scipy_sparse: iraps_classifier.py comparison

comparison iraps_classifier.py @ 24:b9ed7b774ba3 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c

author	bgruening
date	Wed, 15 May 2019 07:43:48 -0400
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-:27c0b1a050df
+:b9ed7b774ba3
+"""
+class IRAPSCore
+class IRAPSClassifier
+class BinarizeTargetClassifier
+class BinarizeTargetRegressor
+class _BinarizeTargetScorer
+class _BinarizeTargetProbaScorer
+binarize_auc_scorer
+binarize_average_precision_scorer
+binarize_accuracy_scorer
+binarize_balanced_accuracy_scorer
+binarize_precision_scorer
+binarize_recall_scorer
+"""
+import numpy as np
+import random
+import warnings
+from abc import ABCMeta
+from scipy.stats import ttest_ind
+from sklearn import metrics
+from sklearn.base import BaseEstimator, clone, RegressorMixin
+from sklearn.externals import six
+from sklearn.feature_selection.univariate_selection import _BaseFilter
+from sklearn.metrics.scorer import _BaseScorer
+from sklearn.pipeline import Pipeline
+from sklearn.utils import as_float_array, check_X_y
+from sklearn.utils._joblib import Parallel, delayed
+from sklearn.utils.validation import (check_array, check_is_fitted,
+check_memory, column_or_1d)
+VERSION = '0.1.1'
+class IRAPSCore(six.with_metaclass(ABCMeta, BaseEstimator)):
+"""
+Base class of IRAPSClassifier
+From sklearn BaseEstimator:
+get_params()
+set_params()
+Parameters
+----------
+n_iter : int
+sample count
+positive_thres : float
+z_score shreshold to discretize positive target values
+negative_thres : float
+z_score threshold to discretize negative target values
+verbose : int
+0 or geater, if not 0, print progress
+n_jobs : int, default=1
+The number of CPUs to use to do the computation.
+pre_dispatch : int, or string.
+Controls the number of jobs that get dispatched during parallel
+execution. Reducing this number can be useful to avoid an
+explosion of memory consumption when more jobs get dispatched
+than CPUs can process. This parameter can be:
+- None, in which case all the jobs are immediately
+created and spawned. Use this for lightweight and
+fast-running jobs, to avoid delays due to on-demand
+spawning of the jobs
+- An int, giving the exact number of total jobs that are
+spawned
+- A string, giving an expression as a function of n_jobs,
+as in '2*n_jobs'
+random_state : int or None
+"""
+def __init__(self, n_iter=1000, positive_thres=-1, negative_thres=0,
+verbose=0, n_jobs=1, pre_dispatch='2*n_jobs',
+random_state=None):
+"""
+IRAPS turns towwards general Anomaly Detection
+It comapares positive_thres with negative_thres,
+and decide which portion is the positive target.
+e.g.:
+(positive_thres=-1, negative_thres=0)
+=> positive = Z_score of target < -1
+(positive_thres=1, negative_thres=0)
+=> positive = Z_score of target > 1
+Note: The positive targets here is always the
+abnormal minority group.
+"""
+self.n_iter = n_iter
+self.positive_thres = positive_thres
+self.negative_thres = negative_thres
+self.verbose = verbose
+self.n_jobs = n_jobs
+self.pre_dispatch = pre_dispatch
+self.random_state = random_state
+def fit(self, X, y):
+"""
+X: array-like (n_samples x n_features)
+y: 1-d array-like (n_samples)
+"""
+X, y = check_X_y(X, y, ['csr', 'csc'], multi_output=False)
+def _stochastic_sampling(X, y, random_state=None, positive_thres=-1,
+negative_thres=0):
+# each iteration select a random number of random subset of
+# training samples. this is somewhat different from the original
+# IRAPS method, but effect is almost the same.
+SAMPLE_SIZE = [0.25, 0.75]
+n_samples = X.shape[0]
+if random_state is None:
+n_select = random.randint(int(n_samples * SAMPLE_SIZE[0]),
+int(n_samples * SAMPLE_SIZE[1]))
+index = random.sample(list(range(n_samples)), n_select)
+else:
+n_select = random.Random(random_state).randint(
+int(n_samples * SAMPLE_SIZE[0]),
+int(n_samples * SAMPLE_SIZE[1]))
+index = random.Random(random_state).sample(
+list(range(n_samples)), n_select)
+X_selected, y_selected = X[index], y[index]
+# Spliting by z_scores.
