Hi Kathy, The negation annotator used in the default clinical pipeline is based upon machine learning and trained on real data. It is possible that such "denies" lists were underrepresented in the training data. One thing that you can try is adding another negation annotator. The ContextAnnotator in ctakes-ne-contexts will add negation to terms without removing existing negation. It also has configurable scope/distance that may be helpful.
To use this, create a new piper file containing the two lines load DefaultFastPipeline add ContextAnnotator MaxLeftScopeSize=10 MaxRightScopeSize=10 The default scope sizes are 7, but increasing the MaxRight* might help with your "denies" discoveries. 7 might be ok for the left, so feel free to remove "MaxLeftScopeSize=10" from the line. Then run your piper file (command line, gui, maven profile, etc.) https://cwiki.apache.org/confluence/display/CTAKES/Piper+Files Sean -----Original Message----- From: Kathy Ferro [mailto:[email protected]] Sent: Monday, November 27, 2017 8:10 PM To: [email protected] Subject: polarity tag in output for mention/concept. [EXTERNAL] Good evening, I ran a few sentences through default clinical pipeline. It really reliable if it's only one term after negative, but I am get in-consistent value for polarity for the list of terms. Please see example below. 1. denies fatigue, malaise, fever, weight loss SignSymthomMention: polarity = -1: fatigue, malaise,fever polarity = 1: weight loss. Why does weight loss got single out? 2. denies ear pain or discharge, nasal obstruction or discharge, sore throat polarity = -1: ear pain or discharge polarity = 1: nasal obstruction or discharge, obstruction, sore throat Doesn't even acknowledge the list. 3. denies back pain, joint swelling, joint stiffness, joint pain polarity = -1: back pain, Swelling polarity = 1: Joint swelling, Stiffness, pain What! totally messy the pattern. 4. denied back pain, joint swelling, joint stiffness, joint pain Ok, may be it doesn't like the word denies; I changed to denied, deny, etc.. polarity = -1 : Swelling everything else is 1. My question is: How do I handle the negative claims in the document? Thank you Kathy
