Recursive Feature Elimination (RFE) by Using Tree Based and Gradient Based Estimators | Machine Learning | KGP Talkie

Published by Srishailam Sri on

Recursive Feature Elimination (RFE)

Playlist: https://www.youtube.com/playlist?list=PLc2rvfiptPSQYzmDIFuq2PqN2n28ZjxDH

As it’s name suggests, it eliminates the features recursively and build a model using remaining attributes then again calculates the model accuracy of the model..Moreover how it do it train the model on all the dataset and it tries to remove the least performing feature and again it trains the model and find out the feature importance among the remaining features and so on it’s kind of recursive so it tries to eliminate the features recursively.

Scikit Learn does most of the heavy lifting just import RFE from sklearn. feature_selection and pass any classifier model to the RFE() method with the number of features to select. Using familiar Scikit Learn syntax, the .fit() method must then be called.

Importing required libraries

import numpy as np
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
%matplotlib inline
from sklearn.model_selection import train_test_split
from sklearn.ensemble import RandomForestClassifier
from sklearn.feature_selection import SelectFromModel
from sklearn.metrics import accuracy_score

As this is the classification problem, we need to load the breast cancer dataset into data variable.

from sklearn.datasets import load_breast_cancer
data = load_breast_cancer()
data.keys()
dict_keys(['data', 'target', 'target_names', 'DESCR', 'feature_names', 'filename'])

Let’s see the description of the breast cancer data:

print(data.DESCR)
.. _breast_cancer_dataset:

Breast cancer wisconsin (diagnostic) dataset
--------------------------------------------

**Data Set Characteristics:**

    :Number of Instances: 569

    :Number of Attributes: 30 numeric, predictive attributes and the class

    :Attribute Information:
        - radius (mean of distances from center to points on the perimeter)
        - texture (standard deviation of gray-scale values)
        - perimeter
        - area
        - smoothness (local variation in radius lengths)
        - compactness (perimeter^2 / area - 1.0)
        - concavity (severity of concave portions of the contour)
        - concave points (number of concave portions of the contour)
        - symmetry 
        - fractal dimension ("coastline approximation" - 1)

        The mean, standard error, and "worst" or largest (mean of the three
        largest values) of these features were computed for each image,
        resulting in 30 features.  For instance, field 3 is Mean Radius, field
        13 is Radius SE, field 23 is Worst Radius.

        - class:
                - WDBC-Malignant
                - WDBC-Benign

    :Summary Statistics:

    ===================================== ====== ======
                                           Min    Max
    ===================================== ====== ======
    radius (mean):                        6.981  28.11
    texture (mean):                       9.71   39.28
    perimeter (mean):                     43.79  188.5
    area (mean):                          143.5  2501.0
    smoothness (mean):                    0.053  0.163
    compactness (mean):                   0.019  0.345
    concavity (mean):                     0.0    0.427
    concave points (mean):                0.0    0.201
    symmetry (mean):                      0.106  0.304
    fractal dimension (mean):             0.05   0.097
    radius (standard error):              0.112  2.873
    texture (standard error):             0.36   4.885
    perimeter (standard error):           0.757  21.98
    area (standard error):                6.802  542.2
    smoothness (standard error):          0.002  0.031
    compactness (standard error):         0.002  0.135
    concavity (standard error):           0.0    0.396
    concave points (standard error):      0.0    0.053
    symmetry (standard error):            0.008  0.079
    fractal dimension (standard error):   0.001  0.03
    radius (worst):                       7.93   36.04
    texture (worst):                      12.02  49.54
    perimeter (worst):                    50.41  251.2
    area (worst):                         185.2  4254.0
    smoothness (worst):                   0.071  0.223
    compactness (worst):                  0.027  1.058
    concavity (worst):                    0.0    1.252
    concave points (worst):               0.0    0.291
    symmetry (worst):                     0.156  0.664
    fractal dimension (worst):            0.055  0.208
    ===================================== ====== ======

    :Missing Attribute Values: None

    :Class Distribution: 212 - Malignant, 357 - Benign

    :Creator:  Dr. William H. Wolberg, W. Nick Street, Olvi L. Mangasarian

    :Donor: Nick Street

    :Date: November, 1995

This is a copy of UCI ML Breast Cancer Wisconsin (Diagnostic) datasets.
https://goo.gl/U2Uwz2

Features are computed from a digitized image of a fine needle
aspirate (FNA) of a breast mass.  They describe
characteristics of the cell nuclei present in the image.

