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https://issues.apache.org/jira/browse/CTAKES-449?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16560128#comment-16560128
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Dmitriy Dligach commented on CTAKES-449:
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First of all, thank you Sean for looking into this issue.
We tested this and unfortunately it looks like the problem is still there. It
takes a day to process two files (one about 6M and the other about 1M in
size)...
> 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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