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://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+-+NE+Contexts > 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, > > > > > >
