Scikit-learn feature selection for regression data

Question

I am trying to apply a univariate feature selection method using the Python module scikit-learn to a regression (i.e. continuous valued response values) dataset in svmlight format.

I am working with scikit-learn version 0.11.

I have tried two approaches - the first of which failed and the second of which worked for my toy dataset but I believe would give meaningless results for a real dataset.

I would like advice regarding an appropriate univariate feature selection approach I could apply to select the top N features for a regression dataset. I would either like (a) to work out how to make the f_regression function work or (b) to hear alternative suggestions.

The two approaches mentioned above:

1. I tried using sklearn.feature_selection.f_regression(X,Y).

This failed with the following error message: "TypeError: copy() takes exactly 1 argument (2 given)"

1. I tried using chi2(X,Y). This "worked" but I suspect this is because the two response values 0.1 and 1.8 in my toy dataset were being treated as class labels? Presumably, this would not yield a meaningful chi-squared statistic for a real dataset for which there would be a large number of possible response values and the number in each cell [with a particular response value and value for the attribute being tested] would be low?

Please find my toy dataset pasted into the end of this message.

The following code snippet should give the results I describe above.

from sklearn.datasets import load_svmlight_file

X_train_data, Y_train_data = load_svmlight_file(svmlight_format_train_file) #i.e. change this to the name of my toy dataset file

from sklearn.feature_selection import SelectKBest
featureSelector = SelectKBest(score_func="one of the two functions I refer to above",k=2) #sorry, I hope this message is clear
featureSelector.fit(X_train_data,Y_train_data)
print [1+zero_based_index for zero_based_index in list(featureSelector.get_support(indices=True))] #This should print the indices of the top 2 features

Thanks in advance.

Richard

Contents of my contrived svmlight file - with additional blank lines inserted for clarity:

1.8 1:1.000000 2:1.000000 4:1.000000 6:1.000000#mA

1.8 1:1.000000 2:1.000000#mB

0.1 5:1.000000#mC

1.8 1:1.000000 2:1.000000#mD

0.1 3:1.000000 4:1.000000#mE

0.1 3:1.000000#mF

1.8 2:1.000000 4:1.000000 5:1.000000 6:1.000000#mG

1.8 2:1.000000#mH

Answer 1

As larsmans noted, chi2 cannot be used for feature selection with regression data.

Upon updating to scikit-learn version 0.13, the following code selected the top two features (according to the f_regression test) for the toy dataset described above.

def f_regression(X,Y):
   import sklearn
   return sklearn.feature_selection.f_regression(X,Y,center=False) #center=True (the default) would not work ("ValueError: center=True only allowed for dense data") but should presumably work in general

from sklearn.datasets import load_svmlight_file

X_train_data, Y_train_data = load_svmlight_file(svmlight_format_train_file) #i.e. change this to  the name of my toy dataset file

from sklearn.feature_selection import SelectKBest
featureSelector = SelectKBest(score_func=f_regression,k=2)
featureSelector.fit(X_train_data,Y_train_data)
print [1+zero_based_index for zero_based_index in list(featureSelector.get_support(indices=True))]