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.natara...@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.fi...@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....@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" <sean.fi...@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....@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" ><gandhi.natara...@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....@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" >><gandhi.natara...@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. 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