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Posted to dev@ctakes.apache.org by Gandhi Rajan Natarajan <Ga...@arisglobal.com> on 2018/02/12 12:50:37 UTC
Regarding cTAKES Tlinks
Hi,
I have a question related to cTAKES Tlinks.
Is there any particular reason why FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator is commented in TemporalSubPipe.piper?
Also if I run the following text - "I had fever due to smoking so took paracetomol on 12th June 2018" in temporal demo link - http://54.68.117.30:8080/index.jsp , I get the following TLinks:
"June 2018 CONTAINS fever , June 2018 CONTAINS smoking , June 2018 CONTAINS paracetomol"
But if I run the same text in the latest cTAKES using TemporalSubPipe.piper, I get only "12th June 2018 CONTAINS paracetomol" as Tlinks.
Is it due to any recent changes in cTAKES?
Please advise.
Regards,
Gandhi
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
RE: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
[SUSPICIOUS]
Posted by Gandhi Rajan Natarajan <Ga...@arisglobal.com>.
Thanks a lot for the response Chen. Appreciate your time.
Regards,
Gandhi
-----Original Message-----
From: Lin, Chen [mailto:Chen.Lin@childrens.harvard.edu]
Sent: Wednesday, March 14, 2018 9:20 PM
To: dev@ctakes.apache.org
Subject: Re: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
Thank you for testing the temporal model in detail. As I can recall, the changes made between the two versions include added features and tuned parameters. We do see significant improvement in our test corpus so that we switch to the new model. The improvement is gauged statistically, not for every single instance. I am sure there would be some instances that the demo version cannot pick up but our new model can.
For your listed case, it's an event-event temporal relation. Event-event relations generally have a lower annotation quality (lower Inter Annotator Agreement). Through development we do observe the annotation quality decreases as the distance increases. We did try enforcing to reason event-event arguments that are within a certain distance like six-word.
But for your case, it's still considered as a good distance. So I would say it's a system error, assuming you can identify both events("HBA1c" and
"good") correctly using the current system.
Best,
Chen
On 3/14/18, 11:20 AM, "Gandhi Rajan Natarajan"
<Ga...@arisglobal.com> wrote:
>Hi Chen/Sean,
>
>As per our earlier discussion, I was under the impression that tlinks
>will not be able to pick only the long distance relationship in the
>latest version of cTAKES. But even when I try smaller text like the one
>below, the tlinks is not getting picked up:
>
>"HBA1c is normal which is good"
>
>But when I try out the same text in demo URL -
>https://urldefense.proofpoint.com/v2/url?u=http-3A__54.68.117.30-3A8080
>_in
>dex.jsp&d=DwIFAw&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=PZ241C
>wYZ
>3AszaTEBtM2wl3EcIjNNNeKX8q7N_mt-aI&m=SEMrHyMpFRLj8NCb6iYM5ST92ybV8iqKkY
>2b2 iu7brc&s=iC5PBgT3lI7HbZ0xGDGBRF_ADnEnyWlgTTGOHbTCjMo&e= , I get the
>following tlink:
>
>" HBA1c CONTAINS good"
>
>Any change in the latest version impacted this functionality or is it
>the expected behavior? Could you please provide some more info on this?
>
>Regards,
>Gandhi
>
>-----Original Message-----
>From: Gandhi Rajan Natarajan [mailto:Gandhi.Natarajan@arisglobal.com]
>Sent: Monday, February 12, 2018 11:00 PM
>To: dev@ctakes.apache.org
>Subject: RE: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS]
>[SUSPICIOUS] [SUSPICIOUS]
>
>Thanks Sean and Chen for your response. I really appreciate your time.
>
>Regards,
>Gandhi
>
>
>-----Original Message-----
>From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
>Sent: Monday, February 12, 2018 9:18 PM
>To: dev@ctakes.apache.org
>Subject: RE: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS]
>[SUSPICIOUS] [SUSPICIOUS]
>
>Hi Chen,
>
>No worries! I often throw out answers before checking code myself. We
>are all busy with other items. Besides, If I recall (without checking
>code), it is because of an improvement in the Event annotator code that
>the Copy*** was no longer needed ... and you wrote that improvement!
>hurrah!
>
>I thank you for taking the time to answer questions on temporal
>matters, as well as being one of the developers involved working on the module!
>
>Cheers,
>Sean
>
>-----Original Message-----
>From: Lin, Chen [mailto:Chen.Lin@childrens.harvard.edu]
>Sent: Monday, February 12, 2018 10:43 AM
>To: dev@ctakes.apache.org
>Subject: Re: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS]
>[SUSPICIOUS] [SUSPICIOUS]
>
>Thanks to Sean. My bad, I should check the code first before any answer
>attempt.
>
>Best,
>Chen
>
>On 2/12/18, 10:40 AM, "Finan, Sean" <Se...@childrens.harvard.edu>
>wrote:
>
>>It should have nothing to do with the tlink extraction. It copied
>>properties from events to eventmentions and was in the pipeline after
>>the tlink annotation, not before.
>>
>>-----Original Message-----
>>From: Lin, Chen [mailto:Chen.Lin@childrens.harvard.edu]
>>Sent: Monday, February 12, 2018 10:33 AM
>>To: dev@ctakes.apache.org
>>Subject: Re: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS]
>>
>>Mmm. Frankly, I don't know the rational behind commenting out
>>"FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator"
>>in that piper file. The TLINK model does take some of the event
>>properties (polarity, uncertainty, contextual modality, semantic
>>types,
>>etc.) for classification features. Without those features the
>>classifier may lose its grip. Have you tried commenting back the line?
>>
>>Best,
>>Chen
>>
>>On 2/12/18, 10:23 AM, "Gandhi Rajan Natarajan"
>><Ga...@arisglobal.com> wrote:
>>
>>>Hi Chen,
>>>
>>>Thanks a lot for your response.
>>>
>>>So I guess this behavior is nothing to do with commented out
>>>'FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator'
>>>in ' TemporalSubPipe.piper'?
>>>
>>>Thanks again.
>>>
>>>Regards,
>>>Gandhi
>>>
>>>-----Original Message-----
>>>From: Lin, Chen [mailto:Chen.Lin@childrens.harvard.edu]
>>>Sent: Monday, February 12, 2018 8:47 PM
>>>To: dev@ctakes.apache.org
>>>Subject: Re: Regarding cTAKES Tlinks [EXTERNAL]
>>>
>>>Hi Gandhi,
>>>
>>>It looks like the newest version is picking up the temporal
>>>expression complete, ³12th June 2018². The previous version only
>>>partially pick up ³June 2018². It is due to the the improvement of the timex annotator.
>>>As for the relations(tlinks), the current distributed TLINK model is
>>>a conventional SVM-based model which is tuned to favor close relation
>>>for high precision, like "12th June 2018 CONTAINS paracetamol². It
>>>can pick up some longer-distance relationship as well, but
>>>obliviously it fails for your case for long distance relations. We
>>>are currently researching a LSTM-based model, which can take more
>>>consideration of sentence structure and long-distance relationship.
>>>Will update more details in the future.
