[CTAKES-449] PolarityCleartkAnalysisEngine slow for large documents

• Type: Improvement
• Status: Closed
• Priority: Critical
• Resolution: Workaround
• Fix Version/s: 4.0.1
• Component/s: ctakes-assertion
• Flags: Important
• Assignee: Sean Finan
• Reporter: Dmitriy Dligach
• Created: 30/Jun/17 14:59
• Updated: 20/Dec/22 17:30
• Resolved: 20/Dec/22 17:30

Description

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