sklearn_estimator_attributes: feature

annotate feature_selectors.py @ 1:84ddbf61e107 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 49522db5f2dc8a571af49e3f38e80c22571068f4

author	bgruening
date	Tue, 09 Jul 2019 19:32:22 -0400
parents	2ad4c2798be7
children

rev	line source
0 2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	1 """
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	2 DyRFE
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	3 DyRFECV
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	4 MyPipeline
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	5 MyimbPipeline
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	6 check_feature_importances
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	7 """
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	8 import numpy as np
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	9
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	10 from imblearn import under_sampling, over_sampling, combine
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	11 from imblearn.pipeline import Pipeline as imbPipeline
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	12 from sklearn import (cluster, compose, decomposition, ensemble,
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	13 feature_extraction, feature_selection,
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	14 gaussian_process, kernel_approximation,
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	15 metrics, model_selection, naive_bayes,
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	16 neighbors, pipeline, preprocessing,
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	17 svm, linear_model, tree, discriminant_analysis)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	18
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	19 from sklearn.base import BaseEstimator
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	20 from sklearn.base import MetaEstimatorMixin, clone, is_classifier
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	21 from sklearn.feature_selection.rfe import _rfe_single_fit, RFE, RFECV
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	22 from sklearn.model_selection import check_cv
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	23 from sklearn.metrics.scorer import check_scoring
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	24 from sklearn.utils import check_X_y, safe_indexing, safe_sqr
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	25 from sklearn.utils._joblib import Parallel, delayed, effective_n_jobs
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	26
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	27
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	28 class DyRFE(RFE):
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	29 """
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	30 Mainly used with DyRFECV
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	31
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	32 Parameters
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	33 ----------
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	34 estimator : object
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	35 A supervised learning estimator with a ``fit`` method that provides
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	36 information about feature importance either through a ``coef_``
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	37 attribute or through a ``feature_importances_`` attribute.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	38 n_features_to_select : int or None (default=None)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	39 The number of features to select. If `None`, half of the features
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	40 are selected.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	41 step : int, float or list, optional (default=1)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	42 If greater than or equal to 1, then ``step`` corresponds to the
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	43 (integer) number of features to remove at each iteration.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	44 If within (0.0, 1.0), then ``step`` corresponds to the percentage
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	45 (rounded down) of features to remove at each iteration.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	46 If list, a series of steps of features to remove at each iteration.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	47 Iterations stops when steps finish
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	48 verbose : int, (default=0)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	49 Controls verbosity of output.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	50
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	51 """
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	52 def __init__(self, estimator, n_features_to_select=None, step=1,
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	53 verbose=0):
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	54 super(DyRFE, self).__init__(estimator, n_features_to_select,
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	55 step, verbose)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	56
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	57 def _fit(self, X, y, step_score=None):
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	58
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	59 if type(self.step) is not list:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	60 return super(DyRFE, self)._fit(X, y, step_score)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	61
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	62 # dynamic step
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	63 X, y = check_X_y(X, y, "csc")
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	64 # Initialization
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	65 n_features = X.shape[1]
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	66 if self.n_features_to_select is None:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	67 n_features_to_select = n_features // 2
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	68 else:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	69 n_features_to_select = self.n_features_to_select
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	70
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	71 step = []
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	72 for s in self.step:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	73 if 0.0 < s < 1.0:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	74 step.append(int(max(1, s * n_features)))
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	75 else:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	76 step.append(int(s))
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	77 if s <= 0:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	78 raise ValueError("Step must be >0")
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	79
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	80 support_ = np.ones(n_features, dtype=np.bool)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	81 ranking_ = np.ones(n_features, dtype=np.int)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	82
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	83 if step_score:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	84 self.scores_ = []
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	85
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	86 step_i = 0
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	87 # Elimination
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	88 while np.sum(support_) > n_features_to_select and step_i < len(step):
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	89
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	90 # if last step is 1, will keep loop