>>>
>>>Best,
>>>Chen
>>>
>>>On 2/12/18, 7:50 AM, "Gandhi Rajan Natarajan"
>>><Ga...@arisglobal.com> wrote:
>>>
>>>>Hi,
>>>>
>>>>I have a question related to cTAKES Tlinks.
>>>>
>>>>Is there any particular reason why
>>>>FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotato
>>>>r is commented in TemporalSubPipe.piper?
>>>>
>>>>Also if I run the following text - "I had fever due to smoking so
>>>>took paracetomol on 12th June 2018" in temporal demo link -
>>>>https://urldefense.proofpoint.com/v2/url?u=http-3A__54.68.117.30-3A8
>>>>0
>>>>8
>>>>0
>>>>_in
>>>>dex.jsp&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=PZ2
>>>>4
>>>>1
>>>>C
>>>>wYZ
>>>>3AszaTEBtM2wl3EcIjNNNeKX8q7N_mt-aI&m=CTJyQ3_c8JXxv2h1gPaq-jZ6hwp-2dK
>>>>T G q IrJ RkC7Yk&s=dOVZEd9mrbu0NtEHUZorIzmzEFC_ghg3l8l53ed4O_M&e= ,
>>>>I get the following TLinks:
>>>>
>>>>"June 2018 CONTAINS fever , June 2018 CONTAINS smoking , June 2018
>>>>CONTAINS paracetomol"
>>>>
>>>>But if I run the same text in the latest cTAKES using
>>>>TemporalSubPipe.piper, I get only "12th June 2018 CONTAINS paracetomol"
>>>>as Tlinks.
>>>>
>>>>Is it due to any recent changes in cTAKES?
>>>>
>>>>Please advise.
>>>>
>>>>
>>>>Regards,
>>>>Gandhi
>>>>
>>>>This email and any files transmitted with it are confidential and
>>>>intended solely for the use of the individual or entity to whom they
>>>>are addressed. If you are not the named addressee you should not
>>>>disseminate, distribute or copy this e-mail. Please notify the
>>>>sender or system manager by email immediately if you have received
>>>>this e-mail by mistake and delete this e-mail from your system. If
>>>>you are not the intended recipient you are notified that disclosing,
>>>>copying, distributing or taking any action in reliance on the
>>>>contents of this information is strictly prohibited and against the law.
>>>
>>>This email and any files transmitted with it are confidential and
>>>intended solely for the use of the individual or entity to whom they
>>>are addressed. If you are not the named addressee you should not
>>>disseminate, distribute or copy this e-mail. Please notify the sender
>>>or system manager by email immediately if you have received this
>>>e-mail by mistake and delete this e-mail from your system. If you are
>>>not the intended recipient you are notified that disclosing, copying,
>>>distributing or taking any action in reliance on the contents of this
>>>information is strictly prohibited and against the law.
>>
>
>This email and any files transmitted with it are confidential and
>intended solely for the use of the individual or entity to whom they
>are addressed. If you are not the named addressee you should not
>disseminate, distribute or copy this e-mail. Please notify the sender
>or system manager by email immediately if you have received this e-mail
>by mistake and delete this e-mail from your system. If you are not the
>intended recipient you are notified that disclosing, copying,
>distributing or taking any action in reliance on the contents of this
>information is strictly prohibited and against the law.
>This email and any files transmitted with it are confidential and
>intended solely for the use of the individual or entity to whom they
>are addressed. If you are not the named addressee you should not
>disseminate, distribute or copy this e-mail. Please notify the sender
>or system manager by email immediately if you have received this e-mail
>by mistake and delete this e-mail from your system. If you are not the
>intended recipient you are notified that disclosing, copying,
>distributing or taking any action in reliance on the contents of this
>information is strictly prohibited and against the law.
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
Re: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
[SUSPICIOUS]
Posted by "Lin, Chen" <Ch...@childrens.harvard.edu>.
Thank you for testing the temporal model in detail. As I can recall, the
changes made between the two versions include added features and tuned
parameters. We do see significant improvement in our test corpus so that
we switch to the new model. The improvement is gauged statistically, not
for every single instance. I am sure there would be some instances that
the demo version cannot pick up but our new model can.
For your listed case, it’s an event-event temporal relation. Event-event
relations generally have a lower annotation quality (lower Inter Annotator
Agreement). Through development we do observe the annotation quality
decreases as the distance increases. We did try enforcing to reason
event-event arguments that are within a certain distance like six-word.
But for your case, it’s still considered as a good distance. So I would
say it’s a system error, assuming you can identify both events(“HBA1c" and
"good") correctly using the current system.
Best,
Chen
On 3/14/18, 11:20 AM, "Gandhi Rajan Natarajan"
<Ga...@arisglobal.com> wrote:
>Hi Chen/Sean,
>
>As per our earlier discussion, I was under the impression that tlinks
>will not be able to pick only the long distance relationship in the
>latest version of cTAKES. But even when I try smaller text like the one
>below, the tlinks is not getting picked up:
>
>"HBA1c is normal which is good"
>
>But when I try out the same text in demo URL -
>https://urldefense.proofpoint.com/v2/url?u=http-3A__54.68.117.30-3A8080_in
>dex.jsp&d=DwIFAw&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=PZ241CwYZ
>3AszaTEBtM2wl3EcIjNNNeKX8q7N_mt-aI&m=SEMrHyMpFRLj8NCb6iYM5ST92ybV8iqKkY2b2
>iu7brc&s=iC5PBgT3lI7HbZ0xGDGBRF_ADnEnyWlgTTGOHbTCjMo&e= , I get the
>following tlink:
>
>" HBA1c CONTAINS good"
>
>Any change in the latest version impacted this functionality or is it the
>expected behavior? Could you please provide some more info on this?
>
>Regards,
>Gandhi
>
>-----Original Message-----
>From: Gandhi Rajan Natarajan [mailto:Gandhi.Natarajan@arisglobal.com]
>Sent: Monday, February 12, 2018 11:00 PM
>To: dev@ctakes.apache.org
>Subject: RE: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
>[SUSPICIOUS]
>
>Thanks Sean and Chen for your response. I really appreciate your time.
>
>Regards,
>Gandhi
>
>
>-----Original Message-----
>From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
>Sent: Monday, February 12, 2018 9:18 PM
>To: dev@ctakes.apache.org
>Subject: RE: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
>[SUSPICIOUS]
>
>Hi Chen,
>
>No worries! I often throw out answers before checking code myself. We
>are all busy with other items. Besides, If I recall (without checking
>code), it is because of an improvement in the Event annotator code that
>the Copy*** was no longer needed ... and you wrote that improvement!
>hurrah!
>
>I thank you for taking the time to answer questions on temporal matters,
>as well as being one of the developers involved working on the module!
>
>Cheers,
>Sean
>
>-----Original Message-----
>From: Lin, Chen [mailto:Chen.Lin@childrens.harvard.edu]
>Sent: Monday, February 12, 2018 10:43 AM
>To: dev@ctakes.apache.org
>Subject: Re: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
>[SUSPICIOUS]
>
>Thanks to Sean. My bad, I should check the code first before any answer
>attempt.
