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Programs
jbjorne edited this page Jul 17, 2012
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Many TEES modules can be used as independent programs. In addition to the main programs classify, train, batch and configure, the most important ones are the external tool wrappers, which allow running these tools on any interaction XML file. This page lists the TEES files that can be run as independent programs. Additionally, there is a number of small interaction XML processing utilities in the subdirectory Utils/InteractionXML.
| Program | Description | |:-----------|:-----------|:-----------| | batch.py | Batch process a tree of input files | | classify.py | Predict events/relations | | configure.py | Configure TEES | | train.py | Train a new event/relation extraction model |
| Program | Location | Description |
|---|---|---|
| Preprocessor.py | Detectors | A tool chain for making interaction XML, sentence splitting, NER and parsing |
| BANNER.py | Tools | BANNER named entity recognizer wrapper |
| BLLIPParser.py | Tools | BLLIP parser wrapper |
| GeniaSentenceSplitter.py | Tools | GENIA Sentence Splitter wrapper |
| SentenceSplitter.py | Tools | For inserting an existing sentence splitting |
| StanfordParser.py | Tools | Stanford Parser dependency converter wrapper |
| Program | Location | Description |
|---|---|---|
| Analyze.py | Utils/STFormat | ST format statistics |
| BioNLP11GeniaTools.py | Evaluators | Evaluate BioNLP Shared Task predictions |
| BioTextExampleWriter.py | ExampleWriters | Write predicted examples to interaction XML |
| Compare.py | Utils/STFormat | Compare event distribution |
| CompareExamples.py | Utils | Analyze SVM example files |
| CompareFeatures.py | Utils | Analyze SVM example files |
| ConvertXML.py | Utils/STFormat | Conversion between BioNLP ST format and Interaction XML |
| DDITools.py | Utils/Convert | Tools for the DDI'11 Shared Task |
| DetectHeads.py | Utils | Recalculate head token offsets |
| Equiv.py | Utils/STFormat | Resolve annotated equivalences |
| Evaluator.py | Evaluators | Calculate f-score and other statistics |
| ExampleBuilder.py | ExampleBuilders | Build machine learning examples from interaction XML |
| FindHeads.py | Utils | Recalculate head token offsets |
| Release.py | Utils | Make TEES release files |
| RoundTrip.py | Utils/STFormat | Convert ST format to interaction XML and back |
| STTools.py | Utils/STFormat | ST format input and output |
| SVMMultiClassClassifier.py | Classifiers | Joachims SVM Multiclass classifier wrapper |
| SVMMultiClassModelUtils.py | Classifiers | Joachims SVM Multiclass model file processing |
| Scores.py | Utils/STFormat | Analyze confidence scores |
| SubtiWiki.py | Utils/Convert | Extract information from SubtiWiki for the BioNLP'11 REN task |
| Validate.py | Utils/STFormat | Validate BioNLP'11 event constraints |
| convertBioNLP.py | Utils/Convert | BioNLP'11 Shared Task corpus conversion |
| convertDDI.py | Utils/Convert | DDI'11 Shared Task corpus conversion |