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Posted to user@ctakes.apache.org by "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu> on 2016/06/24 21:03:57 UTC

update on temporal relations

There was some mention previously (June 2015, I think) on the mailing list about the next release of cTAKES including improved temporal relation extraction. Can anyone share information about what improvements or new features will be included and when the release is expected?

Thanks,
Sean

Re: update on temporal relations

Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.

Glad you enjoyed it! Unfortunately a paper whose takeaway message is "existing simple models work well on this new task" is not as easy to get published (and usually does not make as big a splash) as the "cool complex model obtains 0.5 F1 improvement" paper.

Tim

________________________________
From: buddha <bu...@yahoo.com>
Sent: Wednesday, July 6, 2016 8:00 PM
To: user@ctakes.apache.org
Subject: Re: update on temporal relations

Hi Tim,

I live for papers that include a variant of your phrase "First, it is very interesting that the best per- forming systems are the simplest and fastest. Despite the theoretical advantages of the con- ditional random field's global sequence opti- mization, the BIO approaches using local clas- sifiers typically obtain the best performance."

 I really enjoyed the paper!

~~~~~
May All Your Sequences Converge

On Jul 6, 2016, at 6:35 AM, Miller, Timothy <Ti...@childrens.harvard.edu>> wrote:

Sean, for temporal expressions specifically, see this paper from BioNLP
last year:

http://aclweb.org/anthology/W/W15/W15-3809.pdf<https://urldefense.proofpoint.com/v2/url?u=http-3A__aclweb.org_anthology_W_W15_W15-2D3809.pdf&d=CwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=ynYoryhR7Jc3mvPFCGBAp1o0JUPGbchTFnPifSLa1kQ&s=Bc2CRWQJd5P4XJZ1j7u9m1_maRY1OdPysu9HFMBHmiw&e=>
Timothy Miller; Steven Bethard; Dmitriy Dligach; Chen Lin; Guergana
Savova
Extracting Time Expressions from Clinical Text

in short, yes the SVM-based BIO taggers showed better performance than
the CRF or constituency-tree classifiers.

Tim

On Tue, 2016-07-05 at 21:41 +0000, Mullane, Sean *HS wrote:
Thank you for the links. Does that mean that the SVM-based approach
from your first link has performed better than the CRF-based approach
in CRFTimeAnnotator.java?

Thanks,

Sean

From: Savova, Guergana [mailto:Guergana.Savova@childrens.harvard.edu]
Sent: Friday, June 24, 2016 6:24 PM
To: 'user@ctakes.apache.org'
Subject: RE: update on temporal relations

The best performing methods thus far have been released. They are
described in http://www.ncbi.nlm.nih.gov/pubmed/26521301

The results are state-of-the-art, see the recent community shared task
http://alt.qcri.org/semeval2016/task12/

We are actively working on the topic and will be releasing novel
methods as we investigate them.

Hope this helps.

--Guergana

Guergana Savova, PhD, FACMI

Associate Professor

PI Natural Language Processing Lab

Boston Children's Hospital and Harvard Medical School

300 Longwood Avenue

Mailstop: BCH3092

Enders 144.1

Boston, MA 02115

Tel: (617) 919-2972

Fax: (617) 730-0817

Harvard Scholar: http://scholar.harvard.edu/guergana_k_savova/biocv

From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu]
Sent: Friday, June 24, 2016 5:04 PM
To: 'user@ctakes.apache.org' <us...@ctakes.apache.org>
Subject: update on temporal relations

There was some mention previously (June 2015, I think) on the mailing
list about the next release of cTAKES including improved temporal
relation extraction. Can anyone share information about what
improvements or new features will be included and when the release is
expected?

Thanks,

Sean

Re: update on temporal relations

Posted by buddha <bu...@yahoo.com>.

Hi Tim,

I live for papers that include a variant of your phrase "First, it is very interesting that the best per- forming systems are the simplest and fastest. Despite the theoretical advantages of the con- ditional random field’s global sequence opti- mization, the BIO approaches using local clas- sifiers typically obtain the best performance."
 I really enjoyed the paper!