>
>Best,
>Chen
>
>On 2/12/18, 10:40 AM, "Finan, Sean" <Se...@childrens.harvard.edu>
>wrote:
>
>>It should have nothing to do with the tlink extraction. It copied
>>properties from events to eventmentions and was in the pipeline after
>>the tlink annotation, not before.
>>
>>-----Original Message-----
>>From: Lin, Chen [mailto:Chen.Lin@childrens.harvard.edu]
>>Sent: Monday, February 12, 2018 10:33 AM
>>To: dev@ctakes.apache.org
>>Subject: Re: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS]
>>
>>Mmm. Frankly, I don't know the rational behind commenting out
>>"FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator"
>>in that piper file. The TLINK model does take some of the event
>>properties (polarity, uncertainty, contextual modality, semantic types,
>>etc.) for classification features. Without those features the
>>classifier may lose its grip. Have you tried commenting back the line?
>>
>>Best,
>>Chen
>>
>>On 2/12/18, 10:23 AM, "Gandhi Rajan Natarajan"
>><Ga...@arisglobal.com> wrote:
>>
>>>Hi Chen,
>>>
>>>Thanks a lot for your response.
>>>
>>>So I guess this behavior is nothing to do with commented out
>>>'FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator'
>>>in ' TemporalSubPipe.piper'?
>>>
>>>Thanks again.
>>>
>>>Regards,
>>>Gandhi
>>>
>>>-----Original Message-----
>>>From: Lin, Chen [mailto:Chen.Lin@childrens.harvard.edu]
>>>Sent: Monday, February 12, 2018 8:47 PM
>>>To: dev@ctakes.apache.org
>>>Subject: Re: Regarding cTAKES Tlinks [EXTERNAL]
>>>
>>>Hi Gandhi,
>>>
>>>It looks like the newest version is picking up the temporal expression
>>>complete, ³12th June 2018². The previous version only partially pick
>>>up ³June 2018². It is due to the the improvement of the timex annotator.
>>>As for the relations(tlinks), the current distributed TLINK model is a
>>>conventional SVM-based model which is tuned to favor close relation
>>>for high precision, like "12th June 2018 CONTAINS paracetamol². It can
>>>pick up some longer-distance relationship as well, but obliviously it
>>>fails for your case for long distance relations. We are currently
>>>researching a LSTM-based model, which can take more consideration of
>>>sentence structure and long-distance relationship. Will update more
>>>details in the future.
>>>
>>>Best,
>>>Chen
>>>
>>>On 2/12/18, 7:50 AM, "Gandhi Rajan Natarajan"
>>><Ga...@arisglobal.com> wrote:
>>>
>>>>Hi,
>>>>
>>>>I have a question related to cTAKES Tlinks.
>>>>
>>>>Is there any particular reason why
>>>>FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator
>>>>is commented in TemporalSubPipe.piper?
>>>>
>>>>Also if I run the following text - "I had fever due to smoking so
>>>>took paracetomol on 12th June 2018" in temporal demo link -
>>>>https://urldefense.proofpoint.com/v2/url?u=http-3A__54.68.117.30-3A80
>>>>8
>>>>0
>>>>_in
>>>>dex.jsp&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=PZ24
>>>>1
>>>>C
>>>>wYZ
>>>>3AszaTEBtM2wl3EcIjNNNeKX8q7N_mt-aI&m=CTJyQ3_c8JXxv2h1gPaq-jZ6hwp-2dKT
>>>>G q IrJ RkC7Yk&s=dOVZEd9mrbu0NtEHUZorIzmzEFC_ghg3l8l53ed4O_M&e= , I
>>>>get the following TLinks:
>>>>
>>>>"June 2018 CONTAINS fever , June 2018 CONTAINS smoking , June 2018
>>>>CONTAINS paracetomol"
>>>>
>>>>But if I run the same text in the latest cTAKES using
>>>>TemporalSubPipe.piper, I get only "12th June 2018 CONTAINS paracetomol"
>>>>as Tlinks.
>>>>
>>>>Is it due to any recent changes in cTAKES?
>>>>
>>>>Please advise.
>>>>
>>>>
>>>>Regards,
>>>>Gandhi
>>>>
>>>>This email and any files transmitted with it are confidential and
>>>>intended solely for the use of the individual or entity to whom they
>>>>are addressed. If you are not the named addressee you should not
>>>>disseminate, distribute or copy this e-mail. Please notify the sender
>>>>or system manager by email immediately if you have received this
>>>>e-mail by mistake and delete this e-mail from your system. If you are
>>>>not the intended recipient you are notified that disclosing, copying,
>>>>distributing or taking any action in reliance on the contents of this
>>>>information is strictly prohibited and against the law.
>>>
>>>This email and any files transmitted with it are confidential and
>>>intended solely for the use of the individual or entity to whom they
>>>are addressed. If you are not the named addressee you should not
>>>disseminate, distribute or copy this e-mail. Please notify the sender
>>>or system manager by email immediately if you have received this
>>>e-mail by mistake and delete this e-mail from your system. If you are
>>>not the intended recipient you are notified that disclosing, copying,
>>>distributing or taking any action in reliance on the contents of this
>>>information is strictly prohibited and against the law.
>>
>
>This email and any files transmitted with it are confidential and
>intended solely for the use of the individual or entity to whom they are
>addressed. If you are not the named addressee you should not disseminate,
>distribute or copy this e-mail. Please notify the sender or system
>manager by email immediately if you have received this e-mail by mistake
>and delete this e-mail from your system. If you are not the intended
>recipient you are notified that disclosing, copying, distributing or
>taking any action in reliance on the contents of this information is
>strictly prohibited and against the law.
>This email and any files transmitted with it are confidential and
>intended solely for the use of the individual or entity to whom they are
>addressed. If you are not the named addressee you should not disseminate,
>distribute or copy this e-mail. Please notify the sender or system
>manager by email immediately if you have received this e-mail by mistake
>and delete this e-mail from your system. If you are not the intended
>recipient you are notified that disclosing, copying, distributing or
>taking any action in reliance on the contents of this information is
>strictly prohibited and against the law.
RE: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
[SUSPICIOUS]
Posted by Gandhi Rajan Natarajan <Ga...@arisglobal.com>.
Hi Chen/Sean,
As per our earlier discussion, I was under the impression that tlinks will not be able to pick only the long distance relationship in the latest version of cTAKES. But even when I try smaller text like the one below, the tlinks is not getting picked up:
"HBA1c is normal which is good"
But when I try out the same text in demo URL - http://54.68.117.30:8080/index.jsp , I get the following tlink:
" HBA1c CONTAINS good"
Any change in the latest version impacted this functionality or is it the expected behavior? Could you please provide some more info on this?
Regards,
Gandhi
-----Original Message-----
From: Gandhi Rajan Natarajan [mailto:Gandhi.Natarajan@arisglobal.com]
Sent: Monday, February 12, 2018 11:00 PM
To: dev@ctakes.apache.org
Subject: RE: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
Thanks Sean and Chen for your response. I really appreciate your time.
Regards,
Gandhi
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: Monday, February 12, 2018 9:18 PM
To: dev@ctakes.apache.org
Subject: RE: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
Hi Chen,
No worries! I often throw out answers before checking code myself. We are all busy with other items. Besides, If I recall (without checking code), it is because of an improvement in the Event annotator code that the Copy*** was no longer needed ... and you wrote that improvement! hurrah!
