Greg,
Thank you.
Questions :)
1) I'm getting the following error message:
nms.remove('MolecularFormula')
ValueError: list.remove(x): x not in list
when I check the list of descriptor names indeed I don't see
MolecularFormula,
2) I'm getting the warning message:
[11:27:24] WARNING: The AvailDescriptors module is deprecated. Please
switch to using the Descriptors module.
3) Does the following means that each descriptors is effectively
binarized?
# number of possible values of each descriptor:
nPossible = [0]+[2]*ndescrs+[2]
4) Is this the correct way to build RandomForest? The wiki page sadly
stops at "bag of decision trees", I tried to extrapolate example from
RandomForest for binary fingerprint:
cmp.Grow(pts,attrs=attrs,nPossibleVals=nPossible,nTries=100,randomDescriptors=20,
buildDriver=CrossValidate.CrossValidationDriver,
treeBuilder=QuantTreeBoot,needsQuantization=False,nQuantBounds=boundsPerVar,maxDepth=100)
I'm specifically concerned that needsQuantization=False (should it be
True in this case?), also maxDepth parameter - from what I understand
the randomForest trees should not be pruned, why is there maxDepth
parameter at all?
5) How do I suppress output of
Cycle: 0
Cycle: 10
...
?
6) The wiki seems to stop abruptly at
"Composite models can be also be pickled to disk and then reloaded to
classify new points:"
7) For some strange reason the model i build in this way predicts
nothing but zeros! The previous model - with fingerprints was predicting
something at least...
Do I still use ClassifyExample similar to as before?
cmp.ClassifyExample([i]+list(test_descrs[i])+[act])
Best regards,
Igor
On Thu, 2011-05-05 at 05:24 -0400, Greg Landrum wrote:
> Igor,
>
> On Tue, May 3, 2011 at 6:03 PM, Igor Filippov <[email protected]>
> wrote:
> > Questions:
> >
> > 1) How can I use real-valued descriptors, such as MOE-like descriptors
> > for such modeling? Do I need to pick descriptors one-by-one or is there
> > something like "AllDescriptors" which computes all of them in one pass?
>
> An initial version of this is now here:
> http://code.google.com/p/rdkit/wiki/BuildingModelsUsingDescriptors1
>
> -greg
>
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