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From "Dligach, Dmitriy" <ddlig...@luc.edu>
Subject negation/uncertainty: pipeline runs very slowly
Date Wed, 24 May 2017 14:33:40 GMT
Dear cTAKES developers, 

I am observing something strange. As soon as I add at the end of my pipeline the uncertainty/negation
AEs:

aggregateBuilder.add( PolarityCleartkAnalysisEngine.createAnnotatorDescription() );
aggregateBuilder.add( UncertaintyCleartkAnalysisEngine.createAnnotatorDescription() );

the pipeline becomes 10-20 times slower. I just confirmed this again. As soon as I remove
these two AEs at the end of my pipeline, it runs very fast again.

It seems to get stuck often right after it outputs this warning:
WARN DocumentIDAnnotationUtil - Unable to find DocumentIDAnnotation

If I remove the two AEs, this warning disappears.

The full pipeline is here:
https://github.com/dmitriydligach/ctakes-misc/blob/master/src/main/java/org/apache/ctakes/pipelines/UmlsLookupPipeline.java

Any clues?

Thank you very much,

Dima




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