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From "Miller, Timothy" <Timothy.Mil...@childrens.harvard.edu>
Subject Re: Scaling cTakes
Date Tue, 09 Dec 2014 19:57:04 GMT
Brandon, depending on your use case you may be able to remove the
dependency parser and constituency parser from the pipeline. This might
also reduce the memory footprint substantially and make multi-jvm
pipelines possible.
Tim


On 12/09/2014 01:28 PM, Finan, Sean wrote:
> Hi Brandon,
>
> You are welcome.  I was hoping that you'd get the note processing time down to under
a second with the different lookup, but I guess not.  I think that any optimization from here
really depends upon what information you want to extract from the notes.
>
> Sean
> ________________________________________
> From: Geise, Brandon D. [bdgeise@geisinger.edu]
> Sent: Tuesday, December 09, 2014 9:13 AM
> To: dev@ctakes.apache.org
> Subject: RE: Scaling cTakes
>
> Thanks again Sean for the advice.  Just by changing the pipeline to use the fast dictionary
led to quadrupling the processing speed.  Any other suggestions on performance tuning would
be great!
>
> Thanks,
> Brandon
>
> -----Original Message-----
> From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
> Sent: Friday, December 05, 2014 1:14 PM
> To: dev@ctakes.apache.org
> Subject: RE: Scaling cTakes
>
> Hi Brandon,
>
> It sounds like you've got  a decent pipeline set up.  To increase the speed you could
try swapping out use of ctakes-dictionary-lookup with ctakes-dictionary-lookup-fast in the
AE.  Check ctakes-clinical-pipeline/desc/[ae]/AggregatePlaintextFastUMLSProcessor.xml for
an example.  As for the CASPool, I don't think that it will make any difference for cTakes.
>
> Sean
> ________________________________________
> From: Geise, Brandon D. [bdgeise@geisinger.edu]
> Sent: Friday, December 05, 2014 12:40 PM
> To: dev@ctakes.apache.org
> Subject: Scaling cTakes
>
> Hi,
>
> I'm new to cTakes and the UIMA framework.  I've read most of the UIMA documentation and
was able to take the BagofCUIGenerator example and modify to read notes from a DB, process
using the UMLS AE in the clinical-pipeline using a local DB version of UMLS, and output the
CUIs to a DB.  However, the problem I'm having is it's extremely slow; ~3.5-4 notes a minute.
 I was hoping I could get some hints or advice on speeding the process up.  I read there's
a patch for LVG, but wasn't quite sure how to implement.  Also from testing using the CPE
GUI, I don't notice any different in processing time by adjusting the CASPool setting.  Some
advice on the CASPool would be appreciated also.
>
> Thanks,
> Brandon
>
>
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