Re: [Rdkit-discuss] ML question
Dear Greg,
> > # actual predicion
> >
> > prediction_dictionary = {}
> > for x in cpds_w_descr:
> > pred,conf=cmp.ClassifyExample(x[1:])
> > NAME=x[0]
> > prediction_dictionary[NAME]=pred,conf
> > i+=1
> > for mol in cpds:
> > mol_name = mol.GetProp('_Name')
> > mol.SetProp('prediction',str(prediction_dictionary[mol_name][0]))
> > mol.SetProp('prediction_confidence',str(prediction_dictionary
> > [mol_name][1]))
> > testset_pred.write(mol)
>
> This is just a guess, but it looks like you're passing ClassifyExample
> a shorter vector for each point than what you passed to Grow.
> Does it work if you do: pred,conf=cmp.ClassifyExample(x)?
>
> -greg
wonderful, thanks for this hint!
i was too much stuck in the code...
cheers,
paul
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Re: [Rdkit-discuss] ML question
Hi Paul,
On Fri, Aug 24, 2012 at 1:57 PM, wrote:
>
>
> please find below a code snippet for a 2class model.
> The confusion matrix looks fine.
>
> But when re-applying the model (for test purposes), I end up with
> predictions that ony give consistently ONE class.
>
>
>
> # descriptor calculation etc...
> cmp.Grow(cpds_w_descr,attrs=attrs,nPossibleVals=nPossible,nTries=10,\
> buildDriver=CrossValidate.CrossValidationDriver,\
> treeBuilder=QuantTreeBoot,
> needsQuantization=False,nQuantBounds=boundsPerVar, maxDepth=3)
>
>
> # actual predicion
>
> prediction_dictionary = {}
> for x in cpds_w_descr:
> pred,conf=cmp.ClassifyExample(x[1:])
> NAME=x[0]
> prediction_dictionary[NAME]=pred,conf
> i+=1
> for mol in cpds:
> mol_name = mol.GetProp('_Name')
> mol.SetProp('prediction',str(prediction_dictionary[mol_name][0]))
> mol.SetProp('prediction_confidence',str(prediction_dictionary
> [mol_name][1]))
> testset_pred.write(mol)
This is just a guess, but it looks like you're passing ClassifyExample
a shorter vector for each point than what you passed to Grow.
Does it work if you do: pred,conf=cmp.ClassifyExample(x)?
-greg
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will include endpoint security, mobile security and the latest in malware
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