, shape (n_samples, n_features)
+ Matrix containing the data which have to be sampled.
+
+ y : ndarray, shape (n_samples, )
+ Corresponding label for each sample in X.
+
+ Returns
+ -------
+ self : object,
+ Return self.
+
+ """
+
+ super(CondensedNearestNeighbour, self).fit(X, y)
+
+ self._validate_estimator()
+
+ return self
 
  def _sample(self, X, y):
  """Resample the dataset.
@@ -167,13 +204,8 @@ def _sample(self, X, y):
  S_x = X[y == key]
  S_y = y[y == key]
 
- # Create a k-NN classifier
- knn = KNeighborsClassifier(n_neighbors=self.n_neighbors,
- n_jobs=self.n_jobs,
- **self.kwargs)
-
  # Fit C into the knn
- knn.fit(C_x, C_y)
+ self.estimator_.fit(C_x, C_y)
 
  good_classif_label = idx_maj_sample.copy()
  # Check each sample in S if we keep it or drop it
@@ -184,7 +216,7 @@ def _sample(self, X, y):
  continue
 
  # Classify on S
- pred_y = knn.predict(x_sam.reshape(1, -1))
+ pred_y = self.estimator_.predict(x_sam.reshape(1, -1))
 
  # If the prediction do not agree with the true label
  # append it in C_x
@@ -198,12 +230,12 @@ def _sample(self, X, y):
  idx_maj_sample.size))
 
  # Fit C into the knn
- knn.fit(C_x, C_y)
+ self.estimator_.fit(C_x, C_y)
 
  # This experimental to speed up the search
  # Classify all the element in S and avoid to test the
  # well classified elements
- pred_S_y = knn.predict(S_x)
+ pred_S_y = self.estimator_.predict(S_x)
  good_classif_label = np.unique(
  np.append(idx_maj_sample,
  np.flatnonzero(pred_S_y == S_y)))