I thank you for taking the time to answer questions on temporal matters, as well as being one of the developers involved working on the module!
Cheers,
Sean
-----Original Message-----
From: Lin, Chen [mailto:Chen.Lin@childrens.harvard.edu]
Sent: Monday, February 12, 2018 10:43 AM
To: dev@ctakes.apache.org
Subject: Re: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
Thanks to Sean. My bad, I should check the code first before any answer attempt.
Best,
Chen
On 2/12/18, 10:40 AM, "Finan, Sean" <Se...@childrens.harvard.edu>
wrote:
>It should have nothing to do with the tlink extraction. It copied
>properties from events to eventmentions and was in the pipeline after
>the tlink annotation, not before.
>
>-----Original Message-----
>From: Lin, Chen [mailto:Chen.Lin@childrens.harvard.edu]
>Sent: Monday, February 12, 2018 10:33 AM
>To: dev@ctakes.apache.org
>Subject: Re: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS]
>
>Mmm. Frankly, I don't know the rational behind commenting out
>"FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator"
>in that piper file. The TLINK model does take some of the event
>properties (polarity, uncertainty, contextual modality, semantic types,
>etc.) for classification features. Without those features the
>classifier may lose its grip. Have you tried commenting back the line?
>
>Best,
>Chen
>
>On 2/12/18, 10:23 AM, "Gandhi Rajan Natarajan"
><Ga...@arisglobal.com> wrote:
>
>>Hi Chen,
>>
>>Thanks a lot for your response.
>>
>>So I guess this behavior is nothing to do with commented out
>>'FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator'
>>in ' TemporalSubPipe.piper'?
>>
>>Thanks again.
>>
>>Regards,
>>Gandhi
>>
>>-----Original Message-----
>>From: Lin, Chen [mailto:Chen.Lin@childrens.harvard.edu]
>>Sent: Monday, February 12, 2018 8:47 PM
>>To: dev@ctakes.apache.org
>>Subject: Re: Regarding cTAKES Tlinks [EXTERNAL]
>>
>>Hi Gandhi,
>>
>>It looks like the newest version is picking up the temporal expression
>>complete, ³12th June 2018². The previous version only partially pick
>>up ³June 2018². It is due to the the improvement of the timex annotator.
>>As for the relations(tlinks), the current distributed TLINK model is a
>>conventional SVM-based model which is tuned to favor close relation
>>for high precision, like "12th June 2018 CONTAINS paracetamol². It can
>>pick up some longer-distance relationship as well, but obliviously it
>>fails for your case for long distance relations. We are currently
>>researching a LSTM-based model, which can take more consideration of
>>sentence structure and long-distance relationship. Will update more
>>details in the future.
>>
>>Best,
>>Chen
>>
>>On 2/12/18, 7:50 AM, "Gandhi Rajan Natarajan"
>><Ga...@arisglobal.com> wrote:
>>
>>>Hi,
>>>
>>>I have a question related to cTAKES Tlinks.
>>>
>>>Is there any particular reason why
>>>FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator
>>>is commented in TemporalSubPipe.piper?
>>>
>>>Also if I run the following text - "I had fever due to smoking so
>>>took paracetomol on 12th June 2018" in temporal demo link -
>>>https://urldefense.proofpoint.com/v2/url?u=http-3A__54.68.117.30-3A80
>>>8
>>>0
>>>_in
>>>dex.jsp&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=PZ24
>>>1
>>>C
>>>wYZ
>>>3AszaTEBtM2wl3EcIjNNNeKX8q7N_mt-aI&m=CTJyQ3_c8JXxv2h1gPaq-jZ6hwp-2dKT
>>>G q IrJ RkC7Yk&s=dOVZEd9mrbu0NtEHUZorIzmzEFC_ghg3l8l53ed4O_M&e= , I
>>>get the following TLinks:
>>>
>>>"June 2018 CONTAINS fever , June 2018 CONTAINS smoking , June 2018
>>>CONTAINS paracetomol"
>>>
>>>But if I run the same text in the latest cTAKES using
>>>TemporalSubPipe.piper, I get only "12th June 2018 CONTAINS paracetomol"
>>>as Tlinks.
>>>
>>>Is it due to any recent changes in cTAKES?
>>>
>>>Please advise.
>>>
>>>
>>>Regards,
>>>Gandhi
>>>
>>>This email and any files transmitted with it are confidential and
>>>intended solely for the use of the individual or entity to whom they
>>>are addressed. If you are not the named addressee you should not
>>>disseminate, distribute or copy this e-mail. Please notify the sender
>>>or system manager by email immediately if you have received this
>>>e-mail by mistake and delete this e-mail from your system. If you are
>>>not the intended recipient you are notified that disclosing, copying,
>>>distributing or taking any action in reliance on the contents of this
>>>information is strictly prohibited and against the law.
>>
>>This email and any files transmitted with it are confidential and
>>intended solely for the use of the individual or entity to whom they
>>are addressed. If you are not the named addressee you should not
>>disseminate, distribute or copy this e-mail. Please notify the sender
>>or system manager by email immediately if you have received this
>>e-mail by mistake and delete this e-mail from your system. If you are
>>not the intended recipient you are notified that disclosing, copying,
>>distributing or taking any action in reliance on the contents of this
>>information is strictly prohibited and against the law.
>
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
RE: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
[SUSPICIOUS]
Posted by Gandhi Rajan Natarajan <Ga...@arisglobal.com>.
Thanks Sean and Chen for your response. I really appreciate your time.
Regards,
Gandhi
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: Monday, February 12, 2018 9:18 PM
To: dev@ctakes.apache.org
Subject: RE: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
Hi Chen,
No worries! I often throw out answers before checking code myself. We are all busy with other items. Besides, If I recall (without checking code), it is because of an improvement in the Event annotator code that the Copy*** was no longer needed ... and you wrote that improvement! hurrah!
I thank you for taking the time to answer questions on temporal matters, as well as being one of the developers involved working on the module!
Cheers,
Sean
-----Original Message-----
From: Lin, Chen [mailto:Chen.Lin@childrens.harvard.edu]
Sent: Monday, February 12, 2018 10:43 AM
To: dev@ctakes.apache.org
Subject: Re: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
Thanks to Sean. My bad, I should check the code first before any answer attempt.
Best,
Chen
On 2/12/18, 10:40 AM, "Finan, Sean" <Se...@childrens.harvard.edu>
wrote:
>It should have nothing to do with the tlink extraction. It copied
>properties from events to eventmentions and was in the pipeline after
>the tlink annotation, not before.
>
>-----Original Message-----
>From: Lin, Chen [mailto:Chen.Lin@childrens.harvard.edu]
>Sent: Monday, February 12, 2018 10:33 AM
>To: dev@ctakes.apache.org
>Subject: Re: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS]
>
>Mmm. Frankly, I don't know the rational behind commenting out
>"FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator"
>in that piper file. The TLINK model does take some of the event
>properties (polarity, uncertainty, contextual modality, semantic types,
>etc.) for classification features. Without those features the
>classifier may lose its grip. Have you tried commenting back the line?
