The sentence detector always ends a sentence where there are newlines.
This is a problem for some notes (e.g. MIMIC radiology notes) where a
line can wrap in the middle of a sentence at specified character
offsets. In the comments for SentenceDetector, it seems to be split up
very logically in tha
On May 21, 2013, at 6:07 AM, "Miller, Timothy"
wrote:
> The sentence detector always ends a sentence where there are newlines.
> This is a problem for some notes (e.g. MIMIC radiology notes) where a
> line can wrap in the middle of a sentence at specified character
> offsets. In the comments for
deals with this issue.
--Guergana
-Original Message-
From: Steven Bethard [mailto:steven.beth...@colorado.edu]
Sent: Tuesday, May 21, 2013 9:59 AM
To: dev@ctakes.apache.org
Subject: Re: sentence detector newline behavior
On May 21, 2013, at 6:07 AM, "Miller, Timothy"
wr
, Timothy
Sent: Tuesday, May 21, 2013 7:07 AM
To: dev@ctakes.apache.org
Subject: sentence detector newline behavior
The sentence detector always ends a sentence where there are newlines.
This is a problem for some notes (e.g. MIMIC radiology notes) where a
line can wrap in the middle of a sentence at
egative would negate
extravascular findings
-Original Message-
From: dev-return-1605-Masanz.James=mayo@ctakes.apache.org
[mailto:dev-return-1605-Masanz.James=mayo@ctakes.apache.org] On Behalf Of
Miller, Timothy
Sent: Tuesday, May 21, 2013 7:07 AM
To: dev@ctakes.apache.org
Subject: sent
And without breaking on the line ending, the word negative would negate
>> extravascular findings
>>
>>
>> -Original Message-
>> From: dev-return-1605-Masanz.James=mayo....@ctakes.apache.org
>> [mailto:dev-return-1605-Masanz.James=mayo@ctakes.apache.org] On Behal
...@colorado.edu]
Sent: Tuesday, May 21, 2013 11:38 AM
To: dev@ctakes.apache.org
Subject: Re: sentence detector newline behavior
On May 21, 2013, at 9:02 AM, Tim Miller
wrote:
> I think the whole reason to use a machine learning approach for
> sentence detection should be to help weigh evidenc
nt: Tuesday, May 21, 2013 11:38 AM
> To: dev@ctakes.apache.org
> Subject: Re: sentence detector newline behavior
>
> On May 21, 2013, at 9:02 AM, Tim Miller
> wrote:
>> I think the whole reason to use a machine learning approach for
>> sentence detection should be to help weigh
es or retraining?)
--Pei
> -Original Message-
> From: Steven Bethard [mailto:steven.beth...@colorado.edu]
> Sent: Tuesday, May 21, 2013 12:07 PM
> To: dev@ctakes.apache.org
> Subject: Re: sentence detector newline behavior
>
> On May 21, 2013, at 9:53 AM, "Savova, Guer
nt: Tuesday, May 21, 2013 11:38 AM
> To: dev@ctakes.apache.org
> Subject: Re: sentence detector newline behavior
>
> On May 21, 2013, at 9:02 AM, Tim Miller
> wrote:
>> I think the whole reason to use a machine learning approach for
>> sentence detection should be to help weigh
ginal Message-
> From: Steven Bethard [mailto:steven.beth...@colorado.edu]
> Sent: Tuesday, May 21, 2013 12:07 PM
> To: dev@ctakes.apache.org
> Subject: Re: sentence detector newline behavior
>
> On May 21, 2013, at 9:53 AM, "Savova, Guergana"
> wrote:
>&
On 05/21/2013 08:00 PM, Steven Bethard wrote:
So perhaps we could re-train it to disambiguate newline characters as well?
Yes, the OpenNLP Sentence Detector now supports that in the new 1.5.3
version out of the box, you can
specify the set of EOS chars to use, but the default is still: !?. If
That's awesome! It might be worth trying at least. How does the training
process change? Previously the training data would be one sentence per
line, but with newlines as possible mid-sentence characters that could
be trouble, is there a new representation for training data? Or would we
have to use
On 05/22/2013 01:17 PM, Miller, Timothy wrote:
That's awesome! It might be worth trying at least. How does the training
process change? Previously the training data would be one sentence per
line, but with newlines as possible mid-sentence characters that could
be trouble, is there a new represen
OK I've started doing this, was able to get training working on a very
small example, will try doing slightly bigger.
Tim
On 05/22/2013 08:03 AM, Jörn Kottmann wrote:
On 05/22/2013 01:17 PM, Miller, Timothy wrote:
That's awesome! It might be worth trying at least. How does the training
process
Hi all,
currently I have quite a bit of time to work on OpenNLP, and would like
to help you
out with this issue.
