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Posted to dev@ctakes.apache.org by Petr Zalesky <pz...@inferscience.com> on 2014/11/15 17:04:27 UTC
Chest pain absent. - polarity
I have been investigating how polarity on a sign/symptom gets set and ran
into interesting issue. If a physician's note in a history of present
illness (HPI) says something like:
“Absence of chest pain.”
“Denied chest pain.”
“Chest pain resolved.”
Then cTAKES picks up the term "chest pain", assigns it the correct SNOMED
codes and sets the polarity to -1. However, some of the de-identified
samples say:
"Chest pain absent."
In this case it is also picked up by cTAKES but in this case the polarity
is set to positive one (1). I have been trying to figure out if there is a
way to configure cTAKES to detect that. Any suggestions?
Re: Chest pain absent. - polarity
Posted by Petr Zalesky <pz...@inferscience.com>.
Pei,
Thank you for your prompt response. I downloaded the current released
binary about a week ago from http://ctakes.apache.org/downloads.cgi
(apache-ctakes-3.2.0-bin.tar.gz) so it would be the 3.2.0. I will try the
3.2.1-rc1/trunk to see if it is makes any difference.
Best,
Petr
On Sat, Nov 15, 2014 at 5:16 PM, Pei Chen <ch...@apache.org> wrote:
> Petr,
> Which version of cTAKES are you using? < 3.2.0 or latest 3.2.1-rc1/trunk?
> Both default to use a Machine Learning based polarity algorithm. If it is
> missed, more training examples is probably the way to go.
> The latest one uses clearTK and trained with different features and
> training data so I would be curious to see if that one picks up your
> examples.
>
> On Sat, Nov 15, 2014 at 11:04 AM, Petr Zalesky <pz...@inferscience.com>
> wrote:
>
> > I have been investigating how polarity on a sign/symptom gets set and ran
> > into interesting issue. If a physician's note in a history of present
> > illness (HPI) says something like:
> >
> > “Absence of chest pain.”
> >
> > “Denied chest pain.”
> >
> > “Chest pain resolved.”
> >
> > Then cTAKES picks up the term "chest pain", assigns it the correct SNOMED
> > codes and sets the polarity to -1. However, some of the de-identified
> > samples say:
> >
> > "Chest pain absent."
> >
> > In this case it is also picked up by cTAKES but in this case the polarity
> > is set to positive one (1). I have been trying to figure out if there
> is a
> > way to configure cTAKES to detect that. Any suggestions?
> >
>
--
Petr Zalesky
CTO
Inferscience, Inc
Re: Chest pain absent. - polarity
Posted by Petr Zalesky <pz...@inferscience.com>.
Pei,
Thank you for your response. I got all the dev tools and checked out and
built ctakes from here:
https://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.2.1-rc1/, updated the
various places with my umls credentials and ran two sentences using CVD and
the AggregatePlainUMLSProcessor:
"Absence of chest pain." yields negative polarity
"Chest pain absent." yields positive polarity (see the attached screen
shot).
Would you mind pointing me to instructions on how to "train" ctakes to pick
up my example?
Thank you for your help.
Best,
Petr
On Sat, Nov 15, 2014 at 5:16 PM, Pei Chen <ch...@apache.org> wrote:
> Petr,
> Which version of cTAKES are you using? < 3.2.0 or latest 3.2.1-rc1/trunk?
> Both default to use a Machine Learning based polarity algorithm. If it is
> missed, more training examples is probably the way to go.
> The latest one uses clearTK and trained with different features and
> training data so I would be curious to see if that one picks up your
> examples.
>
> On Sat, Nov 15, 2014 at 11:04 AM, Petr Zalesky <pz...@inferscience.com>
> wrote:
>
> > I have been investigating how polarity on a sign/symptom gets set and ran
> > into interesting issue. If a physician's note in a history of present
> > illness (HPI) says something like:
> >
> > “Absence of chest pain.”
> >
> > “Denied chest pain.”
> >
> > “Chest pain resolved.”
> >
> > Then cTAKES picks up the term "chest pain", assigns it the correct SNOMED
> > codes and sets the polarity to -1. However, some of the de-identified
> > samples say:
> >
> > "Chest pain absent."
> >
> > In this case it is also picked up by cTAKES but in this case the polarity
> > is set to positive one (1). I have been trying to figure out if there
> is a
> > way to configure cTAKES to detect that. Any suggestions?
> >
>
--
Petr Zalesky
CTO
Inferscience, Inc
Re: Chest pain absent. - polarity
Posted by Pei Chen <ch...@apache.org>.
Petr,
Which version of cTAKES are you using? < 3.2.0 or latest 3.2.1-rc1/trunk?
Both default to use a Machine Learning based polarity algorithm. If it is
missed, more training examples is probably the way to go.
The latest one uses clearTK and trained with different features and
training data so I would be curious to see if that one picks up your
examples.
On Sat, Nov 15, 2014 at 11:04 AM, Petr Zalesky <pz...@inferscience.com>
wrote:
> I have been investigating how polarity on a sign/symptom gets set and ran
> into interesting issue. If a physician's note in a history of present
> illness (HPI) says something like:
>
> “Absence of chest pain.”
>
> “Denied chest pain.”
>
> “Chest pain resolved.”
>
> Then cTAKES picks up the term "chest pain", assigns it the correct SNOMED
> codes and sets the polarity to -1. However, some of the de-identified
> samples say:
>
> "Chest pain absent."
>
> In this case it is also picked up by cTAKES but in this case the polarity
> is set to positive one (1). I have been trying to figure out if there is a
> way to configure cTAKES to detect that. Any suggestions?
>