Separating plane described above was obtained using
Multisurface Method-Tree (MSM-T) [K. P. Bennett, "Decision Tree
Construction Via Linear Programming." Proceedings of the 4th
Midwest Artificial Intelligence and Cognitive Science Society,
pp. 97-101, 1992], a classification method which uses linear
programming to construct a decision tree.  Relevant features
were selected using an exhaustive search in the space of 1-4
features and 1-3 separating planes.

The actual linear program used to obtain the separating plane
in the 3-dimensional space is that described in:
[K. P. Bennett and O. L. Mangasarian: "Robust Linear
Programming Discrimination of Two Linearly Inseparable Sets",
Optimization Methods and Software 1, 1992, 23-34].

This database is also available through the UW CS ftp server:

ftp ftp.cs.wisc.edu
cd math-prog/cpo-dataset/machine-learn/WDBC/
X = pd.DataFrame(data = data.data, columns=data.feature_names)
X.head()
mean radiusmean texturemean perimetermean areamean smoothnessmean compactnessmean concavitymean concave pointsmean symmetrymean fractal dimensionworst radiusworst textureworst perimeterworst areaworst smoothnessworst compactnessworst concavityworst concave pointsworst symmetryworst fractal dimension
017.9910.38122.801001.00.118400.277600.30010.147100.24190.0787125.3817.33184.602019.00.16220.66560.71190.26540.46010.11890
120.5717.77132.901326.00.084740.078640.08690.070170.18120.0566724.9923.41158.801956.00.12380.18660.24160.18600.27500.08902
219.6921.25130.001203.00.109600.159900.19740.127900.20690.0599923.5725.53152.501709.00.14440.42450.45040.24300.36130.08758
311.4220.3877.58386.10.142500.283900.24140.105200.25970.0974414.9126.5098.87567.70.20980.86630.68690.25750.66380.17300
420.2914.34135.101297.00.100300.132800.19800.104300.18090.0588322.5416.67152.201575.00.13740.20500.40000.16250.23640.07678

5 rows × 30 columns

Let’s read the target values into variable y .

y = data.target

Let’s go ahead and train the model with train_test_split().

X_train, X_test, y_train, y_test = train_test_split(X,y, test_size = 0.2, random_state = 0)
X_train.shape, X_test.shape
((455, 30), (114, 30))

Feature selection by feature importance of random forest classifier

Now create the selector for RandomForestClassifier() with number of estimators and random state.
And then fit the model with the function fit().

sel = SelectFromModel(RandomForestClassifier(n_estimators=100, random_state=0, n_jobs=-1))
sel.fit(X_train, y_train)
sel.get_support()
array([ True, False,  True,  True, False, False,  True,  True, False, False, False, False, False,  True, False, False, False, False, False, False,  True, False,  True,  True, False, False, False, True, False, False])

Now, we can observe the features with true are selected from the entire features and features with false are not selected we can do it with the function x_train.columns.

X_train.columns
Index(['mean radius', 'mean texture', 'mean perimeter', 'mean area', 'mean smoothness', 'mean compactness', 'mean concavity',  'mean concave points', 'mean symmetry', 'mean fractal dimension', 'radius error', 'texture error', 'perimeter error', 'area error', 'smoothness error', 'compactness error', 'concavity error', 'concave points error', 'symmetry error', 'fractal dimension error', 'worst radius', 'worst texture', 'worst perimeter', 'worst area', 'worst smoothness', 'worst compactness', 'worst concavity',  'worst concave points', 'worst symmetry', 'worst fractal dimension'], dtype='object')

