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. [bdge...@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.fi...@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. [bdge...@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 > > > IMPORTANT WARNING: The information in this message (and the documents > attached to it, if any) is confidential and may be legally privileged. It is > intended solely for the addressee. Access to this message by anyone else is > unauthorized. If you are not the intended recipient, any disclosure, copying, > distribution or any action taken, or omitted to be taken, in reliance on it > is prohibited and may be unlawful. If you have received this message in > error, please delete all electronic copies of this message (and the documents > attached to it, if any), destroy any hard copies you may have created and > notify me immediately by replying to this email. Thank you. > > Geisinger Health System utilizes an encryption process to safeguard Protected > Health Information and other confidential data contained in external e-mail > messages. If email is encrypted, the recipient will receive an e-mail > instructing them to sign on to the Geisinger Health System Secure E-mail > Message Center to retrieve the encrypted e-mail. > >
