Python sklearn - how to calculate p-values

Question

This is probably a simple question but I am trying to calculate the p-values for my features either using classifiers for a classification problem or regressors for regression. Could someone suggest what is the best method for each case and provide sample code? I want to just see the p-value for each feature rather than keep the k best / percentile of features etc as explained in the documentation.

Thank you

Answer 1

You can use statsmodels

import statsmodels.api as sm
logit_model=sm.Logit(y_train,X_train)
result=logit_model.fit()
print(result.summary())

The results would be something like this

                           Logit Regression Results                           
==============================================================================
Dep. Variable:                      y   No. Observations:               406723
Model:                          Logit   Df Residuals:                   406710
Method:                           MLE   Df Model:                           12
Date:                Fri, 12 Apr 2019   Pseudo R-squ.:                0.001661
Time:                        16:48:45   Log-Likelihood:            -2.8145e+05
converged:                      False   LL-Null:                   -2.8192e+05
                                        LLR p-value:                8.758e-193
==============================================================================
                 coef    std err          z      P>|z|      [0.025      0.975]
------------------------------------------------------------------------------
x1            -0.0037      0.003     -1.078      0.281      -0.010       0.003

Answer 2

Just run the significance test on X, y directly. Example using 20news and chi2:

>>> from sklearn.datasets import fetch_20newsgroups_vectorized
>>> from sklearn.feature_selection import chi2
>>> data = fetch_20newsgroups_vectorized()
>>> X, y = data.data, data.target
>>> scores, pvalues = chi2(X, y)
>>> pvalues
array([  4.10171798e-17,   4.34003018e-01,   9.99999996e-01, ...,
         9.99999995e-01,   9.99999869e-01,   9.99981414e-01])