>From your previous email it sounds like you maybe use two negation modules? 
>Some older modules predate the use of standard definitions and so assign 
>values in {0, -1}, while for the machine learning-based module [1] it uses the 
>constants in CONST.java which have values {1,-1}. That's one thing to consider.
Another is that they may operate over different classes. The machine-learning 
operates over IdentifiedAnnotations so it should give them all values of 1,-1, 
which includes the DiseaseDisorderMention class but many others as well. Is it 
possible that new IdentifiedAnnotation types are being created after the 
negation modules run?
Tim

[1] 
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java?view=markup

________________________________________
From: Nicolas Paris <nipari...@gmail.com>
Sent: Monday, March 5, 2018 5:56 PM
To: user@ctakes.apache.org
Subject: Re: Negation attribute annotator always negative [EXTERNAL]

Hi Tim

I spotted a bug in my code. I wasn't annotating all my token as
basic_tokens. Right now, this works as expected.

Still, when I use DiseaseDisorderMention, it works as expected. However,
when I am annotating as regular IdentifiedAnnotation, the polarity is
always 0. Maybe this means this is the correct behavior (the
documentation says FocusAnnotationClass = 
org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation )


Le 05 mars 2018 à 23:23, Nicolas Paris écrivait :
> Hi Tim,
>
> I am using ctakes 4.0.0.
>
> The input text is a mimic note, and I added those example sentence
> within the text. They are separated by newlines, and/or other sentences.
>
> I have tested two negation modules: one is a custom ContextAnnotator
> configured as described there: 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B4.0-2B-2D-2BNE-2BContexts&d=DwIDAw&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=ERGntOhKdzSedh23cqrhpWrsgv9alDebzh-F52qnIDo&s=jOgRWwgFQrW3ZFU3eYoHCa-D_JVbnXHx9qklFYMpvf8&e=
> The other is by using the default one:
> /org/apache/ctakes/assertion/models/polarity/sharpi2b2mipacqnegex/model.jar
> (I guess this is also a negation module too ?)
>
> The pipeline is based on :
> - sentence detection -> stanford parser that produces ctakes sentence 
> annotations
> - token detection -> idem but produces ctakes basic token annotations
> - pos detection -> opennlp mayo released within ctakes
> - chunk detection -> opennlp released within ctakes, not sure what it is
>
> Interestingly, when I am annotating the "disease" word with
> "DiseaseDisorderMention", the polarity is always 1.
> But when I am annotating it with "IdentifiedAnnotation" the polarity is
> always 0, withou any modification of the source code but the annotation
> kind.
>
> My guess is I am missing an AE or something.
>
> Le 05 mars 2018 à 21:46, Miller, Timothy écrivait :
> > Hi Nicholas,
> > Good to hear from you! This is quite a surprising result, it is much
> > more typical in my experience for the negation module to miss a
> > negation (because of long distances), so I'd like to try to replicate
> > this. Do you get that result for each sentence at a time? Or only if
> > all three sentences are like that in the note (as in, separated by
> > newlines)?
> > What version of cTAKES? And can you let me know the exact pipeline
> > components? (Which negation annotator, are there any custom modules?)
> > Thanks
> > Tim
> >
> > On Mon, 2018-03-05 at 01:03 +0100, Nicolas Paris wrote:
> > > Hello
> > >
> > > I have integrated the ctakes PolarityCleartkAnalysisEngine in a
> > > pipeline
> > > such:
> > > - sentence detection
> > > - token detection
> > > - pos detection
> > > - DiseaseDisorderMention annotation
> > > - negation detection
> > >
> > > My example text is:
> > > I have a disease.
> > > I do not have a disease.
> > > I have some disease.
> > >
> > > "Disease" is an instance of DiseaseDisorderMention.
> > >
> > > However, all my example are tagged to negative:
> > >
> > > 05 mars 2018 00:51:30 DEBUG AssertionCleartkAnalysisEngine -
> > > DECODING/EVAL: NEGATED//-1 [570-577]
> > > (org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention)
> > > 05 mars 2018 00:51:30 DEBUG AssertionCleartkAnalysisEngine -
> > > DECODING/EVAL: NEGATED//-1 [594-601]
> > > (org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention)
> > > 05 mars 2018 00:51:30 DEBUG AssertionCleartkAnalysisEngine -
> > > DECODING/EVAL: NEGATED//-1 [1099-1106]
> > > (org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention)
> > >
> > >
> > > Am I missing something in the pipeline ?
> > >
> > > Thanks,
> > >
> > >

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