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I want to run a feature selection study to select only the most important features, before running a machine learning classification. My data is 30,000 x 17 (Observed objects x Features). I use the R implementation of Boruta, with default parameters. My results is: all my 17 features are green (confirmed as "important"). It is suspicious because it is likely that some are not and should be dropped. When I only use a sub-set of observations (eg 100 randomly chosen observations among 30,000), the Boruta algo then changes drastically: 6 features are red (unimportant) and 11 are green (important). Why do I have such different results, is it overfitting? How should I perform to make sure I correctly identify the less and most relevant features among the initial set of 17?

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  • $\begingroup$ Have you studied the features yourself? What does subject matter expertise tell you? 17 features is not so many that you need an automated procedure, so perhaps you have other requirements that would be helpful to help answer the question? $\endgroup$
    – Wayne
    Aug 25 '16 at 13:07
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I had similar experience as yours with real-life data. Boruta does not give you any guarantees, you should treat it's output rather as a "suggestion", then definite answer.

This was even discussed by Kursa and Rudnicki (2010) in their paper about Boruta:

One should note that the Boruta is a heuristic procedure designed to find all relevant attributes, including weakly relevant attributes. Following Nilsson et al. (2007), we say that attribute is weakly important when one can find a subset of attributes among which this attribute is not redundant. The heuristic used in Boruta implies that the attributes which are significantly correlated with the decision variables are relevant, and the significance here means that correlation is higher than that of the randomly generated attributes.

You could try also other methods, e.g. entropy-based (check FSelectorRcpp project).

Feature selection algorithms are far from perfect. Marcin Kosiński compared performance of three different methods and got three different solutions from each.

enter image description here

(source: r-addict.com)


Kursa, M.B., & Rudnicki, W.R. (2010). Feature selection with the Boruta package. Journal of Statistical Software, 36(11), 1-12.

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  • $\begingroup$ Downvoted unintentionally $\endgroup$
    – drake
    Oct 17 '18 at 20:11
  • $\begingroup$ @drake nothing can be done. For the future, you can undo vote within 5 minutes from voting, or after question or answer that you voted on has been edited, see meta.stackexchange.com/questions/75339/… $\endgroup$
    – Tim
    Oct 17 '18 at 20:22
  • $\begingroup$ I've just realized it. I was in my mobile last night when I must tapped by mistake. I apologize. If you edit your answer, I will undo my downvote. $\endgroup$
    – drake
    Oct 17 '18 at 20:30
  • $\begingroup$ @drake no bad feelings $\endgroup$
    – Tim
    Oct 17 '18 at 20:33

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