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	91 if step_i == len(step) - 1 and step[step_i] != 0:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	92 step.append(step[step_i])
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	93
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	94 # Remaining features
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	95 features = np.arange(n_features)[support_]
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	96
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	97 # Rank the remaining features
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	98 estimator = clone(self.estimator)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	99 if self.verbose > 0:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	100 print("Fitting estimator with %d features." % np.sum(support_))
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	101
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	102 estimator.fit(X[:, features], y)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	103
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	104 # Get coefs
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	105 if hasattr(estimator, 'coef_'):
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	106 coefs = estimator.coef_
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	107 else:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	108 coefs = getattr(estimator, 'feature_importances_', None)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	109 if coefs is None:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	110 raise RuntimeError('The classifier does not expose '
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	111 '"coef_" or "feature_importances_" '
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	112 'attributes')
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	113
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	114 # Get ranks
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	115 if coefs.ndim > 1:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	116 ranks = np.argsort(safe_sqr(coefs).sum(axis=0))
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	117 else:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	118 ranks = np.argsort(safe_sqr(coefs))
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	119
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	120 # for sparse case ranks is matrix
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	121 ranks = np.ravel(ranks)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	122
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	123 # Eliminate the worse features
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	124 threshold =\
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	125 min(step[step_i], np.sum(support_) - n_features_to_select)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	126
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	127 # Compute step score on the previous selection iteration
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	128 # because 'estimator' must use features
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	129 # that have not been eliminated yet
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	130 if step_score:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	131 self.scores_.append(step_score(estimator, features))
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	132 support_[features[ranks][:threshold]] = False
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	133 ranking_[np.logical_not(support_)] += 1
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	134
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	135 step_i += 1
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	136
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	137 # Set final attributes
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	138 features = np.arange(n_features)[support_]
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	139 self.estimator_ = clone(self.estimator)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	140 self.estimator_.fit(X[:, features], y)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	141
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	142 # Compute step score when only n_features_to_select features left
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	143 if step_score:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	144 self.scores_.append(step_score(self.estimator_, features))
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	145 self.n_features_ = support_.sum()
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	146 self.support_ = support_
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	147 self.ranking_ = ranking_
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	148
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	149 return self
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	150
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	151
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	152 class DyRFECV(RFECV, MetaEstimatorMixin):
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	153 """
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	154 Compared with RFECV, DyRFECV offers flexiable `step` to eleminate
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	155 features, in the format of list, while RFECV supports only fixed number
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	156 of `step`.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	157
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	158 Parameters
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	159 ----------
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	160 estimator : object
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	161 A supervised learning estimator with a ``fit`` method that provides
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	162 information about feature importance either through a ``coef_``
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	163 attribute or through a ``feature_importances_`` attribute.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	164 step : int or float, optional (default=1)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	165 If greater than or equal to 1, then ``step`` corresponds to the
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	166 (integer) number of features to remove at each iteration.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	167 If within (0.0, 1.0), then ``step`` corresponds to the percentage
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	168 (rounded down) of features to remove at each iteration.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	169 If list, a series of step to remove at each iteration. iteration stopes
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	170 when finishing all steps
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	171 Note that the last iteration may remove fewer than ``step`` features in
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	172 order to reach ``min_features_to_select``.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	173 min_features_to_select : int, (default=1)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	174 The minimum number of features to be selected. This number of features
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	175 will always be scored, even if the difference between the original
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	176 feature count and ``min_features_to_select`` isn't divisible by
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	177 ``step``.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	178 cv : int, cross-validation generator or an iterable, optional
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	179 Determines the cross-validation splitting strategy.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	180 Possible inputs for cv are:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	181 - None, to use the default 3-fold cross-validation,
