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July 2007

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Subject:
From:
William Shannon <[log in to unmask]>
Reply To:
Classification, clustering, and phylogeny estimation
Date:
Mon, 2 Jul 2007 07:18:55 -0700
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Here is a simple experiment that can be done easily in R.

1. Simulate a dataset consisting of 1,000 data points and 900 covariates where each covariate value comes from a normal(0,1) (or any other distribution) -- everything independent from each other.

2. Randomly assign the first 500 data points to group 1 and the second 500 data points to group 2

3. Fit your favorite discriminator to predict these two groups and see how well you can with random data.

4. After identifying the best fitting model removes those covariates and redo the analysis.


I predict you will be able to discriminate the two groups well through several iterations of this procedure.  If we can discriminate well with noise then we should be cautious about saying that in the real problem the discriminator is real and not noise.

Bill
 

Peter Flom <[log in to unmask]> wrote:     RE: Tree software     William Shannon  wrote
 <<<
 I am unaware of SPINA and am downloading party now to look into that software.  I generally have used rpart (because Salford is so expensive) but have never dealt with this many variables with rpart.
 >>>
 
 party is very cool.  Hothorn has a couple papers where he gets into the theory.  The essential idea is to try to provide significance testing for trees.
 
 <<<
 Do you have anyway to reduce the number of covariates before partitioning?  I would be concerned about the curse of dimensionality with 900 variables and 1,000 data points.  It would be very easy to find excellent classifiers based on noise.  Some suggest that a split data set (train on one subset randomly selected from the 1,000 data points and test on the remaining) overcomes this.  However, if X by chance due to the curse of dimensionality discriminates well than it will discriminate well in both the training and test data sets.
 
 Can you reduce the 900 covariates by PCA or perhaps use an upfront stepwise linear discriminant analysis with a high P value threshold to retain the covariate (say p = .2).  We have a paper where we proposed and tested a genetic algorithm to reduce the number of variables in microarray data that I can send you in a couple of weeks when I get back to St. Louis.  It is being published in Sept. in the Interface Proceedings.
 >>>
 
 We can reduce the number of variables to about 500 relatively easily.  Further reduction is hard.  We don't want to use principal components because our goal is to get a method that uses relatively few of the independent variables, and PCA makes linear combinations of all the variables. 
 
 I am not sure I follow your point about a variable discriminating well due to the curse of dimensionality even on the test data.  I had been in the 'some suggest' camp, which, on intuition, feels right.  But if it's not right, that would be good to know.
 
 Thanks for our help, and I look forward to reading your paper
 
 
  Peter L. Flom, PhD
  Brainscope, Inc.
  212 263 7863 (MTW)
  212 845 4485 (Th)
  917 488 7176 (F)
 
 
  
  
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