Tim Miller commented on CTAKES-449:

Found an issue with the evals, it was grabbing the polarity flag from the 
system cas instead of the cas so it wasn't finding any training instances. 
Checking in a fix shortly.

> PolarityCleartkAnalysisEngine slow for large documents
> ------------------------------------------------------
>                 Key: CTAKES-449
>                 URL: https://issues.apache.org/jira/browse/CTAKES-449
>             Project: cTAKES
>          Issue Type: Improvement
>          Components: ctakes-assertion
>            Reporter: Dmitriy Dligach
>            Assignee: Sean Finan
>            Priority: Major
>             Fix For: 4.0.1
> As soon as I add at the end of my pipeline the negation AE:
> aggregateBuilder.add( 
> PolarityCleartkAnalysisEngine.createAnnotatorDescription() );
> The pipeline becomes 50-100 times slower. This likely has to do with the line:
> List<Sentence> sents = new ArrayList<>(JCasUtil.selectCovering(jCas, 
> Sentence.class, entityOrEventMention.getBegin(), 
> entityOrEventMention.getEnd()));
> in AssertionCleartkAnalysisEngine. I am running the pipeline on large files 
> (i.e. having a large number of sentences). The slowdown is caused by the 
> code's obtaining all sentences in a document for each identified annotation.
> The full pipeline is here:
> https://github.com/dmitriydligach/ctakes-misc/blob/master/src/main/java/org/apache/ctakes/pipelines/UmlsLookupPipeline.java

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