>
>Best,
>Chen
>
>On 2/12/18, 10:23 AM, "Gandhi Rajan Natarajan"
><Ga...@arisglobal.com> wrote:
>
>>Hi Chen,
>>
>>Thanks a lot for your response.
>>
>>So I guess this behavior is nothing to do with commented out
>>'FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator'
>>in ' TemporalSubPipe.piper'?
>>
>>Thanks again.
>>
>>Regards,
>>Gandhi
>>
>>-----Original Message-----
>>From: Lin, Chen [mailto:Chen.Lin@childrens.harvard.edu]
>>Sent: Monday, February 12, 2018 8:47 PM
>>To: dev@ctakes.apache.org
>>Subject: Re: Regarding cTAKES Tlinks [EXTERNAL]
>>
>>Hi Gandhi,
>>
>>It looks like the newest version is picking up the temporal expression
>>complete, ³12th June 2018². The previous version only partially pick
>>up ³June 2018². It is due to the the improvement of the timex annotator.
>>As for the relations(tlinks), the current distributed TLINK model is a
>>conventional SVM-based model which is tuned to favor close relation
>>for high precision, like "12th June 2018 CONTAINS paracetamol². It can
>>pick up some longer-distance relationship as well, but obliviously it
>>fails for your case for long distance relations. We are currently
>>researching a LSTM-based model, which can take more consideration of
>>sentence structure and long-distance relationship. Will update more
>>details in the future.
>>
>>Best,
>>Chen
>>
>>On 2/12/18, 7:50 AM, "Gandhi Rajan Natarajan"
>><Ga...@arisglobal.com> wrote:
>>
>>>Hi,
>>>
>>>I have a question related to cTAKES Tlinks.
>>>
>>>Is there any particular reason why
>>>FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator
>>>is commented in TemporalSubPipe.piper?
>>>
>>>Also if I run the following text - "I had fever due to smoking so
>>>took paracetomol on 12th June 2018" in temporal demo link -
>>>https://urldefense.proofpoint.com/v2/url?u=http-3A__54.68.117.30-3A80
>>>8
>>>0
>>>_in
>>>dex.jsp&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=PZ24
>>>1
>>>C
>>>wYZ
>>>3AszaTEBtM2wl3EcIjNNNeKX8q7N_mt-aI&m=CTJyQ3_c8JXxv2h1gPaq-jZ6hwp-2dKT
>>>G q IrJ RkC7Yk&s=dOVZEd9mrbu0NtEHUZorIzmzEFC_ghg3l8l53ed4O_M&e= , I
>>>get the following TLinks:
>>>
>>>"June 2018 CONTAINS fever , June 2018 CONTAINS smoking , June 2018
>>>CONTAINS paracetomol"
>>>
>>>But if I run the same text in the latest cTAKES using
>>>TemporalSubPipe.piper, I get only "12th June 2018 CONTAINS paracetomol"
>>>as Tlinks.
>>>
>>>Is it due to any recent changes in cTAKES?
>>>
>>>Please advise.
>>>
>>>
>>>Regards,
>>>Gandhi
>>>
>>>This email and any files transmitted with it are confidential and
>>>intended solely for the use of the individual or entity to whom they
>>>are addressed. If you are not the named addressee you should not
>>>disseminate, distribute or copy this e-mail. Please notify the sender
>>>or system manager by email immediately if you have received this
>>>e-mail by mistake and delete this e-mail from your system. If you are
>>>not the intended recipient you are notified that disclosing, copying,
>>>distributing or taking any action in reliance on the contents of this
>>>information is strictly prohibited and against the law.
>>
>>This email and any files transmitted with it are confidential and
>>intended solely for the use of the individual or entity to whom they
>>are addressed. If you are not the named addressee you should not
>>disseminate, distribute or copy this e-mail. Please notify the sender
>>or system manager by email immediately if you have received this
>>e-mail by mistake and delete this e-mail from your system. If you are
>>not the intended recipient you are notified that disclosing, copying,
>>distributing or taking any action in reliance on the contents of this
>>information is strictly prohibited and against the law.
>
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
RE: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
[SUSPICIOUS]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Chen,
No worries! I often throw out answers before checking code myself. We are all busy with other items. Besides, If I recall (without checking code), it is because of an improvement in the Event annotator code that the Copy*** was no longer needed ... and you wrote that improvement! hurrah!
I thank you for taking the time to answer questions on temporal matters, as well as being one of the developers involved working on the module!
Cheers,
Sean
-----Original Message-----
From: Lin, Chen [mailto:Chen.Lin@childrens.harvard.edu]
Sent: Monday, February 12, 2018 10:43 AM
To: dev@ctakes.apache.org
Subject: Re: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
Thanks to Sean. My bad, I should check the code first before any answer attempt.
Best,
Chen
On 2/12/18, 10:40 AM, "Finan, Sean" <Se...@childrens.harvard.edu>
wrote:
>It should have nothing to do with the tlink extraction. It copied
>properties from events to eventmentions and was in the pipeline after
>the tlink annotation, not before.
>
>-----Original Message-----
>From: Lin, Chen [mailto:Chen.Lin@childrens.harvard.edu]
>Sent: Monday, February 12, 2018 10:33 AM
>To: dev@ctakes.apache.org
>Subject: Re: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS]
>
>Mmm. Frankly, I don't know the rational behind commenting out
>"FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator"
>in that piper file. The TLINK model does take some of the event
>properties (polarity, uncertainty, contextual modality, semantic types,
>etc.) for classification features. Without those features the
>classifier may lose its grip. Have you tried commenting back the line?
>
>Best,
>Chen
>
>On 2/12/18, 10:23 AM, "Gandhi Rajan Natarajan"
><Ga...@arisglobal.com> wrote:
>
>>Hi Chen,
>>
>>Thanks a lot for your response.
>>
>>So I guess this behavior is nothing to do with commented out
>>'FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator'
>>in ' TemporalSubPipe.piper'?
>>
>>Thanks again.
>>
>>Regards,
>>Gandhi
>>
>>-----Original Message-----
>>From: Lin, Chen [mailto:Chen.Lin@childrens.harvard.edu]
>>Sent: Monday, February 12, 2018 8:47 PM
>>To: dev@ctakes.apache.org
>>Subject: Re: Regarding cTAKES Tlinks [EXTERNAL]
>>
>>Hi Gandhi,
>>
>>It looks like the newest version is picking up the temporal expression
>>complete, ³12th June 2018². The previous version only partially pick
>>up ³June 2018². It is due to the the improvement of the timex annotator.
>>As for the relations(tlinks), the current distributed TLINK model is a
>>conventional SVM-based model which is tuned to favor close relation
>>for high precision, like "12th June 2018 CONTAINS paracetamol². It can
>>pick up some longer-distance relationship as well, but obliviously it
>>fails for your case for long distance relations. We are currently
>>researching a LSTM-based model, which can take more consideration of
>>sentence structure and long-distance relationship. Will update more
>>details in the future.
>>
>>Best,
>>Chen
>>
>>On 2/12/18, 7:50 AM, "Gandhi Rajan Natarajan"
>><Ga...@arisglobal.com> wrote:
>>
>>>Hi,
>>>
>>>I have a question related to cTAKES Tlinks.