Let’s go ahead and see which features are selected with the following script:

features = X_train.columns[sel.get_support()]
features
Index(['mean radius', 'mean perimeter', 'mean area', 'mean concavity', 'mean concave points', 'area error', 'worst radius', 'worst perimeter', 'worst area', 'worst concave points'],dtype='object')
len(features)
10

Now, get the mean of the selected features with the funcion mean().

np.mean(sel.estimator_.feature_importances_)
0.03333333333333333
sel.estimator_.feature_importances_
array([0.03699612, 0.01561296, 0.06016409, 0.0371452 , 0.0063401 ,
       0.00965994, 0.0798662 , 0.08669071, 0.00474992, 0.00417092,
       0.02407355, 0.00548033, 0.01254423, 0.03880038, 0.00379521,
       0.00435162, 0.00452503, 0.00556905, 0.00610635, 0.00528878,
       0.09556258, 0.01859305, 0.17205401, 0.05065305, 0.00943096,
       0.01565491, 0.02443166, 0.14202709, 0.00964898, 0.01001304])

From this we can observe that the features which have more than mean have more importance and whic has less than mean are less importance.

Let’s go ahead and select the features. First we will train the model from the following code. So have a look at this script.

X_train_rfc = sel.transform(X_train)
X_test_rfc = sel.transform(X_test)

Here, we have two datasets those are training dataset and testing dataset. Since we have these two let’s move further and write an algorithm for random forest.

def run_randomForest(X_train, X_test, y_train, y_test):
    clf = RandomForestClassifier(n_estimators=100, random_state=0, n_jobs=-1)
    clf.fit(X_train, y_train)
    y_pred = clf.predict(X_test)
    print('Accuracy: ', accuracy_score(y_test, y_pred))

Then, we are going to call the method and there we pass dataset after the feature selection.

%%time
run_randomForest(X_train_rfc, X_test_rfc, y_train, y_test)
Accuracy:  0.9473684210526315
Wall time: 250 ms

Let’s see the accuracy on the original dataset from the following script.

%%time
run_randomForest(X_train, X_test, y_train, y_test)
Accuracy:  0.9649122807017544
Wall time: 256 ms

Here, we can observe we are getting almost 2% less than original dataset with decreasing features from 30 to 10.

Recursive Feature Elimination (RFE)

Let’s go ahead with Recursive Feature Elimination(RFE) for the feature selection. Have a look at following code.

from sklearn.feature_selection import RFE
sel = RFE(RandomForestClassifier(n_estimators=100, random_state=0, n_jobs=-1), n_features_to_select = 15)
sel.fit(X_train, y_train)
RFE(estimator=RandomForestClassifier(bootstrap=True, class_weight=None, criterion='gini',
            max_depth=None, max_features='auto', max_leaf_nodes=None,
            min_impurity_decrease=0.0, min_impurity_split=None,
            min_samples_leaf=1, min_samples_split=2,
            min_weight_fraction_leaf=0.0, n_estimators=100, n_jobs=-1,
            oob_score=False, random_state=0, verbose=0, warm_start=False),
  n_features_to_select=15, step=1, verbose=0)

Now we will see which features have been selected and which are not selected.

sel.get_support()
array([ True,  True,  True,  True, False, False,  True,  True, False,
       False, False, False, False,  True, False, False, False, False,
       False, False,  True,  True,  True,  True,  True, False,  True,
        True,  True, False])
features = X_train.columns[sel.get_support()]
features
Index(['mean radius', 'mean texture', 'mean perimeter', 'mean area',
       'mean concavity', 'mean concave points', 'area error', 'worst radius',
       'worst texture', 'worst perimeter', 'worst area', 'worst smoothness',
       'worst concavity', 'worst concave points', 'worst symmetry'],
      dtype='object')

Let’s see the number of features from the following code.

len(features)
15

Let’s get training dataset and testing dataset for RFE.

