Re: [VOTE] Release Apache cTAKES 3.2.1 (rc2)
Yep, sounds like a plan. +1 from me! Tim On 12/05/2014 11:20 AM, Chen, Pei wrote: Thanks for testing Tim. I don't think AggregatePlaintextProcessor.xml (w/o UMLS) does much actually. We can fix the descriptor xml in the next patch irrespective [1]. I updated the documentation[2] to say - if you want something simple to test, try the SentencesAndTokensAggregate.xml in the meantime. - default to AggregatePlaintextFastUMLSProcessor.xml - made UMLS 'Recommended' rather than 'Optional'. Otherwise, you'll just have a dictionary with 5 dummy terms. [1] https://issues.apache.org/jira/browse/CTAKES-340 [2] https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2 -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Thursday, December 04, 2014 9:34 AM To: dev@ctakes.apache.org Subject: Re: [VOTE] Release Apache cTAKES 3.2.1 (rc2) I downloaded the src and bin and did the following (in xubuntu): * Compiled src from command line using mvn compile * Ran fast dictionary pipeline in src package (using mvn compile -P runCVD) -- required setting umls user password in dictionary descriptor * Extracted resources into bin release and successfully ran runCVD.sh -- require setting umls user password in dictionary descriptor There was one issue with the non-UMLS pipeline -- was missing a close bracket in the descriptor xml. Added it back in and it worked fine. Is there a way to just patch that file w/o re-doing the whole RC? Tim On 12/01/2014 03:21 PM, Pei Chen wrote: This is a call for a vote on releasing the following candidate (rc2) as Apache cTAKES 3.2.1. The major changes include: - New optional Temporal component (Time + Event Relationships models now available) - Other bug fixes/enhancements from Jira I manually downloaded the bin as well as resources and tried the CVD with the AggregatePlaintextFastUMLSProcessor.xml and AggregatePlaintextUMLSProcessor.xml. Would be great if folks have time to test/verify especially if you opened any of the Jira's below to ensure the bugs have been fixed/integrated. For more detailed information on the changes/release notes, please visit: https://issues.apache.org/jira/secure/ReleaseNote.jspa?projectId=12313621version=12326778 The release was made using the cTAKES release process documented here: http://ctakes.apache.org/ctakes-release-guide.html The candidate is available at: https://dist.apache.org/repos/dist/dev/ctakes/ctakes-3.2.1-rc2/apache-ctakes-3.2.1-src.tar.gz /.zip The tag to be voted on: http://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.2.1-rc2 The MD5 checksum of the tarball can be found at: https://dist.apache.org/repos/dist/dev/ctakes/ctakes-3.2.1-rc2/apache-ctakes-3.2.1-src.tar.gz.md5 /.zip.md5 The signature of the tarball can be found at: https://dist.apache.org/repos/dist/dev/ctakes/ctakes-3.2.1-rc2/apache-ctakes-3.2.1-src.tar.gz.asc /.zip.asc Apache cTAKES' KEYS file, containing the PGP keys used to sign the release: https://dist.apache.org/repos/dist/release/ctakes/KEYS Please vote on releasing these packages as Apache cTAKES 3.2.1. The vote is open for at least the next 72 hours. The vote passes if at least three binding +1 votes are cast. [ ] +1 Release the packages as Apache cTAKES 3.2.1 [ ] -1 Do not release the packages because... Also, the convenience binary can be found at: https://dist.apache.org/repos/dist/dev/ctakes/ctakes-3.2.1-rc2/apache-ctakes-3.2.1-bin.tar.gz.md5 /.zip Thanks!
RE: Scaling cTakes
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.