>>>
>>>Is there any particular reason why
>>>FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator
>>>is commented in TemporalSubPipe.piper?
>>>
>>>Also if I run the following text - "I had fever due to smoking so
>>>took paracetomol on 12th June 2018" in temporal demo link -
>>>https://urldefense.proofpoint.com/v2/url?u=http-3A__54.68.117.30-3A80
>>>8
>>>0
>>>_in
>>>dex.jsp&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=PZ24
>>>1
>>>C
>>>wYZ
>>>3AszaTEBtM2wl3EcIjNNNeKX8q7N_mt-aI&m=CTJyQ3_c8JXxv2h1gPaq-jZ6hwp-2dKT
>>>G q IrJ RkC7Yk&s=dOVZEd9mrbu0NtEHUZorIzmzEFC_ghg3l8l53ed4O_M&e= , I
>>>get the following TLinks:
>>>
>>>"June 2018 CONTAINS fever , June 2018 CONTAINS smoking , June 2018
>>>CONTAINS paracetomol"
>>>
>>>But if I run the same text in the latest cTAKES using
>>>TemporalSubPipe.piper, I get only "12th June 2018 CONTAINS paracetomol"
>>>as Tlinks.
>>>
>>>Is it due to any recent changes in cTAKES?
>>>
>>>Please advise.
>>>
>>>
>>>Regards,
>>>Gandhi
>>>
>>>This email and any files transmitted with it are confidential and
>>>intended solely for the use of the individual or entity to whom they
>>>are addressed. If you are not the named addressee you should not
>>>disseminate, distribute or copy this e-mail. Please notify the sender
>>>or system manager by email immediately if you have received this
>>>e-mail by mistake and delete this e-mail from your system. If you are
>>>not the intended recipient you are notified that disclosing, copying,
>>>distributing or taking any action in reliance on the contents of this
>>>information is strictly prohibited and against the law.
>>
>>This email and any files transmitted with it are confidential and
>>intended solely for the use of the individual or entity to whom they
>>are addressed. If you are not the named addressee you should not
>>disseminate, distribute or copy this e-mail. Please notify the sender
>>or system manager by email immediately if you have received this
>>e-mail by mistake and delete this e-mail from your system. If you are
>>not the intended recipient you are notified that disclosing, copying,
>>distributing or taking any action in reliance on the contents of this
>>information is strictly prohibited and against the law.
>
Re: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Posted by "Lin, Chen" <Ch...@childrens.harvard.edu>.
Thanks to Sean. My bad, I should check the code first before any answer
attempt.
Best,
Chen
On 2/12/18, 10:40 AM, "Finan, Sean" <Se...@childrens.harvard.edu>
wrote:
>It should have nothing to do with the tlink extraction. It copied
>properties from events to eventmentions and was in the pipeline after the
>tlink annotation, not before.
>
>-----Original Message-----
>From: Lin, Chen [mailto:Chen.Lin@childrens.harvard.edu]
>Sent: Monday, February 12, 2018 10:33 AM
>To: dev@ctakes.apache.org
>Subject: Re: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS]
>
>Mmm. Frankly, I don't know the rational behind commenting out
>"FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator"
>in that piper file. The TLINK model does take some of the event
>properties (polarity, uncertainty, contextual modality, semantic types,
>etc.) for classification features. Without those features the classifier
>may lose its grip. Have you tried commenting back the line?
>
>Best,
>Chen
>
>On 2/12/18, 10:23 AM, "Gandhi Rajan Natarajan"
><Ga...@arisglobal.com> wrote:
>
>>Hi Chen,
>>
>>Thanks a lot for your response.
>>
>>So I guess this behavior is nothing to do with commented out
>>'FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator'
>>in ' TemporalSubPipe.piper'?
>>
>>Thanks again.
>>
>>Regards,
>>Gandhi
>>
>>-----Original Message-----
>>From: Lin, Chen [mailto:Chen.Lin@childrens.harvard.edu]
>>Sent: Monday, February 12, 2018 8:47 PM
>>To: dev@ctakes.apache.org
>>Subject: Re: Regarding cTAKES Tlinks [EXTERNAL]
>>
>>Hi Gandhi,
>>
>>It looks like the newest version is picking up the temporal expression
>>complete, ³12th June 2018². The previous version only partially pick up
>>³June 2018². It is due to the the improvement of the timex annotator.
>>As for the relations(tlinks), the current distributed TLINK model is a
>>conventional SVM-based model which is tuned to favor close relation for
>>high precision, like "12th June 2018 CONTAINS paracetamol². It can pick
>>up some longer-distance relationship as well, but obliviously it fails
>>for your case for long distance relations. We are currently researching
>>a LSTM-based model, which can take more consideration of sentence
>>structure and long-distance relationship. Will update more details in
>>the future.
>>
>>Best,
>>Chen
>>
>>On 2/12/18, 7:50 AM, "Gandhi Rajan Natarajan"
>><Ga...@arisglobal.com> wrote:
>>
>>>Hi,
>>>
>>>I have a question related to cTAKES Tlinks.
>>>
>>>Is there any particular reason why
>>>FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator
>>>is commented in TemporalSubPipe.piper?
>>>
>>>Also if I run the following text - "I had fever due to smoking so took
>>>paracetomol on 12th June 2018" in temporal demo link -
>>>https://urldefense.proofpoint.com/v2/url?u=http-3A__54.68.117.30-3A808
>>>0
>>>_in
>>>dex.jsp&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=PZ241
>>>C
>>>wYZ
>>>3AszaTEBtM2wl3EcIjNNNeKX8q7N_mt-aI&m=CTJyQ3_c8JXxv2h1gPaq-jZ6hwp-2dKTG
>>>q IrJ RkC7Yk&s=dOVZEd9mrbu0NtEHUZorIzmzEFC_ghg3l8l53ed4O_M&e= , I get
>>>the following TLinks:
>>>
>>>"June 2018 CONTAINS fever , June 2018 CONTAINS smoking , June 2018
>>>CONTAINS paracetomol"
>>>
>>>But if I run the same text in the latest cTAKES using
>>>TemporalSubPipe.piper, I get only "12th June 2018 CONTAINS paracetomol"
>>>as Tlinks.
>>>
>>>Is it due to any recent changes in cTAKES?
>>>
>>>Please advise.
>>>
>>>
>>>Regards,
>>>Gandhi
>>>
>>>This email and any files transmitted with it are confidential and
>>>intended solely for the use of the individual or entity to whom they
>>>are addressed. If you are not the named addressee you should not
>>>disseminate, distribute or copy this e-mail. Please notify the sender
>>>or system manager by email immediately if you have received this
>>>e-mail by mistake and delete this e-mail from your system. If you are
>>>not the intended recipient you are notified that disclosing, copying,
>>>distributing or taking any action in reliance on the contents of this
>>>information is strictly prohibited and against the law.
>>
>>This email and any files transmitted with it are confidential and
>>intended solely for the use of the individual or entity to whom they
>>are addressed. If you are not the named addressee you should not
>>disseminate, distribute or copy this e-mail. Please notify the sender
>>or system manager by email immediately if you have received this e-mail
>>by mistake and delete this e-mail from your system. If you are not the
>>intended recipient you are notified that disclosing, copying,
>>distributing or taking any action in reliance on the contents of this
>>information is strictly prohibited and against the law.
