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From: "Chen, Pei" <Pei.Chen@childrens.harvard.edu>
To: "dev@ctakes.apache.org" <dev@ctakes.apache.org>
Subject: RE: Preparing for an Apache cTAKES 3.2 Release?
Thread-Topic: Preparing for an Apache cTAKES 3.2 Release?
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Date: Wed, 18 Jun 2014 17:49:19 +0000
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Renamed to *-fast. =20
Again, this is only temporary... this will eventually just replace the exis=
ting dictionary lookup (next minor release?).

> -----Original Message-----
> From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
> Sent: Tuesday, June 17, 2014 10:14 AM
> To: dev@ctakes.apache.org
> Subject: RE: Preparing for an Apache cTAKES 3.2 Release?
>=20
> Yes.  It's only temporary to give folks a chance try out and transition t=
o the
> new lookup algorithm (hence, the +1 for the -fast suffix rename).
> But open to biting the bullet and defaulting it now if folks are compelle=
d to
> do so.
>=20
> > -----Original Message-----
> > From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
> > Sent: Monday, June 16, 2014 11:36 AM
> > To: dev@ctakes.apache.org
> > Subject: RE: Preparing for an Apache cTAKES 3.2 Release?
> >
> > I guess that I've got one question at this point:
> >
> > Is the name being given to the -new- dictionary lookup module
> > temporary or permanent?
> >
> > I was under the assumption that it was temporary and that with the
> > switch to it being default (and eventually only) the module would
> > simply be named "dictionary-lookup".
> >
> >
> >
> > -----Original Message-----
> > From: Masanz, James J. [mailto:Masanz.James@mayo.edu]
> > Sent: Monday, June 16, 2014 11:24 AM
> > To: 'dev@ctakes.apache.org'
> > Subject: RE: Preparing for an Apache cTAKES 3.2 Release?
> >
> > I'd rather something else than "dictionary-lookup-fast". If we come up
> > with something even faster than this one, having an older one called
> > "fast" could be confusing.
> >
> > -----Original Message-----
> > From: Dligach, Dmitriy [mailto:Dmitriy.Dligach@childrens.harvard.edu]
> > Sent: Monday, June 16, 2014 9:55 AM
> > To: cTAKES Developer list
> > Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
> >
> > +1
> >
> > Dima
> >
> >
> >
> >
> > On Jun 16, 2014, at 9:42, Miller, Timothy
> > <Timothy.Miller@childrens.harvard.edu> wrote:
> >
> > > Sorry to weigh in so late on this -- just returned from vacation. If
> > > we want to have a one release delay before making dictionary2
> > > default for testing/documentation/configuration purposes, and there
> > > isn't an obvious function-related name, and the main difference is
> > > speed, maybe we could call it dictionary-lookup-fast? Besides being
> > > accurate and more descriptive than "2", it might lure people into
> > > trying it and give us some feedback.
> > >
> > > Tim
> > >
> > >
> > > On 06/16/2014 10:34 AM, Chen, Pei wrote:
> > >> I'm making some significant updates to trunk that may cause some
> > instability for this release.
> > >> It should be mostly transparent, but let me know if you encounter
> > >> any
> > issues with trunk.
> > >>
> > >> Also, regarding the dictionary-lookup2.  If there are no strong
> > >> objections,
> > we can leave default to as-is (old behavior).  Folks who wish to give
> > the new one a try are welcome to do so and we can change the default
> > behavior in a future release.
> > >>
> > >> [ducks for cover now]
> > >> --Pei
> > >>
> > >>> -----Original Message-----
> > >>> From: ksarma@gmail.com [mailto:ksarma@gmail.com] On Behalf Of
> > >>> Karthik Sarma
> > >>> Sent: Wednesday, June 11, 2014 9:58 AM
> > >>> To: dev@ctakes.apache.org
> > >>> Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
> > >>>
> > >>> Agreed
> > >>>
> > >>> On Wednesday, June 11, 2014, vijay garla <vngarla@gmail.com> wrote:
> > >>>
> > >>>> regardless of the name, I think it would be incredibly helpful to
> > >>>> have thorough documentation on the dictionary lookup, how to
> > >>>> configure it, and how to create new dictionaries.  I would
> > >>>> venture to say that this is the most important component in
> > >>>> cTAKES, and probably the one that has generated the most
> > >>>> questions on the
> > newsgroup.
> > >>>>
> > >>>>
> > >>>>
> > >>>> On Wed, Jun 11, 2014 at 9:21 AM, Finan, Sean <
> > >>>> Sean.Finan@childrens.harvard.edu> wrote:
> > >>>>
> > >>>>>> . The newer NER should have in its name the Behavior...
> > >>>>> I agree, but the *2 module is a complete replacement for the
> > >>>>> current lookup.  It does not (really) have any different
> > >>>>> behavior, just a
> > >>>> different
> > >>>>> implementation and performance.  We plan to swap out the old
> > >>>>> with the new in the next release and get rid of the *2 suffix.