+y_selected = (y_selected - y_selected.mean()) / y_selected.std()
+if positive_thres < negative_thres:
+X_selected_positive = X_selected[y_selected < positive_thres]
+X_selected_negative = X_selected[y_selected > negative_thres]
+else:
+X_selected_positive = X_selected[y_selected > positive_thres]
+X_selected_negative = X_selected[y_selected < negative_thres]
+# For every iteration, at least 5 responders are selected
+if X_selected_positive.shape[0] < 5:
+warnings.warn("Warning: fewer than 5 positives were selected!")
+return
+# p_values
+_, p = ttest_ind(X_selected_positive, X_selected_negative,
+axis=0, equal_var=False)
+# fold_change == mean change?
+# TODO implement other normalization method
+positive_mean = X_selected_positive.mean(axis=0)
+negative_mean = X_selected_negative.mean(axis=0)
+mean_change = positive_mean - negative_mean
+# mean_change = np.select(
+#       [positive_mean > negative_mean,
+#           positive_mean < negative_mean],
+#       [positive_mean / negative_mean,
+#           -negative_mean / positive_mean])
+# mean_change could be adjusted by power of 2
+# mean_change = 2**mean_change \
+#       if mean_change>0 else -2**abs(mean_change)
+return p, mean_change, negative_mean
+parallel = Parallel(n_jobs=self.n_jobs, verbose=self.verbose,
+pre_dispatch=self.pre_dispatch)
+if self.random_state is None:
+res = parallel(delayed(_stochastic_sampling)(
+X, y, random_state=None,
+positive_thres=self.positive_thres,
+negative_thres=self.negative_thres)
+for i in range(self.n_iter))
+else:
+res = parallel(delayed(_stochastic_sampling)(
+X, y, random_state=seed,
+positive_thres=self.positive_thres,
+negative_thres=self.negative_thres)
+for seed in range(self.random_state,
+self.random_state+self.n_iter))
+res = [_ for _ in res if _]
+if len(res) < 50:
+raise ValueError("too few (%d) valid feature lists "
+"were generated!" % len(res))
+pvalues = np.vstack([x[0] for x in res])
+fold_changes = np.vstack([x[1] for x in res])
+base_values = np.vstack([x[2] for x in res])
+self.pvalues_ = np.asarray(pvalues)
+self.fold_changes_ = np.asarray(fold_changes)
+self.base_values_ = np.asarray(base_values)
+return self
+def _iraps_core_fit(iraps_core, X, y):
+return iraps_core.fit(X, y)
+class IRAPSClassifier(six.with_metaclass(ABCMeta, _BaseFilter,
+BaseEstimator, RegressorMixin)):
+"""
+Extend the bases of both sklearn feature_selector and classifier.
+From sklearn BaseEstimator:
+get_params()
+set_params()
+From sklearn _BaseFilter:
+get_support()
+fit_transform(X)
+transform(X)
+From sklearn RegressorMixin:
+score(X, y): R2
+New:
+predict(X)
+predict_label(X)
+get_signature()
+Properties:
+discretize_value
+Parameters
+----------
+iraps_core: object
+p_thres: float, threshold for p_values
+fc_thres: float, threshold for fold change or mean difference
+occurrence: float, occurrence rate selected by set of p_thres and fc_thres
+discretize: float, threshold of z_score to discretize target value
+memory: None, str or joblib.Memory object
+min_signature_features: int, the mininum number of features in a signature
+"""
+def __init__(self, iraps_core, p_thres=1e-4, fc_thres=0.1,
+occurrence=0.8, discretize=-1, memory=None,
+min_signature_features=1):
+self.iraps_core = iraps_core
+self.p_thres = p_thres
+self.fc_thres = fc_thres
+self.occurrence = occurrence
+self.discretize = discretize
+self.memory = memory
+self.min_signature_features = min_signature_features
+def fit(self, X, y):
+memory = check_memory(self.memory)
+cached_fit = memory.cache(_iraps_core_fit)
+iraps_core = clone(self.iraps_core)
+# allow pre-fitted iraps_core here
+if not hasattr(iraps_core, 'pvalues_'):
+iraps_core = cached_fit(iraps_core, X, y)
+self.iraps_core_ = iraps_core
+pvalues = as_float_array(iraps_core.pvalues_, copy=True)
+# why np.nan is here?
