SubjectClearTkAnalysisEngine not working

[Ratan Sharma <ra...@gmail.com>]

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

Re: SubjectClearTkAnalysisEngine not working [EXTERNAL]

["Miller, Timothy" <Ti...@childrens.harvard.edu>]

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