Here is the follow up issue for this change:
https://issues.apache.org/jira/browse/OPENNLP-602
I am still trying to figure out what would be the best option to
implement this.
In
The sentence detection opennlp model used by ctakes does not split
sentences at newlines - there is additional logic in the takes sentence
splitter that does this (and an alternative impl that doesn't is in the
ytex branch). Afaik no retraining / change to the feature representation is
necessary.
I presume Joern was suggesting that if he supports new lines in the opennlp
SentenceDectector (either part of the trained models or post processing with
some rules?) cTAKES will be able to use it out of the box and we should be able
remove any additional custom logic that we currently have- whic
Yes, exactly, OPENNLP-602 is about training a sentence detector model
which can use a new line as a end-of-sentence character.
In case you have certain rules to split sentences we should have a look
at them. The Sentence Detector could be extended to support
a user provided rule based splitter.
o:dev-return-2390-Masanz.James=mayo@ctakes.apache.org] On Behalf Of
Jörn Kottmann
Sent: Tuesday, January 21, 2014 4:29 AM
To: dev@ctakes.apache.org
Subject: Re: sentence detector newline behavior
Yes, exactly, OPENNLP-602 is about training a sentence detector model
which can use a new line as a end-of-s
7;
Subject: RE: sentence detector newline behavior
The only rule I know of is that cTAKES (prior to ytex integration) always
forces a sentence break at a newline.
This was because the clinical notes cTAKES original processed never had
newlines in the middle of a sentence, but did need sentence b
...@childrens.harvard.edu]
Sent: Wednesday, January 22, 2014 1:33 PM
To: dev@ctakes.apache.org
Subject: RE: sentence detector newline behavior
Just whistling in the wind here ...
Perhaps before any changes are made to universally toggle cTakes in one
direction or the other, we can take a poll of when & w
been prescribed"
-- 2 sentences, 5 lines
Nothing can really be done for the last bit where punctuation is missing.
-Original Message-
From: Masanz, James J. [mailto:masanz.ja...@mayo.edu]
Sent: Wednesday, January 22, 2014 3:07 PM
To: 'dev@ctakes.apache.org'
Subject: RE:
l and Tylenol have
been prescribed"
-- 2 sentences, 5 lines
Nothing can really be done for the last bit where punctuation is missing.
-Original Message-
From: Masanz, James J. [mailto:masanz.ja...@mayo.edu]
Sent: Wednesday, January 22, 2014 3:07 PM
To: 'dev@ctakes.apache.org&
d.edu]
> Sent: Wednesday, January 22, 2014 3:42 PM
> To: dev@ctakes.apache.org
> Subject: RE: sentence detector newline behavior
>
> Thanks James
>
> > but then no typical sentence ending punctuation at the end of the line
>
> Gotcha.
>
> > So simply using Lines w
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
> > Sent: Wednesday, January 22, 2014 3:42 PM
> > To: dev@ctakes.apache.org
> > Subject: RE: sentence detector newline behavior
> >
> > Thanks James
> >
> > > but then no typical sentence ending
Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, January 22, 2014 3:42 PM
To: dev@ctakes.apache.org
Subject: RE: sentence detector newline behavior
Thanks James
but then no typical sentence ending punctuation at the end of the line
Gotcha.
So simply using Li
On 01/23/2014 10:06 PM, Tim Miller wrote:
Just an FYI, a while back I did some of these annotations myself on
MIMIC to get around this issue. I replaced the newline character with
a special (non-English) character, then pre-processed ctakes input to
replace newlines with that character, then di
il and
Tylenol
have been prescribed"
-- 2 sentences, 5 lines
Nothing can really be done for the last bit where punctuation is
missing.
-Original Message-
From: Masanz, James J. [mailto:masanz.ja...@mayo.edu]
Sent: Wednesday, January 22, 2014 3:07 PM
To: 'dev@ctakes.
gt;>>> was in
>>>> the opennlp model, but this requires training data. I don't know
>>>> what the
>>>> training data is, or if the training data has sentences that cross
>>>> newline
>>>> boundaries (if not, won't bu
s requires training data. I don't know
>>>> what the
>>>> training data is, or if the training data has sentences that cross
>>>> newline
>>>> boundaries (if not, won't buy us anything).
>>>>
>>>> vijay
>>>>
&
On 01/25/2014 01:33 PM, Miller, Timothy wrote:
Thanks Joern,
I'll try it. My understanding is I just need to give it my training
data, with the special character I used replaced with the literal string
"" and each line in the file is an example sentence.
Yes, exactly.
Just thinking about the
On 01/25/2014 03:03 PM, Miller, Timothy wrote:
I'm running into one issue, it gets tripped up on sentences with
line-ending spaces. I could easily remove them with a script but by
default they are in there. It happens when a sentence example ends:
...BILAT HEMATOMAS.
