d match".
This is pretty lenient, but seems to work in my tests. "this kinda-sorta
should ..." will not match ... though maybe '-' should be a special case. Let
me know what you think.
Enjoy,
Sean
-----Original Message-
From: Masanz, James J. [mailto:masanz.ja...@
3:57 PM
To: 'dev@ctakes.apache.org'
Subject: dictionary lookup config for best F1 measure [was RE: cTakes
Annotation Comparison
Sean (or others),
Of the various configuration options described below, which values/choices
would you recommend for best F1 measure for something like
4 10:43 AM
To: dev@ctakes.apache.org; kim.eb...@imatsolutions.com
Subject: RE: cTakes Annotation Comparison
Also check out stats that Sean ran before releasing the new component on:
http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-dictionary-lookup-fast/doc/DictionaryLookupStats.docx
From the evaluat
spot checks on the validity”. In other words,
>>> when your script reports that a cui and/or span is missing, manually look
>>> at the data and see if it really is. Just open up one .xmi in the CVD and
>>> see what it looks like.
>>>
>>>
>>>
>>> Th
>> Sorry, I meant “Do some spot checks on the validity”. In other words,
>>> when your script reports that a cui and/or span is missing, manually look
>>> at the data and see if it really is. Just open up one .xmi in the CVD and
>>> see what it looks like.
&
-Original Message-
From: Bruce Tietjen [mailto:bruce.tiet...@perfectsearchcorp.com]
Sent: Friday, December 19, 2014 5:05 PM
To: dev@ctakes.apache.org
Subject: Re: cTakes Annotation Comparison
My apologies to Sean and everyone,
I am happy to report that I found a bug in our analysis tools that
ing, manually
> look
> >> at the data and see if it really is. Just open up one .xmi in the CVD
> and
> >> see what it looks like.
> >>
> >>
> >>
> >> Thanks,
> >>
> >> Sean
> >>
> >>
> >>
> &
>> see what it looks like.
>>
>>
>>
>> Thanks,
>>
>> Sean
>>
>>
>>
>> *From:* Bruce Tietjen [mailto:bruce.tiet...@perfectsearchcorp.com]
>> *Sent:* Friday, December 19, 2014 3:37 PM
>> *To:* dev@ctakes.apache.org
>> *Subject:*
at it looks like.
>
>
>
> Thanks,
>
> Sean
>
>
>
> *From:* Bruce Tietjen [mailto:bruce.tiet...@perfectsearchcorp.com]
> *Sent:* Friday, December 19, 2014 3:37 PM
> *To:* dev@ctakes.apache.org
> *Subject:* Re: cTakes Annotation Comparison
>
>
>
> M
[mailto:bruce.tiet...@perfectsearchcorp.com]
Sent: Friday, December 19, 2014 3:37 PM
To: dev@ctakes.apache.org
Subject: Re: cTakes Annotation Comparison
My original results were using a newly downloaded cTakes 3.2.1 with the
separately downloaded resources copied in. There were no changes to any of the
ld be so horribly
inaccurate.
Thanks
-Original Message-
From: Bruce Tietjen [mailto:bruce.tiet...@perfectsearchcorp.com]
Sent: Friday, December 19, 2014 3:29 PM
To: dev@ctakes.apache.org
Subject: Re: cTakes Annotation Comparison
Correction -- So far, I did steps 1 and 2 of Sean's ema
leaner code base. If this is not the case or if there are issues, we
> > should fix it and move forward.).
> >
> > We can keep the old component around for as long as needed, but it’s
> > likely going to have limited support…
> >
> > --Pei
> >
> >
>
that you'd only have two
matches per document (100 docs?).
Thanks,
Sean
-Original Message-
From: Bruce Tietjen [mailto:bruce.tiet...@perfectsearchcorp.com]
Sent: Friday, December 19, 2014 3:23 PM
To: dev@ctakes.apache.org
Subject: Re: cTakes Annotation Comparison
Sean,
I
should fix it and move
>> forward.).
>>
>> We can keep the old component around for as long as needed, but it’s
>> likely going to have limited support…
>>
>> --Pei
>>
>>
>>
>> *From:* Kim Ebert [mailto:kim.eb...@imatsolutions.com]
>>
...@imatsolutions.com]
> *Sent:* Friday, December 19, 2014 1:47 PM
> *To:* Chen, Pei; dev@ctakes.apache.org
>
> *Subject:* Re: cTakes Annotation Comparison
>
>
>
> Pei,
>
> I don't think bugs/issues should be part of determining if one algorithm
> vs the oth
@ctakes.apache.org
Subject: Re: cTakes Annotation Comparison
Pei,
I don't think bugs/issues should be part of determining if one algorithm vs the
other is superior. Obviously, it is worth mentioning the bugs, but if the fast
lookup method has worse precision and recall but better performanc
lookup
(that is to say: when working with the default lookup).
From: Kim Ebert [mailto:kim.eb...@perfectsearchcorp.com]
Sent: Friday, December 19, 2014 1:40 PM
To: dev@ctakes.apache.org
Subject: Re: cTakes Annotation Comparison
Sean,
I don't think that would be an issue since both the rare
(The old dictionary lookup is essentially obsolete now- plagued with
> bugs/issues as you mentioned.)
