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Commit 4bb038a0 authored by Baptiste Bauvin's avatar Baptiste Bauvin
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SK tests correction

parent 78dd68e7
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multimodal/boosting/combo.py
View file @ 4bb038a0
......@@ -48,11 +48,11 @@ estimator for classification implemented in the ``MuComboClassifier`` class.
import numpy as np
from sklearn.base import ClassifierMixin
from sklearn.ensemble import BaseEnsemble
from sklearn.ensemble.forest import BaseForest
from sklearn.ensemble._forest import BaseForest
from sklearn.metrics import accuracy_score
from sklearn.tree import DecisionTreeClassifier
from sklearn.tree._tree import DTYPE
from sklearn.tree.tree import BaseDecisionTree
from sklearn.tree import BaseDecisionTree
from sklearn.utils import check_array, check_X_y, check_random_state
from sklearn.utils.multiclass import check_classification_targets
from sklearn.utils.validation import check_is_fitted, has_fit_parameter
......@@ -141,11 +141,11 @@ class MuComboClassifier(BaseEnsemble, ClassifierMixin, UBoosting):
>>> base_estimator = DecisionTreeClassifier(max_depth=2)
>>> clf = MuComboClassifier(base_estimator=base_estimator, random_state=1)
>>> clf.fit(X, y, views_ind) # doctest: +NORMALIZE_WHITESPACE
MuComboClassifier(base_estimator=DecisionTreeClassifier(class_weight=None, criterion='gini', max_depth=2,
MuComboClassifier(base_estimator=DecisionTreeClassifier(ccp_alpha=0.0, class_weight=None, criterion='gini', max_depth=2,
max_features=None, max_leaf_nodes=None,
min_impurity_decrease=0.0, min_impurity_split=None,
min_samples_leaf=1, min_samples_split=2,
min_weight_fraction_leaf=0.0, presort=False, random_state=None,
min_weight_fraction_leaf=0.0, presort='deprecated', random_state=None,
splitter='best'),
n_estimators=50, random_state=1)
>>> print(clf.predict([[ 5., 3., 1., 1.]]))
......@@ -222,8 +222,9 @@ class MuComboClassifier(BaseEnsemble, ClassifierMixin, UBoosting):
dist = np.empty(cost.shape[:2], dtype=cost.dtype, order="C")
# NOTE: In Sokol's PhD thesis, the formula for dist is mistakenly given
# with a minus sign in section 2.2.2 page 31
dist[:, :] = cost[:, np.arange(n_samples), y] \
/ np.sum(cost[:, np.arange(n_samples), y], axis=1)[:, np.newaxis]
sum_cost = np.sum(cost[:, np.arange(n_samples), y], axis=1)[:, np.newaxis]
sum_cost[sum_cost==0] = 1
dist[:, :] = cost[:, np.arange(n_samples), y] / sum_cost
return dist
def _indicatrice(self, predicted_classes, y_i):
......@@ -444,6 +445,8 @@ class MuComboClassifier(BaseEnsemble, ClassifierMixin, UBoosting):
views_ind_, n_views = self.X_._validate_views_ind(self.X_.views_ind,
self.X_.shape[1])
check_X_y(self.X_, y)
if not isinstance(y, np.ndarray):
y = np.asarray(y)
check_classification_targets(y)
self._validate_estimator()
......
multimodal/boosting/mumbo.py
View file @ 4bb038a0
......@@ -48,10 +48,10 @@ import numpy as np
from sklearn.base import ClassifierMixin
from sklearn.ensemble import BaseEnsemble
from sklearn.ensemble.forest import BaseForest
from sklearn.ensemble._forest import BaseForest
from sklearn.metrics import accuracy_score
from sklearn.tree import DecisionTreeClassifier
from sklearn.tree.tree import BaseDecisionTree
from sklearn.tree import BaseDecisionTree
from sklearn.tree._tree import DTYPE
from sklearn.utils import check_array, check_X_y, check_random_state
from sklearn.utils.multiclass import check_classification_targets
......@@ -143,11 +143,11 @@ class MumboClassifier(BaseEnsemble, ClassifierMixin, UBoosting):
>>> base_estimator = DecisionTreeClassifier(max_depth=2)
>>> clf = MumboClassifier(base_estimator=base_estimator, random_state=0)
>>> clf.fit(X, y, views_ind) # doctest: +NORMALIZE_WHITESPACE
MumboClassifier(base_estimator=DecisionTreeClassifier(class_weight=None,
MumboClassifier(base_estimator=DecisionTreeClassifier(ccp_alpha=0.0, class_weight=None,
criterion='gini', max_depth=2, max_features=None,
max_leaf_nodes=None, min_impurity_decrease=0.0,
min_impurity_split=None, min_samples_leaf=1, min_samples_split=2,
min_weight_fraction_leaf=0.0, presort=False, random_state=None,
min_weight_fraction_leaf=0.0, presort='deprecated', random_state=None,
splitter='best'),
best_view_mode='edge', n_estimators=50, random_state=0)
>>> print(clf.predict([[ 5., 3., 1., 1.]]))
