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The model files can be found at target/eval/thyme/train_and_test/event-event.
Evaluating DocTimeRel and Contextual Modality
The evaluation program is org.apache.ctakes.temporal.eval.EvaluationOfEventProperties.java
EvaluationOfEventProperties
uses org.apache.ctakes.temporal.ae.DocTimeRelAnnotator
and org.apache.ctakes.temporal.ae.ContextualModalityAnnotator
The parameters are the same as event-time parameters.
The model files for DocTimeRel can be found at target/eval/event-properties/train_and_test/docTimeRel
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.
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