>
> --Pei
>
>
>
> *From:* Kim Ebert [mailto:kim.eb...@perfectsearchcorp.com
> ]
> *Sent:* Friday, December 19, 2014 10:25 AM
> *To:* dev@ctakes.apache.org
> *Subject:* Re: c
kim.eb...@perfectsearchcorp.com]
> *Sent:* Friday, December 19, 2014 10:25 AM
> *To:* dev@ctakes.apache.org
> *Subject:* Re: cTakes Annotation Comparison
>
>
>
> Guergana,
>
> I'm curious to the number of records that are in your gold standard
> sets,
I’m bringing it up in case the Human Annotations were done using a different
version.
From: Kim Ebert [mailto:kim.eb...@perfectsearchcorp.com]
Sent: Friday, December 19, 2014 1:40 PM
To: dev@ctakes.apache.org
Subject: Re: cTakes Annotation Comparison
Sean,
I don't think that would be an
and moved from one TUI to another.
>
> Sean
>
> -Original Message-
> From: Savova, Guergana [mailto:guergana.sav...@childrens.harvard.edu]
> Sent: Friday, December 19, 2014 1:28 PM
> To: dev@ctakes.apache.org
> Subject: RE: cTakes Annotation Comparison
>
> Several thoughts:
onths cuis are added, removed, deprecated, and
moved from one TUI to another.
Sean
-Original Message-
From: Savova, Guergana [mailto:guergana.sav...@childrens.harvard.edu]
Sent: Friday, December 19, 2014 1:28 PM
To: dev@ctakes.apache.org
Subject: RE: cTakes Annotation Comparison
Se
@ctakes.apache.org
Subject: Re: cTakes Annotation Comparison
Our analysis against the human adjudicated gold standard from this SHARE corpus
is using a simple check to see if the cTakes output included the annotation
specified by the gold standard. The initial results I reported were for exact
matches
fast one were
> similar.
>
> Thank you everyone!
> --Guergana
>
> -Original Message-
> From: David Kincaid [mailto:kincaid.d...@gmail.com]
> Sent: Friday, December 19, 2014 9:02 AM
> To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org>
> Subject: Re: cTakes Annota
look up and the fast
> one were similar.
>
> Thank you everyone!
> --Guergana
>
> -Original Message-
> From: David Kincaid [mailto:kincaid.d...@gmail.com]
> Sent: Friday, December 19, 2014 9:02 AM
> To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org>
> Subject
To: dev@ctakes.apache.org; kim.eb...@imatsolutions.com
Subject: RE: cTakes Annotation Comparison
Also check out stats that Sean ran before releasing the new component on:
http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-dictionary-lookup-fast/doc/DictionaryLookupStats.docx
From the evaluation and experie
F1 results from the old dictionary look up and the fast one were similar.
Thank you everyone!
--Guergana
-Original Message-
From: David Kincaid [mailto:kincaid.d...@gmail.com]
Sent: Friday, December 19, 2014 9:02 AM
To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org>
Subject: R
To: dev@ctakes.apache.org
Subject: Re: cTakes Annotation Comparison
Guergana,
I'm curious to the number of records that are in your gold standard sets, or if
your gold standard set was run through a long running cTAKES process. I know at
some point we fixed a bug in the old dictionary lookup
: David Kincaid [mailto:kincaid.d...@gmail.com]
> Sent: Friday, December 19, 2014 9:02 AM
> To: dev@ctakes.apache.org
> Subject: Re: cTakes Annotation Comparison
>
> Thanks for this, Bruce! Very interesting work. It confirms what I've seen in
> my small tests that I've d
gt; -Original Message-
> From: David Kincaid [mailto:kincaid.d...@gmail.com]
> Sent: Friday, December 19, 2014 9:02 AM
> To: dev@ctakes.apache.org
> Subject: Re: cTakes Annotation Comparison
>
> Thanks for this, Bruce! Very interesting work. It confirms what I've seen
> in my s
were similar.
Thank you everyone!
--Guergana
-Original Message-
From: David Kincaid [mailto:kincaid.d...@gmail.com]
Sent: Friday, December 19, 2014 9:02 AM
To: dev@ctakes.apache.org
Subject: Re: cTakes Annotation Comparison
Thanks for this, Bruce! Very interesting work. It confirms what
to compare to an adjudicated human
> > annotated gold standard.
> >
> > --Pei
> >
> > -----Original Message-
> > From: Bruce Tietjen [mailto:bruce.tiet...@perfectsearchcorp.com]
> > Sent: Thursday, December 18, 2014 1:45 PM
> > To: dev@ctakes.ap
gt; From: Bruce Tietjen [mailto:bruce.tiet...@perfectsearchcorp.com]
>> Sent: Thursday, December 18, 2014 1:45 PM
>> To: dev@ctakes.apache.org
>> Subject: cTakes Annotation Comparison
>>
>> With the recent release of cTakes 3.2.1, we were very interested in
>> checki
.
>
> --Pei
>
> -Original Message-
> From: Bruce Tietjen [mailto:bruce.tiet...@perfectsearchcorp.com]
> Sent: Thursday, December 18, 2014 1:45 PM
> To: dev@ctakes.apache.org
> Subject: cTakes Annotation Comparison
>
> With the recent release of cTakes 3.2.1, we were
er 18, 2014 1:45 PM
To: dev@ctakes.apache.org
Subject: cTakes Annotation Comparison
With the recent release of cTakes 3.2.1, we were very interested in checking
for any differences in annotations between using the
AggregatePlaintextUMLSProcessor pipeline and the
AggregatePlanetextFastUMLSProc
With the recent release of cTakes 3.2.1, we were very interested in
checking for any differences in annotations between using the
AggregatePlaintextUMLSProcessor pipeline and the
AggregatePlanetextFastUMLSProcessor pipeline within this release of cTakes
with its associated set of UMLS resources.
W
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