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.