>
RE: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
It should have nothing to do with the tlink extraction. It copied properties from events to eventmentions and was in the pipeline after the tlink annotation, not before.
-----Original Message-----
From: Lin, Chen [mailto:Chen.Lin@childrens.harvard.edu]
Sent: Monday, February 12, 2018 10:33 AM
To: dev@ctakes.apache.org
Subject: Re: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS]
Mmm. Frankly, I don't know the rational behind commenting out "FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator" in that piper file. The TLINK model does take some of the event properties (polarity, uncertainty, contextual modality, semantic types, etc.) for classification features. Without those features the classifier may lose its grip. Have you tried commenting back the line?
Best,
Chen
On 2/12/18, 10:23 AM, "Gandhi Rajan Natarajan"
<Ga...@arisglobal.com> wrote:
>Hi Chen,
>
>Thanks a lot for your response.
>
>So I guess this behavior is nothing to do with commented out
>'FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator'
>in ' TemporalSubPipe.piper'?
>
>Thanks again.
>
>Regards,
>Gandhi
>
>-----Original Message-----
>From: Lin, Chen [mailto:Chen.Lin@childrens.harvard.edu]
>Sent: Monday, February 12, 2018 8:47 PM
>To: dev@ctakes.apache.org
>Subject: Re: Regarding cTAKES Tlinks [EXTERNAL]
>
>Hi Gandhi,
>
>It looks like the newest version is picking up the temporal expression
>complete, ³12th June 2018². The previous version only partially pick up
>³June 2018². It is due to the the improvement of the timex annotator.
>As for the relations(tlinks), the current distributed TLINK model is a
>conventional SVM-based model which is tuned to favor close relation for
>high precision, like "12th June 2018 CONTAINS paracetamol². It can pick
>up some longer-distance relationship as well, but obliviously it fails
>for your case for long distance relations. We are currently researching
>a LSTM-based model, which can take more consideration of sentence
>structure and long-distance relationship. Will update more details in the future.
>
>Best,
>Chen
>
>On 2/12/18, 7:50 AM, "Gandhi Rajan Natarajan"
><Ga...@arisglobal.com> wrote:
>
>>Hi,
>>
>>I have a question related to cTAKES Tlinks.
>>
>>Is there any particular reason why
>>FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator
>>is commented in TemporalSubPipe.piper?
>>
>>Also if I run the following text - "I had fever due to smoking so took
>>paracetomol on 12th June 2018" in temporal demo link -
>>https://urldefense.proofpoint.com/v2/url?u=http-3A__54.68.117.30-3A808
>>0
>>_in
>>dex.jsp&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=PZ241
>>C
>>wYZ
>>3AszaTEBtM2wl3EcIjNNNeKX8q7N_mt-aI&m=CTJyQ3_c8JXxv2h1gPaq-jZ6hwp-2dKTG
>>q IrJ RkC7Yk&s=dOVZEd9mrbu0NtEHUZorIzmzEFC_ghg3l8l53ed4O_M&e= , I get
>>the following TLinks:
>>
>>"June 2018 CONTAINS fever , June 2018 CONTAINS smoking , June 2018
>>CONTAINS paracetomol"
>>
>>But if I run the same text in the latest cTAKES using
>>TemporalSubPipe.piper, I get only "12th June 2018 CONTAINS paracetomol"
>>as Tlinks.
>>
>>Is it due to any recent changes in cTAKES?
>>
>>Please advise.
>>
>>
>>Regards,
>>Gandhi
>>
>>This email and any files transmitted with it are confidential and
>>intended solely for the use of the individual or entity to whom they
>>are addressed. If you are not the named addressee you should not
>>disseminate, distribute or copy this e-mail. Please notify the sender
>>or system manager by email immediately if you have received this
>>e-mail by mistake and delete this e-mail from your system. If you are
>>not the intended recipient you are notified that disclosing, copying,
>>distributing or taking any action in reliance on the contents of this
>>information is strictly prohibited and against the law.
>
>This email and any files transmitted with it are confidential and
>intended solely for the use of the individual or entity to whom they
>are addressed. If you are not the named addressee you should not
>disseminate, distribute or copy this e-mail. Please notify the sender
>or system manager by email immediately if you have received this e-mail
>by mistake and delete this e-mail from your system. If you are not the
>intended recipient you are notified that disclosing, copying,
>distributing or taking any action in reliance on the contents of this
>information is strictly prohibited and against the law.
Re: Regarding cTAKES Tlinks [EXTERNAL]
Posted by "Lin, Chen" <Ch...@childrens.harvard.edu>.
Mmm. Frankly, I don’t know the rational behind commenting out
“FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator” in
that piper file. The TLINK model does take some of the event properties
(polarity, uncertainty, contextual modality, semantic types, etc.) for
classification features. Without those features the classifier may lose
its grip. Have you tried commenting back the line?
Best,
Chen
On 2/12/18, 10:23 AM, "Gandhi Rajan Natarajan"
<Ga...@arisglobal.com> wrote:
>Hi Chen,
>
>Thanks a lot for your response.
>
>So I guess this behavior is nothing to do with commented out
>'FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator'
>in ' TemporalSubPipe.piper'?
>
>Thanks again.
>
>Regards,
>Gandhi
>
>-----Original Message-----
>From: Lin, Chen [mailto:Chen.Lin@childrens.harvard.edu]
>Sent: Monday, February 12, 2018 8:47 PM
>To: dev@ctakes.apache.org
>Subject: Re: Regarding cTAKES Tlinks [EXTERNAL]
>
>Hi Gandhi,
>
>It looks like the newest version is picking up the temporal expression
>complete, ³12th June 2018². The previous version only partially pick up
>³June 2018². It is due to the the improvement of the timex annotator.
>As for the relations(tlinks), the current distributed TLINK model is a
>conventional SVM-based model which is tuned to favor close relation for
>high precision, like "12th June 2018 CONTAINS paracetamol². It can pick
>up some longer-distance relationship as well, but obliviously it fails
>for your case for long distance relations. We are currently researching a
>LSTM-based model, which can take more consideration of sentence structure
>and long-distance relationship. Will update more details in the future.
>
>Best,
>Chen
>
>On 2/12/18, 7:50 AM, "Gandhi Rajan Natarajan"
><Ga...@arisglobal.com> wrote:
>
>>Hi,
>>
>>I have a question related to cTAKES Tlinks.
>>
>>Is there any particular reason why
>>FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator
>>is commented in TemporalSubPipe.piper?
