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From "Savova, Guergana" <Guergana.Sav...@childrens.harvard.edu>
Subject RE: cTakes polarity problem
Date Wed, 31 Dec 2014 16:24:07 GMT
cTAKES also implements a rule-based approach to the negation/polarity problem. It was the default
until the latest release. You are free to use the rule-based implementation and compare results
with the ML approach.
--Guergana

-----Original Message-----
From: Michael J Gurley [mailto:m-gurley@northwestern.edu] 
Sent: Wednesday, December 31, 2014 11:22 AM
To: dev@ctakes.apache.org
Subject: Re: cTakes polarity problem

I think this demonstrates that machine learning is not the right approach to the negation/polarity
problem.


Michael Gurley
m-gurley@northwestern.edu
312 925 3268
Northwestern University Clinical and Translational Sciences Institute
(NUCATS)
http://www.nucats.northwestern.edu
Rubloff Building
750 N Lake Shore Drive, 11th Floor
Chicago, IL 60611







On 12/31/14 9:13 AM, "Miller, Timothy"
<Timothy.Miller@childrens.harvard.edu> wrote:

>Hi Yu,
>
>The new polarity module is machine-learning based so it is not always 
>easy to diagnose accuracy issues. But generally it might mean there was 
>no example like that in the training data. It was trained on multiple 
>corpora, but sometimes certain phrases slip through the cracks, and 
>"Deny hepatitis," while possible in the truncated language of clinical 
>notes, seems like an unlikely phrase and so it may not be in our data.
>Is that a real example you saw or just a minimum (not) working example?
>If not do you have a real example (i.e. a whole sentence) where "deny"
>should cause a negation but does not? If so I will look into it. We 
>have had a few reports like this so it may be worth keeping track of 
>missed examples for future iterations of the module. It is important 
>that they be real examples "from the wild" though.
>
>(As an aside, machine learning methods don't understand language the 
>way people do so even if it seems obvious to a human that "Deny <disease>."
>should be negated, if it looks different enough from the context of an 
>example from the training data the ML will sometimes fall back to the 
>majority class of "Not negated".)
>
>Tim
>
>
>On 12/31/2014 10:03 AM, Yu Liang wrote:
>> I have a quick question about CTAKES.
>> I am using AE ³AggregatePlaintextUMLSProcessor.xml² and want to get 
>>some negation results by referring to polarity attribute.
>> However, it turns out, for example ³Negative for hepatitis², is not 
>>negated. I think it is weird and I tried ³No hepatitis², ³ Denies 
>>hepatitis² which return ³polarity= -1², but ³Deny hepatitis.² returns 
>>³polarity=1².
>>
>> any one could give me some clue that what is wrong? Thank you!
>


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