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	182 - integer, to specify the number of folds.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	183 - :term:`CV splitter`,
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	184 - An iterable yielding (train, test) splits as arrays of indices.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	185 For integer/None inputs, if ``y`` is binary or multiclass,
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	186 :class:`sklearn.model_selection.StratifiedKFold` is used. If the
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	187 estimator is a classifier or if ``y`` is neither binary nor multiclass,
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	188 :class:`sklearn.model_selection.KFold` is used.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	189 Refer :ref:`User Guide <cross_validation>` for the various
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	190 cross-validation strategies that can be used here.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	191 .. versionchanged:: 0.20
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	192 ``cv`` default value of None will change from 3-fold to 5-fold
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	193 in v0.22.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	194 scoring : string, callable or None, optional, (default=None)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	195 A string (see model evaluation documentation) or
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	196 a scorer callable object / function with signature
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	197 ``scorer(estimator, X, y)``.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	198 verbose : int, (default=0)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	199 Controls verbosity of output.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	200 n_jobs : int or None, optional (default=None)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	201 Number of cores to run in parallel while fitting across folds.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	202 ``None`` means 1 unless in a :obj:`joblib.parallel_backend` context.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	203 ``-1`` means using all processors. See :term:`Glossary <n_jobs>`
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	204 for more details.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	205 """
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	206 def __init__(self, estimator, step=1, min_features_to_select=1, cv='warn',
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	207 scoring=None, verbose=0, n_jobs=None):
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	208 super(DyRFECV, self).__init__(
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	209 estimator, step=step,
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	210 min_features_to_select=min_features_to_select,
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	211 cv=cv, scoring=scoring, verbose=verbose,
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	212 n_jobs=n_jobs)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	213
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	214 def fit(self, X, y, groups=None):
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	215 """Fit the RFE model and automatically tune the number of selected
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	216 features.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	217 Parameters
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	218 ----------
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	219 X : {array-like, sparse matrix}, shape = [n_samples, n_features]
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	220 Training vector, where `n_samples` is the number of samples and
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	221 `n_features` is the total number of features.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	222 y : array-like, shape = [n_samples]
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	223 Target values (integers for classification, real numbers for
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	224 regression).
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	225 groups : array-like, shape = [n_samples], optional
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	226 Group labels for the samples used while splitting the dataset into
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	227 train/test set.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	228 """
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	229 if type(self.step) is not list:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	230 return super(DyRFECV, self).fit(X, y, groups)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	231
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	232 X, y = check_X_y(X, y, "csr")
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	233
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	234 # Initialization
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	235 cv = check_cv(self.cv, y, is_classifier(self.estimator))
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	236 scorer = check_scoring(self.estimator, scoring=self.scoring)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	237 n_features = X.shape[1]
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	238
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	239 step = []
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	240 for s in self.step:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	241 if 0.0 < s < 1.0:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	242 step.append(int(max(1, s * n_features)))
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	243 else:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	244 step.append(int(s))
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	245 if s <= 0:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	246 raise ValueError("Step must be >0")
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	247
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	248 # Build an RFE object, which will evaluate and score each possible
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	249 # feature count, down to self.min_features_to_select
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	250 rfe = DyRFE(estimator=self.estimator,
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	251 n_features_to_select=self.min_features_to_select,
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	252 step=self.step, verbose=self.verbose)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	253
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	254 # Determine the number of subsets of features by fitting across
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	255 # the train folds and choosing the "features_to_select" parameter
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	256 # that gives the least averaged error across all folds.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	257
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	258 # Note that joblib raises a non-picklable error for bound methods
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	259 # even if n_jobs is set to 1 with the default multiprocessing
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	260 # backend.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	261 # This branching is done so that to
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	262 # make sure that user code that sets n_jobs to 1
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	263 # and provides bound methods as scorers is not broken with the
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	264 # addition of n_jobs parameter in version 0.18.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	265
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	266 if effective_n_jobs(self.n_jobs) == 1:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	267 parallel, func = list, _rfe_single_fit
