Re: Negation attribute annotator always negative [EXTERNAL]
Thanks. I probably use two negation modules. The first one is based on the documentation there https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+-+NE+Contexts It only produces 0 when I am using it (a ContextAnnotator) The second one works quite well and is based on this code org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE; It produces 1 and -1. About the DiseaseDisorderMention versus IdentifiedAnnotation, I just switched them to test, at the same piece of code level. The former works, the other not. Do you recommend to use the [1] negex based on cleartk ML ? Thanks. Le 06 mars 2018 à 12:28, Miller, Timothy écrivait : > 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 > 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 > > > > >
Re: Negation attribute annotator always negative [EXTERNAL]
>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 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, > > > > > >
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://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, > > > > > >
Re: Negation attribute annotator always negative [EXTERNAL]
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, > > > >
Re: Negation attribute annotator always negative [EXTERNAL]
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, > >