+pvalues[np.isnan(pvalues)] = np.finfo(pvalues.dtype).max
+fold_changes = as_float_array(iraps_core.fold_changes_, copy=True)
+fold_changes[np.isnan(fold_changes)] = 0.0
+base_values = as_float_array(iraps_core.base_values_, copy=True)
+p_thres = self.p_thres
+fc_thres = self.fc_thres
+occurrence = self.occurrence
+mask_0 = np.zeros(pvalues.shape, dtype=np.int32)
+# mark p_values less than the threashold
+mask_0[pvalues <= p_thres] = 1
+# mark fold_changes only when greater than the threashold
+mask_0[abs(fold_changes) < fc_thres] = 0
+# count the occurrence and mask greater than the threshold
+counts = mask_0.sum(axis=0)
+occurrence_thres = int(occurrence * iraps_core.n_iter)
+mask = np.zeros(counts.shape, dtype=bool)
+mask[counts >= occurrence_thres] = 1
+# generate signature
+fold_changes[mask_0 == 0] = 0.0
+signature = fold_changes[:, mask].sum(axis=0) / counts[mask]
+signature = np.vstack((signature, base_values[:, mask].mean(axis=0)))
+# It's not clearn whether min_size could impact prediction
+# performance
+if signature is None\
+or signature.shape[1] < self.min_signature_features:
+raise ValueError("The classifier got None signature or the number "
+"of sinature feature is less than minimum!")
+self.signature_ = np.asarray(signature)
+self.mask_ = mask
+# TODO: support other discretize method: fixed value, upper
+# third quater, etc.
+self.discretize_value = y.mean() + y.std() * self.discretize
+if iraps_core.negative_thres > iraps_core.positive_thres:
+self.less_is_positive = True
+else:
+self.less_is_positive = False
+return self
+def _get_support_mask(self):
+"""
+return mask of feature selection indices
+"""
+check_is_fitted(self, 'mask_')
+return self.mask_
+def get_signature(self):
+"""
+return signature
+"""
+check_is_fitted(self, 'signature_')
+return self.signature_
+def predict(self, X):
+"""
+compute the correlation coefficient with irpas signature
+"""
+signature = self.get_signature()
+X = as_float_array(X)
+X_transformed = self.transform(X) - signature[1]
+corrcoef = np.array(
+[np.corrcoef(signature[0], e)[0][1] for e in X_transformed])
+corrcoef[np.isnan(corrcoef)] = np.finfo(np.float32).min
+return corrcoef
+def predict_label(self, X, clf_cutoff=0.4):
+return self.predict(X) >= clf_cutoff
+class BinarizeTargetClassifier(BaseEstimator, RegressorMixin):
+"""
+Convert continuous target to binary labels (True and False)
+and apply a classification estimator.
+Parameters
+----------
+classifier: object
+Estimator object such as derived from sklearn `ClassifierMixin`.
+z_score: float, default=-1.0
+Threshold value based on z_score. Will be ignored when
+fixed_value is set
+value: float, default=None
+Threshold value
+less_is_positive: boolean, default=True
+When target is less the threshold value, it will be converted
+to True, False otherwise.
+Attributes
+----------
+classifier_: object
+Fitted classifier
+discretize_value: float
+The threshold value used to discretize True and False targets
+"""
+def __init__(self, classifier, z_score=-1, value=None,
+less_is_positive=True):
+self.classifier = classifier
+self.z_score = z_score
+self.value = value
+self.less_is_positive = less_is_positive
+def fit(self, X, y, sample_weight=None):
+"""
+Convert y to True and False labels and then fit the classifier
+with X and new y
+Returns
+------
+self: object
+"""
+y = check_array(y, accept_sparse=False, force_all_finite=True,
+ensure_2d=False, dtype='numeric')
+y = column_or_1d(y)
+if self.value is None:
+discretize_value = y.mean() + y.std() * self.z_score
+else:
+discretize_value = self.Value
+self.discretize_value = discretize_value
+if self.less_is_positive:
+y_trans = y < discretize_value
+else:
+y_trans = y > discretize_value
+self.classifier_ = clone(self.classifier)
+if sample_weight is not None:
+self.classifier_.fit(X, y_trans, sample_weight=sample_weight)
+else:
+self.classifier_.fit(X, y_trans)
+if hasattr(self.classifier_, 'feature_importances_'):
+self.feature_importances_ = self.classifier_.feature_importances_
+if hasattr(self.classifier_, 'coef_'):
+self.coef_ = self.classifier_.coef_
+if hasattr(self.classifier_, 'n_outputs_'):
+self.n_outputs_ = self.classifier_.n_outputs_
+if hasattr(self.classifier_, 'n_features_'):
+self.n_features_ = self.classifier_.n_features_
+return self
+def predict(self, X):
+"""
+Predict class probabilities of X.
