Re: Chest pain absent. - polarity
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 chen...@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 pzale...@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
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
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 pzale...@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?
Re: Chest pain absent. - polarity
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 chen...@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 pzale...@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