> > >>>>> So, any name provided now is just temporary - unless people
> > >>>>> don't like the name "dictionary-lookup" at all.
> > >>>>>
> > >>>>> In my original sandbox it was named "RareWordLookup", a nod to
> > >>>>> its implementation.  However, this doesn't help any users.
> > >>>>>
> > >>>>> Sean
> > >>>>>
> > >>>>> -----Original Message-----
> > >>>>> From: andy mcmurry [mailto:mcmurry.andy@gmail.com]
> > >>>>> Sent: Wednesday, June 11, 2014 3:09 AM
> > >>>>> To: dev@ctakes.apache.org
> > >>>>> Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
> > >>>>>
> > >>>>> "2" doesn't mean much. The newer NER should have in its name the
> > >>>>> Behavior...
> > >>>>>
> > >>>>> Perhaps something like MetaMap Usage
> > >>>>> <http://metamap.nlm.nih.gov/Docs/MM09_Usage.shtml> "--
> > >>> allow_overmatches"
> > >>>>> or  "--allow_concept_gaps" or .....other?
> > >>>>>
> > >>>>> Since yTex already provides a pluggable *DictionaryLookup, *that
> > >>>>> seems like the best place to define the differing Behavior /  Usa=
ge.
> > >>>>>
> > >>>>> https://cwiki.apache.org/confluence/display/CTAKES/User's+Guide
> > >>>>> https://code.google.com/p/ytex/wiki/DictionaryLookup_V05
> > >>>>>
> > >>>>>
> > >>>>> AndyMC
> > >>>>>
> > >>>>> On Tue, Jun 10, 2014 at 9:55 AM, britt fitch
> > >>>>> <britt.fitch@gmail.com>
> > >>>>> wrote:
> > >>>>>
> > >>>>>> I don't have an issue with the *-2 name. I also don't have any
> > >>>>>> objections to renaming it.
> > >>>>>>
> > >>>>>> It might be nice to keep the old dictionary code around for a
> > >>>>>> release-worth of time but after that I would vote purging it.
> > >>>>>> If someone needs it after that it'll be accessible in the
> > >>>>>> archived releases.
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>> On Jun 10, 2014, at 12:48 PM, Chen, Pei
> > >>>>>> <Pei.Chen@childrens.harvard.edu>
> > >>>>>> wrote:
> > >>>>>>
> > >>>>>>> I think James has a fair point here.
> > >>>>>>> It may be worthwhile biting the bullet here and push forward.
> > >>>>>>>
> > >>>>>>> Since this essentially will be a full replacement of the
> > >>>>>> ctakes-dictionary-lookup module, a good option maybe to just
> > >>>>>> replace the entire module now and rename the existing module to
> > >>>>>> *
> > >>> _deprecated.
> > >>>>>>> How do folks feel about that?  In a nutshell,
> > >>>>>>> ctakes-dictionary-lookup-2
> > >>>>>> is a faster algorithm with a simpler code base- and comparable
> > >>>>>> results (Sean has a full comparison in the documentation for
> > >>>>>> those who are
> > >>>>> curious).
> > >>>>>>> --Pei
> > >>>>>>>
> > >>>>>>>> -----Original Message-----
> > >>>>>>>> From: britt fitch [mailto:britt.fitch@gmail.com]
> > >>>>>>>> Sent: Monday, June 09, 2014 5:42 PM
> > >>>>>>>> To: dev@ctakes.apache.org
> > >>>>>>>> Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
> > >>>>>>>>
> > >>>>>>>> There is some documentation in the dictionary2 module under
> > >>>>>>>> /doc/DictionaryLookupHelp.{txt | docx} that gives some some
> > >>>>>>>> details of
> > >>>>>> the
> > >>>>>>>> different lookup implementation options within that module
> > >>>>>>>> that I found helpful.
> > >>>>>>>>
> > >>>>>>>>
> > >>>>>>>> On Jun 9, 2014, at 5:17 PM, Masanz, James J.
> > >>>>>>>> <
> > >>>
> > >>>
> > >>> --
> > >>>
> > >>>
> > >>>
> > >>>
> > >>> --
> > >>> Karthik Sarma
> > >>> UCLA Medical Scientist Training Program Class of 20??
> > >>> Member, UCLA Medical Imaging & Informatics Lab Member, CA
> > Delegation
> > >>> to the House of Delegates of the American Medical Association
> > >>> ksarma@ksarma.com
> > >>> gchat: ksarma@gmail.com
> > >>> linkedin: www.linkedin.com/in/ksarma
> > >
> > > --
> > > Tim Miller
> > > Instructor
> > > Boston Children's Hospital and Harvard Medical School
> > > timothy.miller@childrens.harvard.edu
> > > 617-919-1223
> > >