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I'm working with a dataset of approximately 150,000 observations and 50 features, using SVM for the final model. To trim down the feature count, I decided to look into using RF so SVM optimization doesn't take too long. I'm currently using the TreeBagger implementation in Matlab and had a few questions.

  1. When investigating feature importances, should the RF be tuned for the highest CV performance? Does the accuracy of the model play into the accuracy of the reported predictor importances?
  2. What is the best way to deal with one of two correlated feature having it's importance underreported? Can this be cancelled out by training the RF multiple times and averaging the feature rankings?
  3. There doesn't seem to be any way to manually select split criterion in TreeBagger, nor could I find any documentation on what the default is. Does anyone know? If not, would it be safe to assume it's using Gini?
  4. How do the feature importances from TreeBagger compare to those generated by Matlab's fitensemble? This has support for bagging and different boosting algorithms, as well as different split criteria. But, as far as I know, these don't invoke Breiman's RF algorithm. The only Matlab function which does is TreeBagger, when specifying a number of features to sample. Please correct me if I'm wrong. As it stands, fitensemble is looking more attractive due to more options and better documentation.
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  1. What you describe would be one approach. For classification, TreeBagger by default randomly selects sqrt(p) predictors for each decision split (setting recommended by Breiman). Depending on your data and tree depth, some of your 50 predictors could be considered fewer times than others for splits just because they get unlucky. This is why for estimation of predictor importance I usually set 'nvartosample' to 'all'. This gives a model with somewhat lower accuracy ensures that every predictor is sensibly included.

  2. If you run TreeBagger at the default settings, this is generally not a problem. For example, if you have two strongly correlated features and one of them is included in the 7 predictors selected at random for a split, the other is likely not included in these 7. If you want to adopt my scheme by inspecting all predictors for each split, use surrogate splits by setting 'surrogate' to 'all'. Training will take longer but you will have full information about predictor importance, irrespective of other predictors, associations among predictors.

  3. The TreeBagger doc and help have this statement at the bottom:

"In addition to the optional arguments above, this method accepts all optional fitctree and fitrtree arguments with the exception of 'minparent'. Refer to the documentation for fitctree and fitrtree for more detail."

Look at the doc for fitctree and fitrtree.

  1. fitensemble for the 'Bag' method implements Breiman's random forest with the same default settings as in TreeBagger. You can change the number of features to sample to whatever you like; just read the doc for templateTree. The object returned by fitensemble has a predictorImportance method which shows cumulative gains due to splits on each predictor. The TreeBagger's equivalent of that the DeltaCriterionDecisionSplit property (or something like that). In addition, TreeBagger has 3 OOBPermuted properties that are alternative measures of predictor importance.
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  • $\begingroup$ One more question with regards to Question 1. I was under the impression that if all predictors are sampled per split it is not truly an RF because we are not examining a subset of the features. From the documentation on TreeBagger, under the 'NumPredictorsToSample' says the same thing. Does sampling all predictors hurt the model accuracy but still return equally valid predictor importances? $\endgroup$
    – Thorbjorn Henriksen
    Dec 5, 2015 at 2:40
  • $\begingroup$ I don't agree with 1). Why would a less accurate (i.e. overfit) model have more accurate feature importances? Isn't some of that feature importance allocated to parts of the model that overfit? The feature importances is a model dependent measure, it would better be called "model participation", the name is a very unfortunate choice. $\endgroup$
    – Matthew Drury
    Aug 27, 2016 at 20:06
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Yes, sampling all predictors would typically hurt the model accuracy. It is predictor importance values we are after, not accuracy. Either way, this is a heuristic procedure. Using random forest to estimate predictor importance for SVM can only give you a notion of what predictors could be important. One can construct datasets in which RF fails to identify predictors that are important for SVM (false negatives) and the other way around (false positives). If you want to have more trust in your predictor selection procedure, do sequential backward elimination using SVM as the underlying learner.

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