......@@ -377,6 +377,8 @@ class MumboClassifier(BaseEnsemble, ClassifierMixin, UBoosting):
views_ind_, n_views = self.X_._validate_views_ind(self.X_.views_ind,
self.X_.shape[1])
check_X_y(self.X_, y, accept_sparse=accept_sparse, dtype=dtype)
if not isinstance(y, np.ndarray):
y = np.asarray(y)
check_classification_targets(y)
self._validate_estimator()
......
multimodal/kernels/mvml.py
View file @ 4bb038a0
......@@ -230,9 +230,10 @@ class MVML(MKernel, BaseEstimator, ClassifierMixin, RegressorMixin):
# if type_of_target(y) not in "binary":
# raise ValueError("target should be binary")
check_classification_targets(y)
if type_of_target(y) in "binary":
check_classification_targets(y)
self.classes_, y = np.unique(y, return_inverse=True)
y[y==0] = -1.0
self.n_classes = len(self.classes_)
......@@ -342,7 +343,7 @@ class MVML(MKernel, BaseEstimator, ClassifierMixin, RegressorMixin):
else:
# A_inv = self._inverse_precond_LU(A + 1e-8 * np.eye(views * self.n_approx), pos="precond_A") # self._inverse_precond_jacobi(A + 1e-8 * np.eye(views * self.n_approx), pos="precond_A")
A_inv = self._inv_best_precond(A + 1e-8 * np.eye(views * self.n_approx), pos="precond_A")
except spli.LinAlgError:
except spli.LinAlgError: # pragma: no cover
self.warning_message["LinAlgError"] = self.warning_message.get("LinAlgError", 0) + 1
try:
A_inv = spli.pinv(A + 1e-07 * np.eye(views * self.n_approx))
......@@ -352,7 +353,7 @@ class MVML(MKernel, BaseEstimator, ClassifierMixin, RegressorMixin):
except ValueError:
self.warning_message["ValueError"] = self.warning_message.get("ValueError", 0) + 1
return A_prev, g_prev
except ValueError:
except ValueError: # pragma: no cover
self.warning_message["ValueError"] = self.warning_message.get("ValueError", 0) + 1
return A_prev, g_prev, w_prev
# print("A_inv ",np.sum(A_inv))
......@@ -372,7 +373,7 @@ class MVML(MKernel, BaseEstimator, ClassifierMixin, RegressorMixin):
else:
# g = np.dot(self._inverse_precond_LU(A_inv, pos="precond_A_1"), g)
g = np.dot(self._inv_best_precond(A_inv, pos="precond_A_1"), g)
except spli.LinAlgError:
except spli.LinAlgError: # pragma: no cover
self.warning_message["LinAlgError"] = self.warning_message.get("LinAlgError", 0) + 1
g = spli.solve(A_inv, g)
......@@ -428,7 +429,7 @@ class MVML(MKernel, BaseEstimator, ClassifierMixin, RegressorMixin):
A_inv = spli.pinv(A)
return A_inv
def _inverse_precond_jacobi(self, A, pos="precond_A"):
def _inverse_precond_jacobi(self, A, pos="precond_A"): # pragma: no cover
J_1 = np.diag(1.0/np.diag(A))
# J_1 = np.linalg.inv(J)
P = np.dot(J_1, A)
......@@ -438,10 +439,9 @@ class MVML(MKernel, BaseEstimator, ClassifierMixin, RegressorMixin):
self.warning_message[pos] = self.warning_message.get(pos, 0) + 1
else:
A_inv = self._inverse_precond_LU(A, pos=pos)
return A_inv
def _inverse_precond_LU(self, A, pos="precond_A"):
def _inverse_precond_LU(self, A, pos="precond_A"): # pragma: no cover
P, L, U = spli.lu(A)
M = spli.inv(np.dot(L, U))
P = np.dot(M, A)
......@@ -606,17 +606,17 @@ class MVML(MKernel, BaseEstimator, ClassifierMixin, RegressorMixin):
try:
# minA_inv = np.min(np.absolute(A_prev)) , rcond=self.r_cond*minA_inv
A_prev_inv = spli.pinv(A_prev)
except spli.LinAlgError:
except spli.LinAlgError: # pragma: no cover
try:
A_prev_inv = spli.pinv(A_prev + 1e-6 * np.eye(views * m))
except spli.LinAlgError:
return A_prev
except ValueError:
return A_prev
except ValueError:
except ValueError: # pragma: no cover
return A_prev
if np.any(np.isnan(A_prev_inv)):
if np.any(np.isnan(A_prev_inv)): # pragma: no cover
# just in case the inverse didn't return a proper solution (happened once or twice)
return A_prev
......@@ -625,9 +625,9 @@ class MVML(MKernel, BaseEstimator, ClassifierMixin, RegressorMixin):
# if there is one small negative eigenvalue this gets rid of it
try:
val, vec = spli.eigh(A_tmp)
except spli.LinAlgError:
except spli.LinAlgError: # pragma: no cover
return A_prev
except ValueError:
except ValueError: # pragma: no cover
return A_prev
val[val < 0] = 0
......
multimodal/tests/test_mvml.py
View file @ 4bb038a0
......@@ -95,6 +95,22 @@ class MVMLTest(unittest.TestCase):
w_expected = np.array([[0.5],[0.5]])
np.testing.assert_almost_equal(mvml.w, w_expected, 8)
def testFitMVMLRegression(self):
#######################################################
# task with dict and not precomputed
#######################################################
y = self.y
y += np.random.uniform(0,1, size=y.shape)
mvml = MVML(lmbda=0.1, eta=1,
kernel=['rbf'], kernel_params=[{'gamma':50}],
nystrom_param=0.2)
views_ind = [120, 240]
mvml.fit(self.kernel_dict, y=y, views_ind=None)
self.assertEqual(mvml.A.shape, (48, 48))
self.assertEqual(mvml.g.shape,(48, 1))
w_expected = np.array([[0.5],[0.5]])
np.testing.assert_almost_equal(mvml.w, w_expected, 8)
def testFitMVMLPrecision(self):
#######################################################
# task with dict and not precomputed
......
setup.cfg
View file @ 4bb038a0
......@@ -14,3 +14,6 @@ branch = True
source = multimodal
include = */multimodal/*
omit = */tests/*
[coverage:report]
exclude_lines = pragma: no cover
\ No newline at end of file
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