Hi Kathy, I am glad that you checked the wiki! I should have pointed to it ...
In the example I sent the "relevant distance" between trigger terms and events would be 10. There isn't any maximum as far as I know, but I think that 10 is the most that I've ever used. The default is 7, and you can try with that (remove "*=*") before increasing the number(s). The piper files aren't source code, they are just plain text and don't require compiling, etc. How are you running the pipeline right now? From a binary with a bin/run* script? Sean -----Original Message----- From: Kathy Ferro [mailto:healthcare1...@gmail.com] Sent: Tuesday, November 28, 2017 12:11 PM To: dev@ctakes.apache.org Subject: Re: polarity tag in output for mention/concept. [EXTERNAL] Sean, Thank you for information. I was reading the document. So, the MaxLeftScopeSize and MaxRightScopeSize are limit up to 10? Is there anyway to adjust it without modify the source code? https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B4.0-2B-2D-2BNE-2BContexts&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=4K9fxMmBiI0QZB0UhriFp_YvXDL8rmXtGRiKVgxMCPE&s=hsCB9xPXLC8fpiwrGXuEW9snw_WZbY0e-E-mhPOO9N8&e= Thanks again, Kathy On Tue, Nov 28, 2017 at 9:31 AM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > 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://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_ > confluence_display_CTAKES_Piper-2BFiles&d=DwIBaQ&c=qS4goWBT7poplM69zy_ > 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao > &m=4K9fxMmBiI0QZB0UhriFp_YvXDL8rmXtGRiKVgxMCPE&s=rXqsHq_poDXmwkCf3L2M5 > ZlsByCbUHcSWD84JQQuh5A&e= > > Sean > > -----Original Message----- > From: Kathy Ferro [mailto:healthcare1...@gmail.com] > Sent: Monday, November 27, 2017 8:10 PM > To: dev@ctakes.apache.org > 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 >