(There is a period, then
On 01/25/2014 12:24 PM, Jörn Kottmann wrote:
> The code which computes the spans tries to remove white space from it.
> Removing the white space from a whitespace only sentence is causing
> the exception your are seeing. Which response would you expect from
> the sentence detector? Should a white
On 01/25/2014 10:03 PM, Miller, Timothy wrote:
On 01/25/2014 12:24 PM, Jörn Kottmann wrote:
The code which computes the spans tries to remove white space from it.
Removing the white space from a whitespace only sentence is causing
the exception your are seeing. Which response would you expect fr
On 01/26/2014 09:59 AM, Jörn Kottmann wrote:
>
> The evaluation should ignore white spaces. I committed now my fix, it
> would be nice if you can
> test it.
>
> There might be still something wrong. In my test data I replaced all
> question marks with white spaces, and the result
> is slightly w
On 01/26/2014 11:29 PM, Miller, Timothy wrote:
Yes, this fixes the whitespace sentence issue but the evaluation issue
remains. I believe the problem is in SentenceSampleStream, where in the
following block the whitespace trim happens before the character is
replaced with the \n character. So tes
OK, with the most recent version I am able to replicate the performance
I was getting before. Thanks a lot Jörn!
Assuming this is in the next incremental release of opennlp, how quickly
can we get a re-trained model into cTAKES? I heard from a researcher at
AMIA who tried cTAKES and because of
> Date: Mon, 27 Jan 2014 09:52:00 -0500
> From: timothy.mil...@childrens.harvard.edu
> To: dev@ctakes.apache.org
> Subject: Re: sentence detector newline behavior
>
> OK, with the most recent version I am able to replicate the performance
> I was getting before. Thanks a lo
or and just using OpenNLP directly.
-- James
-Original Message-
From: Tim Miller [mailto:timothy.mil...@childrens.harvard.edu]
Sent: Monday, January 27, 2014 8:52 AM
To: dev@ctakes.apache.org
Subject: Re: sentence detector newline behavior
OK, with the most recent version I am able to replic
AM
To: dev@ctakes.apache.org
Subject: Re: sentence detector newline behavior
OK, with the most recent version I am able to replicate the performance
I was getting before. Thanks a lot Jörn!
Assuming this is in the next incremental release of opennlp, how quickly
can we get a re-trained model into c
> From: Tim Miller [mailto:timothy.mil...@childrens.harvard.edu]
> Sent: Monday, January 27, 2014 8:52 AM
> To: dev@ctakes.apache.org
> Subject: Re: sentence detector newline behavior
>
> OK, with the most recent version I am able to replicate the performance
> I was getting before. Thank
w with it. I've
> been delving deeper into cTAKES on the machine learning aspect...I'm
> struggling a bit with it and if anything I scratch my head and doubt my
> competence. ;-)
>
> Regards,
> Paula
>
> > Date: Mon, 27 Jan 2014 09:52:00 -0500
> > From: timo
with it. I've
been delving deeper into cTAKES on the machine learning aspect...I'm
struggling a bit with it and if anything I scratch my head and doubt my
competence. ;-)
Regards,
Paula
Date: Mon, 27 Jan 2014 09:52:00 -0500
From: timothy.mil...@childrens.harvard.edu
To: dev@ctakes.apac
month and worked around it with treating narrative as one string.
>
> Anyone who's looked at the code would appreciate and acknowledge that
> cTAKES is a powerful and complex application. I'm overall impressed with
> it and I intend to continue to use it, improve it, and gro
Date: Mon, 27 Jan 2014 09:52:00 -0500
From: timothy.mil...@childrens.harvard.edu
To: dev@ctakes.apache.org
Subject: Re: sentence detector newline behavior
OK, with the most recent version I am able to replicate the performance
I was getting before. Thanks a lot Jörn!
Assuming this is in the next
On 01/27/2014 08:44 PM, Tim Miller wrote:
That is a good point, and something I was wondering about. Having now
looked at both the ctakes and opennlp code for the sentence splitter
it seems like there is a lot of overlap. I would've thought it was
just a matter of converting annotations into
ry 29, 2014 3:55 PM
> To: dev@ctakes.apache.org
> Subject: Re: sentence detector newline behavior
>
> On 01/27/2014 08:44 PM, Tim Miller wrote:
> >
> > That is a good point, and something I was wondering about. Having now
> > looked at both the ctakes and opennlp code fo
On 01/27/2014 03:52 PM, Tim Miller wrote:
OK, with the most recent version I am able to replicate the
performance I was getting before. Thanks a lot Jörn!
Assuming this is in the next incremental release of opennlp, how
quickly can we get a re-trained model into cTAKES?
I am currently worki
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