+"""
+check_is_fitted(self, 'classifier_')
+proba = self.classifier_.predict_proba(X)
+return proba[:, 1]
+def predict_label(self, X):
+"""Predict class label of X
+"""
+check_is_fitted(self, 'classifier_')
+return self.classifier_.predict(X)
+class _BinarizeTargetProbaScorer(_BaseScorer):
+"""
+base class to make binarized target specific scorer
+"""
+def __call__(self, clf, X, y, sample_weight=None):
+clf_name = clf.__class__.__name__
+# support pipeline object
+if isinstance(clf, Pipeline):
+main_estimator = clf.steps[-1][-1]
+# support stacking ensemble estimators
+# TODO support nested pipeline/stacking estimators
+elif clf_name in ['StackingCVClassifier', 'StackingClassifier']:
+main_estimator = clf.meta_clf_
+elif clf_name in ['StackingCVRegressor', 'StackingRegressor']:
+main_estimator = clf.meta_regr_
+else:
+main_estimator = clf
+discretize_value = main_estimator.discretize_value
+less_is_positive = main_estimator.less_is_positive
+if less_is_positive:
+y_trans = y < discretize_value
+else:
+y_trans = y > discretize_value
+y_pred = clf.predict(X)
+if sample_weight is not None:
+return self._sign * self._score_func(y_trans, y_pred,
+sample_weight=sample_weight,
+**self._kwargs)
+else:
+return self._sign * self._score_func(y_trans, y_pred,
+**self._kwargs)
+# roc_auc
+binarize_auc_scorer =\
+_BinarizeTargetProbaScorer(metrics.roc_auc_score, 1, {})
+# average_precision_scorer
+binarize_average_precision_scorer =\
+_BinarizeTargetProbaScorer(metrics.average_precision_score, 1, {})
+# roc_auc_scorer
+iraps_auc_scorer = binarize_auc_scorer
+# average_precision_scorer
+iraps_average_precision_scorer = binarize_average_precision_scorer
+class BinarizeTargetRegressor(BaseEstimator, RegressorMixin):
+"""
+Extend regression estimator to have discretize_value
+Parameters
+----------
+regressor: object
+Estimator object such as derived from sklearn `RegressionMixin`.
+z_score: float, default=-1.0
+Threshold value based on z_score. Will be ignored when
+fixed_value is set
+value: float, default=None
+Threshold value
+less_is_positive: boolean, default=True
+When target is less the threshold value, it will be converted
+to True, False otherwise.
+Attributes
+----------
+regressor_: object
+Fitted regressor
+discretize_value: float
+The threshold value used to discretize True and False targets
+"""
+def __init__(self, regressor, z_score=-1, value=None,
+less_is_positive=True):
+self.regressor = regressor
+self.z_score = z_score
+self.value = value
+self.less_is_positive = less_is_positive
+def fit(self, X, y, sample_weight=None):
+"""
+Calculate the discretize_value fit the regressor with traning data
+Returns
+------
+self: object
+"""
+y = check_array(y, accept_sparse=False, force_all_finite=True,
+ensure_2d=False, dtype='numeric')
+y = column_or_1d(y)
+if self.value is None:
+discretize_value = y.mean() + y.std() * self.z_score
+else:
+discretize_value = self.Value
+self.discretize_value = discretize_value
+self.regressor_ = clone(self.regressor)
+if sample_weight is not None:
+self.regressor_.fit(X, y, sample_weight=sample_weight)
+else:
+self.regressor_.fit(X, y)
+# attach classifier attributes
+if hasattr(self.regressor_, 'feature_importances_'):
+self.feature_importances_ = self.regressor_.feature_importances_
+if hasattr(self.regressor_, 'coef_'):
+self.coef_ = self.regressor_.coef_
+if hasattr(self.regressor_, 'n_outputs_'):
+self.n_outputs_ = self.regressor_.n_outputs_
+if hasattr(self.regressor_, 'n_features_'):
+self.n_features_ = self.regressor_.n_features_
+return self
+def predict(self, X):
+"""Predict target value of X
+"""
+check_is_fitted(self, 'regressor_')
+y_pred = self.regressor_.predict(X)
+if not np.all((y_pred >= 0) & (y_pred <= 1)):
+y_pred = (y_pred - y_pred.min()) / (y_pred.max() - y_pred.min())
+if self.less_is_positive:
+y_pred = 1 - y_pred
+return y_pred
+# roc_auc_scorer
+regression_auc_scorer = binarize_auc_scorer
+# average_precision_scorer
+regression_average_precision_scorer = binarize_average_precision_scorer

Mercurial > repos > bgruening > scipy_sparse

comparison iraps_classifier.py @ 24:b9ed7b774ba3 draft