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The model files for Contextual Modality can be found at  target/eval/event-properties/train_and_test/contextualModality

Creating Temporal Output in Anafora XML Format

Within-sentence event-event and event-time temporal relations can be output in XML format that is used by Anafora using org.apache.ctakes.temporal.eval.EvaluationOfBothEEAndETRelations.java

That program uses the following two annotators:

  org.apache.ctakes.temporal.ae.EventTimeSelfRelationAnnotator

  org.apache.ctakes.temporal.ae.EventEventRelationAnnotator

Required parameters for  EvaluationOfBothEEAndETRelations

--text <path to the folder contains the THYME raw notes>

--format Anafora

--xml <path to the folder contains the THYME gold annotation files in xml format >

--xmi <path to the target folder of xmi file output>

--kernelParams "c 0.001953125 t 0.03125 d 3 g 1.0 S 1 C + L 0.5 T 0.1 N 3"

--patients 1-218

--useGoldAttributes

--test

--skipTrain

  skipTrain is now a required parameter. The system will use pretrained models in the  target/eval/thyme/train_and_test/  folder, and directly predict on the test split.

--anaforaOutput <path to the target folder of xml file output>

Potentially Improving Temporal Pipeline Results

When running the temporal module, you may want to consider using the newer BIO sentence detector instead of the original sentence detector - on the THYME data the BIO sentence detector achieved better results. However, the BIO sentence detector is not better in all cases.

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A demo of the cTAKES Temporal Module can be found at http://5254.2768.22117.20630:8080/index.jsp.

Anchor
ChangingSentenceDetector ChangingSentenceDetector

 Using Using the BIO Sentence Detector with the Temporal Pipeline

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