~~~~~
May All Your Sequences Converge

> On Jul 6, 2016, at 6:35 AM, Miller, Timothy <Ti...@childrens.harvard.edu> wrote:
> 
> Sean, for temporal expressions specifically, see this paper from BioNLP
> last year:
> 
> http://aclweb.org/anthology/W/W15/W15-3809.pdf
> Timothy Miller; Steven Bethard; Dmitriy Dligach; Chen Lin; Guergana
> Savova
> Extracting Time Expressions from Clinical Text
> 
> in short, yes the SVM-based BIO taggers showed better performance than
> the CRF or constituency-tree classifiers.
> 
> Tim
> 
> 
> On Tue, 2016-07-05 at 21:41 +0000, Mullane, Sean *HS wrote:
>> Thank you for the links. Does that mean that the SVM-based approach
>> from your first link has performed better than the CRF-based approach
>> in CRFTimeAnnotator.java?
>> 
>> 
>> 
>> Thanks,
>> 
>> Sean
>> 
>> 
>> 
>> From: Savova, Guergana [mailto:Guergana.Savova@childrens.harvard.edu] 
>> Sent: Friday, June 24, 2016 6:24 PM
>> To: 'user@ctakes.apache.org'
>> Subject: RE: update on temporal relations
>> 
>> 
>> 
>> 
>> The best performing methods thus far have been released. They are
>> described in http://www.ncbi.nlm.nih.gov/pubmed/26521301
>> 
>> The results are state-of-the-art, see the recent community shared task
>> http://alt.qcri.org/semeval2016/task12/
>> 
>> 
>> 
>> We are actively working on the topic and will be releasing novel
>> methods as we investigate them.
>> 
>> Hope this helps.
>> 
>> --Guergana
>> 
>> 
>> 
>> Guergana Savova, PhD, FACMI
>> 
>> Associate Professor
>> 
>> PI Natural Language Processing Lab
>> 
>> Boston Children's Hospital and Harvard Medical School
>> 
>> 300 Longwood Avenue
>> 
>> Mailstop: BCH3092
>> 
>> Enders 144.1
>> 
>> Boston, MA 02115
>> 
>> Tel: (617) 919-2972
>> 
>> Fax: (617) 730-0817
>> 
>> Harvard Scholar: http://scholar.harvard.edu/guergana_k_savova/biocv
>> 
>> 
>> 
>> From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu] 
>> Sent: Friday, June 24, 2016 5:04 PM
>> To: 'user@ctakes.apache.org' <us...@ctakes.apache.org>
>> Subject: update on temporal relations
>> 
>> 
>> 
>> 
>> There was some mention previously (June 2015, I think) on the mailing
>> list about the next release of cTAKES including improved temporal
>> relation extraction. Can anyone share information about what
>> improvements or new features will be included and when the release is
>> expected?
>> 
>> 
>> 
>> Thanks,
>> 
>> Sean
>> 
>> 
>

Re: update on temporal relations

Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.

Sean, for temporal expressions specifically, see this paper from BioNLP
last year:

http://aclweb.org/anthology/W/W15/W15-3809.pdf
Timothy Miller; Steven Bethard; Dmitriy Dligach; Chen Lin; Guergana
Savova
Extracting Time Expressions from Clinical Text

in short, yes the SVM-based BIO taggers showed better performance than
the CRF or constituency-tree classifiers.

Tim


On Tue, 2016-07-05 at 21:41 +0000, Mullane, Sean *HS wrote:
> Thank you for the links. Does that mean that the SVM-based approach
> from your first link has performed better than the CRF-based approach
> in CRFTimeAnnotator.java?
> 
>  
> 
> Thanks,
> 
> Sean
> 
>  
> 
> From: Savova, Guergana [mailto:Guergana.Savova@childrens.harvard.edu] 
> Sent: Friday, June 24, 2016 6:24 PM
> To: 'user@ctakes.apache.org'
> Subject: RE: update on temporal relations
> 
> 
>  
> 
> The best performing methods thus far have been released. They are
> described in http://www.ncbi.nlm.nih.gov/pubmed/26521301
> 
> The results are state-of-the-art, see the recent community shared task
> http://alt.qcri.org/semeval2016/task12/
> 
>  
> 
> We are actively working on the topic and will be releasing novel
> methods as we investigate them.
> 
> Hope this helps.
> 
> --Guergana
> 
>  
> 
> Guergana Savova, PhD, FACMI
> 
> Associate Professor
> 
> PI Natural Language Processing Lab
> 
> Boston Children's Hospital and Harvard Medical School
> 
> 300 Longwood Avenue
> 
> Mailstop: BCH3092
> 
> Enders 144.1
> 
> Boston, MA 02115
> 
> Tel: (617) 919-2972
> 
> Fax: (617) 730-0817
> 
> Harvard Scholar: http://scholar.harvard.edu/guergana_k_savova/biocv
> 
>  
> 
> From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu] 
> Sent: Friday, June 24, 2016 5:04 PM
> To: 'user@ctakes.apache.org' <us...@ctakes.apache.org>
> Subject: update on temporal relations
> 
> 
>  
> 
> There was some mention previously (June 2015, I think) on the mailing
> list about the next release of cTAKES including improved temporal
> relation extraction. Can anyone share information about what
> improvements or new features will be included and when the release is
> expected?
> 
>  
> 
> Thanks,
> 
> Sean
> 
>

RE: update on temporal relations

Posted by "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>.