X_train_rfe = sel.transform(X_train)
X_test_rfe = sel.transform(X_test)
%%time
run_randomForest(X_train_rfe, X_test_rfe, y_train, y_test)
Accuracy:  0.9736842105263158
Wall time: 251 ms
%%time
run_randomForest(X_train, X_test, y_train, y_test)
Accuracy:  0.9649122807017544
Wall time: 254 ms

Here, we can observe 1% of accuracy we have achieved with optimization of 15 features.

Feature selection by GradientBoost Tree Importance

Imporing requires library

from sklearn.ensemble import GradientBoostingClassifier

Let’s go ahead and train the model with gradient boost algorithm with the following code.

sel = RFE(GradientBoostingClassifier(n_estimators=100, random_state=0), n_features_to_select = 12)
sel.fit(X_train, y_train)
RFE(estimator=GradientBoostingClassifier(criterion='friedman_mse', init=None,
              learning_rate=0.1, loss='deviance', max_depth=3,
              max_features=None, max_leaf_nodes=None,
              min_impurity_decrease=0.0, min_impurity_split=None,
              min_samples_leaf=1, min_sampl...      subsample=1.0, tol=0.0001, validation_fraction=0.1,
              verbose=0, warm_start=False),
  n_features_to_select=12, step=1, verbose=0)

Now we will observe which features are selected and which are not selected.

sel.get_support()
array([False,  True, False, False,  True, False, False,  True,  True,
       False, False, False, False,  True, False, False,  True, False,
       False, False,  True,  True,  True,  True, False, False,  True,
        True, False, False])
features = X_train.columns[sel.get_support()]
features
Index(['mean texture', 'mean smoothness', 'mean concave points',
       'mean symmetry', 'area error', 'concavity error', 'worst radius',
       'worst texture', 'worst perimeter', 'worst area', 'worst concavity',
       'worst concave points'],
      dtype='object')
len(features)
12
X_train_rfe = sel.transform(X_train)
X_test_rfe = sel.transform(X_test)
%%time
run_randomForest(X_train_rfe, X_test_rfe, y_train, y_test)
Accuracy:  0.9736842105263158
Wall time: 253 ms
%%time
run_randomForest(X_train, X_test, y_train, y_test)
Accuracy:  0.9649122807017544
Wall time: 253 ms

Get the accuracies of the model for various selected features from the following code.

for index in range(1, 31):
    sel = RFE(GradientBoostingClassifier(n_estimators=100, random_state=0), n_features_to_select = index)
    sel.fit(X_train, y_train)
    X_train_rfe = sel.transform(X_train)
    X_test_rfe = sel.transform(X_test)
    print('Selected Feature: ', index)
    run_randomForest(X_train_rfe, X_test_rfe, y_train, y_test)
    print()
Selected Feature:  1
Accuracy:  0.8771929824561403

