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From: "Miller, Timothy" <Timothy.Miller@childrens.harvard.edu>
To: "dev@ctakes.apache.org" <dev@ctakes.apache.org>
Subject: Re: Scaling cTakes
Thread-Topic: Scaling cTakes
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Date: Tue, 9 Dec 2014 19:57:04 +0000
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Brandon, depending on your use case you may be able to remove the=0A=
dependency parser and constituency parser from the pipeline. This might=0A=
also reduce the memory footprint substantially and make multi-jvm=0A=
pipelines possible.=0A=
Tim=0A=
=0A=
=0A=
On 12/09/2014 01:28 PM, Finan, Sean wrote:=0A=
> Hi Brandon,=0A=
>=0A=
> You are welcome.  I was hoping that you'd get the note processing time do=
wn to under a second with the different lookup, but I guess not.  I think t=
hat any optimization from here really depends upon what information you wan=
t to extract from the notes.=0A=
>=0A=
> Sean=0A=
> ________________________________________=0A=
> From: Geise, Brandon D. [bdgeise@geisinger.edu]=0A=
> Sent: Tuesday, December 09, 2014 9:13 AM=0A=
> To: dev@ctakes.apache.org=0A=
> Subject: RE: Scaling cTakes=0A=
>=0A=
> Thanks again Sean for the advice.  Just by changing the pipeline to use t=
he fast dictionary led to quadrupling the processing speed.  Any other sugg=
estions on performance tuning would be great!=0A=
>=0A=
> Thanks,=0A=
> Brandon=0A=
>=0A=
> -----Original Message-----=0A=
> From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]=0A=
> Sent: Friday, December 05, 2014 1:14 PM=0A=
> To: dev@ctakes.apache.org=0A=
> Subject: RE: Scaling cTakes=0A=
>=0A=
> Hi Brandon,=0A=
>=0A=
> It sounds like you've got  a decent pipeline set up.  To increase the spe=
ed you could try swapping out use of ctakes-dictionary-lookup with ctakes-d=
ictionary-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.=0A=
>=0A=
> Sean=0A=
> ________________________________________=0A=
> From: Geise, Brandon D. [bdgeise@geisinger.edu]=0A=
> Sent: Friday, December 05, 2014 12:40 PM=0A=
> To: dev@ctakes.apache.org=0A=
> Subject: Scaling cTakes=0A=
>=0A=
> Hi,=0A=
>=0A=
> I'm new to cTakes and the UIMA framework.  I've read most of the UIMA doc=
umentation 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 u=
sing 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 h=
oping 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 app=
reciated also.=0A=
>=0A=
> Thanks,=0A=
> Brandon=0A=
>=0A=
>=0A=
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nd notify me immediately by replying to this email. Thank you.=0A=
>=0A=
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