Thank you for the links. Does that mean that the SVM-based approach from your first link has performed better than the CRF-based approach in CRFTimeAnnotator.java?

Thanks,
Sean

From: Savova, Guergana [mailto:Guergana.Savova@childrens.harvard.edu]
Sent: Friday, June 24, 2016 6:24 PM
To: 'user@ctakes.apache.org'
Subject: RE: update on temporal relations

The best performing methods thus far have been released. They are described in http://www.ncbi.nlm.nih.gov/pubmed/26521301
The results are state-of-the-art, see the recent community shared task http://alt.qcri.org/semeval2016/task12/

We are actively working on the topic and will be releasing novel methods as we investigate them.
Hope this helps.
--Guergana

Guergana Savova, PhD, FACMI
Associate Professor
PI Natural Language Processing Lab
Boston Children's Hospital and Harvard Medical School
300 Longwood Avenue
Mailstop: BCH3092
Enders 144.1
Boston, MA 02115
Tel: (617) 919-2972
Fax: (617) 730-0817
Harvard Scholar: http://scholar.harvard.edu/guergana_k_savova/biocv

From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu]
Sent: Friday, June 24, 2016 5:04 PM
To: 'user@ctakes.apache.org' <us...@ctakes.apache.org>>
Subject: update on temporal relations

There was some mention previously (June 2015, I think) on the mailing list about the next release of cTAKES including improved temporal relation extraction. Can anyone share information about what improvements or new features will be included and when the release is expected?

Thanks,
Sean

Re: update on temporal relations

Posted by "Mattmann, Chris A (3980)" <ch...@jpl.nasa.gov>.

Also if folks are interested I have had a lot of luck with GROBID
in collaborative work with P. Lopez (http://github.com/kermit2/grobid/).
Would be happy to talk more.

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Chris Mattmann, Ph.D.
Chief Architect
Instrument Software and Science Data Systems Section (398)
NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
Office: 168-519, Mailstop: 168-527
Email: chris.a.mattmann@nasa.gov
WWW:  http://sunset.usc.edu/~mattmann/
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Director, Information Retrieval and Data Science Group (IRDS)
Adjunct Associate Professor, Computer Science Department
University of Southern California, Los Angeles, CA 90089 USA
WWW: http://irds.usc.edu/
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++









On 6/24/16, 3:23 PM, "Savova, Guergana" <Gu...@childrens.harvard.edu> wrote:

>The best performing methods thus far have been released. They are described in
>http://www.ncbi.nlm.nih.gov/pubmed/26521301
>The results are state-of-the-art, see the recent community shared task
>http://alt.qcri.org/semeval2016/task12/
> 
>We are actively working on the topic and will be releasing novel methods as we investigate them.
>Hope this helps.
>--Guergana
> 
>Guergana Savova, PhD, FACMI
>Associate Professor
>PI Natural Language Processing Lab
>Boston Children's Hospital and Harvard Medical School
>300 Longwood Avenue
>Mailstop: BCH3092
>Enders 144.1
>Boston, MA 02115
>Tel: (617) 919-2972
>Fax: (617) 730-0817
>Harvard Scholar:
>http://scholar.harvard.edu/guergana_k_savova/biocv
> 
>From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu]
>
>Sent: Friday, June 24, 2016 5:04 PM
>To: 'user@ctakes.apache.org' <us...@ctakes.apache.org>
>Subject: update on temporal relations
>
>
> 
>There was some mention previously (June 2015, I think) on the mailing list about the next release of cTAKES including improved temporal relation extraction. Can anyone share information about what improvements or new features will be included
> and when the release is expected?
> 
>Thanks,
>Sean
>

RE: update on temporal relations

Posted by "Savova, Guergana" <Gu...@childrens.harvard.edu>.

The best performing methods thus far have been released. They are described in http://www.ncbi.nlm.nih.gov/pubmed/26521301
The results are state-of-the-art, see the recent community shared task http://alt.qcri.org/semeval2016/task12/

We are actively working on the topic and will be releasing novel methods as we investigate them.
Hope this helps.
--Guergana

Guergana Savova, PhD, FACMI
Associate Professor
PI Natural Language Processing Lab
Boston Children's Hospital and Harvard Medical School
300 Longwood Avenue
Mailstop: BCH3092
Enders 144.1
Boston, MA 02115
Tel: (617) 919-2972
Fax: (617) 730-0817
Harvard Scholar: http://scholar.harvard.edu/guergana_k_savova/biocv

From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu]
Sent: Friday, June 24, 2016 5:04 PM
To: 'user@ctakes.apache.org' <us...@ctakes.apache.org>
Subject: update on temporal relations

There was some mention previously (June 2015, I think) on the mailing list about the next release of cTAKES including improved temporal relation extraction. Can anyone share information about what improvements or new features will be included and when the release is expected?

Thanks,
Sean