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From Ratan Sharma <ratanc...@gmail.com>
Subject Re: SubjectClearTkAnalysisEngine not working [EXTERNAL]
Date Tue, 16 Jan 2018 19:40:12 GMT
I am trying to find out something like If an entity falls in one of these
category, and my understanding was subject can get me these information.

SUBJECT it belongs to like -
*"Vital Signs", "BP", "Physical Examination", "Family Medical History",
"Lab Results"*

Any idea how to achieve this.


On Wed, Jan 17, 2018 at 1:05 AM, Miller, Timothy <
Timothy.Miller@childrens.harvard.edu> wrote:

> What output would you like? What are you expecting?
>
> This field in theory could have a few different values: patient,
> family_member, other, donor(iirc?)
>
> But in reality our training data was very skewed towards the patient
> label, and the representation we used for training is not great at
> picking up section-wide cues that would be helpful (like a family
> history section header). So in practice it almost always will say
> "patient." It may occasionally get something very obvious: "Mother had
> breast cancer"
> I don't know if it will get this exact example, it probably needs to
> look exactly like a training instance because we had very few to
> generalize from.
> Thanks
> Tim
>
>
> On Wed, 2018-01-17 at 00:57 +0530, Ratan Sharma wrote:
> > I am able to pull entity information for different section correctly.
> > But
> > facing issues when it comes to pull subject information. The subject
> > is
> > always pulled as "PATIENT".
> >
> > I do have this added in the AssertionPipeline
> > builder.add(
> > SubjectCleartkAnalysisEngine.createAnnotatorDescription() );
> >
> >
> > Here are some sample output :
> >
> > Entity: 3 === Text: Blood Transfusion === Polarity: 1 === Subject:
> > patient
> > === EntityName:
> > org.apache.ctakes.typesystem.type.textsem.SignSymptomMention
> > Entity: 6 === Text: Blood === Polarity: 1 === Subject: patient ===
> > EntityName:
> > org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention
> > Entity: 3 === Text: Transfusion Reaction === Polarity: 1 === Subject:
> > patient === EntityName:
> > org.apache.ctakes.typesystem.type.textsem.SignSymptomMention
> > Entity: 5 === Text: Transfusion === Polarity: 1 === Subject: patient
> > ===
> > EntityName:
> > org.apache.ctakes.typesystem.type.textsem.ProcedureMention
> > Entity: 2 === Text: HIV === Polarity: 1 === Subject: patient ===
> > EntityName:
> > org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention
> > Entity: 6 === Text: Sickle Cell === Polarity: 1 === Subject: patient
> > ===
> > EntityName:
> > org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention
> > Entity: 2 === Text: Neurologic Disorders === Polarity: 1 === Subject:
> > patient === EntityName:
> > org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention
> > Entity: 2 === Text: Autoimmune Disorders === Polarity: 1 === Subject:
> > patient === EntityName:
> > org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention
> > Entity: 3 === Text: Autoimmune === Polarity: 1 === Subject: patient
> > ===
> > EntityName:
> > org.apache.ctakes.typesystem.type.textsem.SignSymptomMention
> > Entity: 2 === Text: Autoimmune Disorders === Polarity: -1 ===
> > Subject:
> > patient === EntityName:
> > org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention
> > Entity: 3 === Text: Autoimmune === Polarity: 1 === Subject: patient
> > ===
> > EntityName:
> > org.apache.ctakes.typesystem.type.textsem.SignSymptomMention

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