>>
>>Also if I run the following text - "I had fever due to smoking so took
>>paracetomol on 12th June 2018" in temporal demo link -
>>https://urldefense.proofpoint.com/v2/url?u=http-3A__54.68.117.30-3A8080
>>_in
>>dex.jsp&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=PZ241C
>>wYZ
>>3AszaTEBtM2wl3EcIjNNNeKX8q7N_mt-aI&m=CTJyQ3_c8JXxv2h1gPaq-jZ6hwp-2dKTGq
>>IrJ RkC7Yk&s=dOVZEd9mrbu0NtEHUZorIzmzEFC_ghg3l8l53ed4O_M&e= , I get the
>>following TLinks:
>>
>>"June 2018 CONTAINS fever , June 2018 CONTAINS smoking , June 2018
>>CONTAINS paracetomol"
>>
>>But if I run the same text in the latest cTAKES using
>>TemporalSubPipe.piper, I get only "12th June 2018 CONTAINS paracetomol"
>>as Tlinks.
>>
>>Is it due to any recent changes in cTAKES?
>>
>>Please advise.
>>
>>
>>Regards,
>>Gandhi
>>
>>This email and any files transmitted with it are confidential and
>>intended solely for the use of the individual or entity to whom they
>>are addressed. If you are not the named addressee you should not
>>disseminate, distribute or copy this e-mail. Please notify the sender
>>or system manager by email immediately if you have received this e-mail
>>by mistake and delete this e-mail from your system. If you are not the
>>intended recipient you are notified that disclosing, copying,
>>distributing or taking any action in reliance on the contents of this
>>information is strictly prohibited and against the law.
>
>This email and any files transmitted with it are confidential and
>intended solely for the use of the individual or entity to whom they are
>addressed. If you are not the named addressee you should not disseminate,
>distribute or copy this e-mail. Please notify the sender or system
>manager by email immediately if you have received this e-mail by mistake
>and delete this e-mail from your system. If you are not the intended
>recipient you are notified that disclosing, copying, distributing or
>taking any action in reliance on the contents of this information is
>strictly prohibited and against the law.
RE: Regarding cTAKES Tlinks [EXTERNAL]
Posted by Gandhi Rajan Natarajan <Ga...@arisglobal.com>.
Hi Chen,
Thanks a lot for your response.
So I guess this behavior is nothing to do with commented out 'FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator' in ' TemporalSubPipe.piper'?
Thanks again.
Regards,
Gandhi
-----Original Message-----
From: Lin, Chen [mailto:Chen.Lin@childrens.harvard.edu]
Sent: Monday, February 12, 2018 8:47 PM
To: dev@ctakes.apache.org
Subject: Re: Regarding cTAKES Tlinks [EXTERNAL]
Hi Gandhi,
It looks like the newest version is picking up the temporal expression complete, ³12th June 2018². The previous version only partially pick up ³June 2018². It is due to the the improvement of the timex annotator.
As for the relations(tlinks), the current distributed TLINK model is a conventional SVM-based model which is tuned to favor close relation for high precision, like "12th June 2018 CONTAINS paracetamol². It can pick up some longer-distance relationship as well, but obliviously it fails for your case for long distance relations. We are currently researching a LSTM-based model, which can take more consideration of sentence structure and long-distance relationship. Will update more details in the future.
Best,
Chen
On 2/12/18, 7:50 AM, "Gandhi Rajan Natarajan"
<Ga...@arisglobal.com> wrote:
>Hi,
>
>I have a question related to cTAKES Tlinks.
>
>Is there any particular reason why
>FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator
>is commented in TemporalSubPipe.piper?
>
>Also if I run the following text - "I had fever due to smoking so took
>paracetomol on 12th June 2018" in temporal demo link -
>https://urldefense.proofpoint.com/v2/url?u=http-3A__54.68.117.30-3A8080
>_in
>dex.jsp&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=PZ241C
>wYZ
>3AszaTEBtM2wl3EcIjNNNeKX8q7N_mt-aI&m=CTJyQ3_c8JXxv2h1gPaq-jZ6hwp-2dKTGq
>IrJ RkC7Yk&s=dOVZEd9mrbu0NtEHUZorIzmzEFC_ghg3l8l53ed4O_M&e= , I get the
>following TLinks:
>
>"June 2018 CONTAINS fever , June 2018 CONTAINS smoking , June 2018
>CONTAINS paracetomol"
>
>But if I run the same text in the latest cTAKES using
>TemporalSubPipe.piper, I get only "12th June 2018 CONTAINS paracetomol"
>as Tlinks.
>
>Is it due to any recent changes in cTAKES?
>
>Please advise.
>
>
>Regards,
>Gandhi
>
>This email and any files transmitted with it are confidential and
>intended solely for the use of the individual or entity to whom they
>are addressed. If you are not the named addressee you should not
>disseminate, distribute or copy this e-mail. Please notify the sender
>or system manager by email immediately if you have received this e-mail
>by mistake and delete this e-mail from your system. If you are not the
>intended recipient you are notified that disclosing, copying,
>distributing or taking any action in reliance on the contents of this
>information is strictly prohibited and against the law.
This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
Re: Regarding cTAKES Tlinks [EXTERNAL]
Posted by "Lin, Chen" <Ch...@childrens.harvard.edu>.
Hi Gandhi,
It looks like the newest version is picking up the temporal expression
complete, ³12th June 2018². The previous version only partially pick up
³June 2018². It is due to the the improvement of the timex annotator.
As for the relations(tlinks), the current distributed TLINK model is a
conventional SVM-based model which is tuned to favor close relation for
high precision, like "12th June 2018 CONTAINS paracetamol². It can pick up
some longer-distance relationship as well, but obliviously it fails for
your case for long distance relations. We are currently researching a
LSTM-based model, which can take more consideration of sentence structure
and long-distance relationship. Will update more details in the future.
Best,
Chen
On 2/12/18, 7:50 AM, "Gandhi Rajan Natarajan"
<Ga...@arisglobal.com> wrote:
>Hi,
>
>I have a question related to cTAKES Tlinks.
>
>Is there any particular reason why
>FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator is
>commented in TemporalSubPipe.piper?
>
>Also if I run the following text - "I had fever due to smoking so took
>paracetomol on 12th June 2018" in temporal demo link -
>https://urldefense.proofpoint.com/v2/url?u=http-3A__54.68.117.30-3A8080_in
>dex.jsp&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=PZ241CwYZ
>3AszaTEBtM2wl3EcIjNNNeKX8q7N_mt-aI&m=CTJyQ3_c8JXxv2h1gPaq-jZ6hwp-2dKTGqIrJ
>RkC7Yk&s=dOVZEd9mrbu0NtEHUZorIzmzEFC_ghg3l8l53ed4O_M&e= , I get the
>following TLinks:
>
>"June 2018 CONTAINS fever , June 2018 CONTAINS smoking , June 2018
>CONTAINS paracetomol"
>
>But if I run the same text in the latest cTAKES using
>TemporalSubPipe.piper, I get only "12th June 2018 CONTAINS paracetomol"
>as Tlinks.
>
>Is it due to any recent changes in cTAKES?
>
>Please advise.
>
>
>Regards,
>Gandhi
>
>This email and any files transmitted with it are confidential and
>intended solely for the use of the individual or entity to whom they are
>addressed. If you are not the named addressee you should not disseminate,
>distribute or copy this e-mail. Please notify the sender or system
>manager by email immediately if you have received this e-mail by mistake
>and delete this e-mail from your system. If you are not the intended
>recipient you are notified that disclosing, copying, distributing or
>taking any action in reliance on the contents of this information is
>strictly prohibited and against the law.