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From "Geise, Brandon D." <bdge...@geisinger.edu>
Subject RE: Scaling cTakes
Date Tue, 09 Dec 2014 14:11:32 GMT
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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