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	268 else:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	269 parallel = Parallel(n_jobs=self.n_jobs)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	270 func = delayed(_rfe_single_fit)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	271
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	272 scores = parallel(
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	273 func(rfe, self.estimator, X, y, train, test, scorer)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	274 for train, test in cv.split(X, y, groups))
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	275
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	276 scores = np.sum(scores, axis=0)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	277 diff = int(scores.shape[0]) - len(step)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	278 if diff > 0:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	279 step = np.r_[step, [step[-1]] * diff]
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	280 scores_rev = scores[::-1]
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	281 argmax_idx = len(scores) - np.argmax(scores_rev) - 1
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	282 n_features_to_select = max(
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	283 n_features - sum(step[:argmax_idx]),
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	284 self.min_features_to_select)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	285
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	286 # Re-execute an elimination with best_k over the whole set
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	287 rfe = DyRFE(estimator=self.estimator,
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	288 n_features_to_select=n_features_to_select, step=self.step,
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	289 verbose=self.verbose)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	290
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	291 rfe.fit(X, y)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	292
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	293 # Set final attributes
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	294 self.support_ = rfe.support_
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	295 self.n_features_ = rfe.n_features_
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	296 self.ranking_ = rfe.ranking_
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	297 self.estimator_ = clone(self.estimator)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	298 self.estimator_.fit(self.transform(X), y)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	299
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	300 # Fixing a normalization error, n is equal to get_n_splits(X, y) - 1
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	301 # here, the scores are normalized by get_n_splits(X, y)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	302 self.grid_scores_ = scores[::-1] / cv.get_n_splits(X, y, groups)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	303 return self
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	304
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	305
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	306 class MyPipeline(pipeline.Pipeline):
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	307 """
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	308 Extend pipeline object to have feature_importances_ attribute
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	309 """
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	310 def fit(self, X, y=None, **fit_params):
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	311 super(MyPipeline, self).fit(X, y, **fit_params)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	312 estimator = self.steps[-1][-1]
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	313 if hasattr(estimator, 'coef_'):
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	314 coefs = estimator.coef_
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	315 else:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	316 coefs = getattr(estimator, 'feature_importances_', None)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	317 if coefs is None:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	318 raise RuntimeError('The estimator in the pipeline does not expose '
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	319 '"coef_" or "feature_importances_" '
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	320 'attributes')
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	321 self.feature_importances_ = coefs
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	322 return self
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	323
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	324
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	325 class MyimbPipeline(imbPipeline):
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	326 """
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	327 Extend imblance pipeline object to have feature_importances_ attribute
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	328 """
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	329 def fit(self, X, y=None, **fit_params):
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	330 super(MyimbPipeline, self).fit(X, y, **fit_params)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	331 estimator = self.steps[-1][-1]
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	332 if hasattr(estimator, 'coef_'):
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	333 coefs = estimator.coef_
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	334 else:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	335 coefs = getattr(estimator, 'feature_importances_', None)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	336 if coefs is None:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	337 raise RuntimeError('The estimator in the pipeline does not expose '
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	338 '"coef_" or "feature_importances_" '
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	339 'attributes')
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	340 self.feature_importances_ = coefs
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	341 return self
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	342
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	343
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	344 def check_feature_importances(estimator):
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	345 """
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	346 For pipeline object which has no feature_importances_ property,
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	347 this function returns the same comfigured pipeline object with
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	348 attached the last estimator's feature_importances_.
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	349 """
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	350 if estimator.__class__.__module__ == 'sklearn.pipeline':
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	351 pipeline_steps = estimator.get_params()['steps']
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	352 estimator = MyPipeline(pipeline_steps)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	353 elif estimator.__class__.__module__ == 'imblearn.pipeline':
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	354 pipeline_steps = estimator.get_params()['steps']
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	355 estimator = MyimbPipeline(pipeline_steps)
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	356 else:
2ad4c2798be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	357 return estimator

Mercurial > repos > bgruening > sklearn_estimator_attributes

annotate feature_selectors.py @ 1:84ddbf61e107 draft