Selected Feature:  2
Accuracy:  0.9035087719298246

Selected Feature:  3
Accuracy:  0.9649122807017544

Selected Feature:  4
Accuracy:  0.9736842105263158

Selected Feature:  5
Accuracy:  0.9649122807017544

Selected Feature:  6
Accuracy:  0.9912280701754386

Selected Feature:  7
Accuracy:  0.9736842105263158

Selected Feature:  8
Accuracy:  0.9649122807017544

Selected Feature:  9
Accuracy:  0.9736842105263158

Selected Feature:  10
Accuracy:  0.956140350877193

Selected Feature:  11
Accuracy:  0.956140350877193

Selected Feature:  12
Accuracy:  0.9736842105263158

Selected Feature:  13
Accuracy:  0.956140350877193

Selected Feature:  14
Accuracy:  0.9649122807017544

Selected Feature:  15
Accuracy:  0.9649122807017544

Selected Feature:  16
Accuracy:  0.9824561403508771

Selected Feature:  17
Accuracy:  0.9649122807017544

Selected Feature:  18
Accuracy:  0.9736842105263158

Selected Feature:  19
Accuracy:  0.9649122807017544

Selected Feature:  20
Accuracy:  0.956140350877193

Selected Feature:  21
Accuracy:  0.9736842105263158

Selected Feature:  22
Accuracy:  0.9824561403508771

Selected Feature:  23
Accuracy:  0.9649122807017544

Selected Feature:  24
Accuracy:  0.9649122807017544

Selected Feature:  25
Accuracy:  0.9736842105263158

Selected Feature:  26
Accuracy:  0.9736842105263158

Selected Feature:  27
Accuracy:  0.9649122807017544

Selected Feature:  28
Accuracy:  0.9649122807017544

Selected Feature:  29
Accuracy:  0.9649122807017544

Selected Feature:  30
Accuracy:  0.9649122807017544

We are getting almost same accuracy with less number of features also so why should we include all the features. So we will select features which are important.

Now check the accuarcy for 6 number of selected features. Let’s see the following code.

sel = RFE(GradientBoostingClassifier(n_estimators=100, random_state=0), n_features_to_select = 6)
sel.fit(X_train, y_train)
X_train_rfe = sel.transform(X_train)
X_test_rfe = sel.transform(X_test)
print('Selected Feature: ', 6)
run_randomForest(X_train_rfe, X_test_rfe, y_train, y_test)
print()
Selected Feature:  6
Accuracy:  0.9912280701754386

Here, we got 99.12% with 6 features.

Let’s go ahead and see what are those features from the following code.

features = X_train.columns[sel.get_support()]
features
Index(['mean concave points', 'area error', 'worst texture', 'worst perimeter',
       'worst area', 'worst concave points'],
      dtype='object')

Let’s see the accuracy of the model for random forest classifier with changing various number of features which are selected from the following script:

for index in range(1, 31):
    sel = RFE(RandomForestClassifier(n_estimators=100, random_state=0, n_jobs=-1), n_features_to_select = index)
    sel.fit(X_train, y_train)
    X_train_rfe = sel.transform(X_train)
    X_test_rfe = sel.transform(X_test)
    print('Selected Feature: ', index)
    run_randomForest(X_train_rfe, X_test_rfe, y_train, y_test)
    print()
Selected Feature:  1
Accuracy:  0.8947368421052632

Selected Feature:  2
Accuracy:  0.9298245614035088

Selected Feature:  3
Accuracy:  0.9473684210526315

Selected Feature:  4
Accuracy:  0.9649122807017544

Selected Feature:  5
Accuracy:  0.9649122807017544

Selected Feature:  6
Accuracy:  0.956140350877193

Selected Feature:  7
Accuracy:  0.956140350877193

Selected Feature:  8
Accuracy:  0.9649122807017544

Selected Feature:  9
Accuracy:  0.9736842105263158

Selected Feature:  10
Accuracy:  0.9736842105263158

Selected Feature:  11
Accuracy:  0.9649122807017544

Selected Feature:  12
Accuracy:  0.9736842105263158

Selected Feature:  13
Accuracy:  0.9649122807017544

Selected Feature:  14
Accuracy:  0.9736842105263158

Selected Feature:  15
Accuracy:  0.9736842105263158

Selected Feature:  16
Accuracy:  0.9736842105263158

Selected Feature:  17
Accuracy:  0.9824561403508771

Selected Feature:  18
Accuracy:  0.9649122807017544

Selected Feature:  19
Accuracy:  0.9649122807017544

Selected Feature:  20
Accuracy:  0.9736842105263158

Selected Feature:  21
Accuracy:  0.9736842105263158

Selected Feature:  22
Accuracy:  0.9736842105263158

Selected Feature:  23
Accuracy:  0.9649122807017544

Selected Feature:  24
Accuracy:  0.9824561403508771

Selected Feature:  25
Accuracy:  0.956140350877193

Selected Feature:  26
Accuracy:  0.956140350877193

Selected Feature:  27
Accuracy:  0.9649122807017544

Selected Feature:  28
Accuracy:  0.9649122807017544

Selected Feature:  29
Accuracy:  0.9649122807017544

Selected Feature:  30
Accuracy:  0.9649122807017544


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