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Programs
jbjorne edited this page Feb 25, 2013
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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 |
|---|---|---|
| SVMMultiClassClassifier.py | Classifiers | Joachims SVM Multiclass classifier wrapper |
| SVMMultiClassModelUtils.py | Classifiers | Joachims SVM Multiclass model file processing |
| StructureAnalyzer.py | Detectors | Calculate f-score and other statistics |
| AveragingMultiClassEvaluator.py | Evaluators | Calculate f-score and other statistics |
| BioNLP11GeniaTools.py | Evaluators | Evaluate BioNLP Shared Task predictions |
| Evaluator.py | Evaluators | Calculate f-score and other statistics |
| ExampleBuilder.py | ExampleBuilders | Build machine learning examples from interaction XML |
| BioTextExampleWriter.py | ExampleWriters | Write predicted examples to interaction XML |
| CompareExamples.py | Utils | Analyze SVM example files |
| CompareFeatures.py | Utils | Analyze SVM example files |
| DetectHeads.py | Utils | Recalculate head token offsets |
| FindHeads.py | Utils | Recalculate head token offsets |
| Release.py | Utils | Make TEES release files |
| DDITools.py | Utils/Convert | Tools for the DDI'11 Shared Task |
| SubtiWiki.py | Utils/Convert | Extract information from SubtiWiki for the BioNLP'11 REN task |
| convertBioNLP.py | Utils/Convert | BioNLP Shared Task corpus conversion |
| convertDDI.py | Utils/Convert | DDI'11 Shared Task corpus conversion |
| convertDDI13.py | Utils/Convert | DDI'13 Shared Task corpus conversion |
| Analyze.py | Utils/STFormat | ST format statistics |
| Compare.py | Utils/STFormat | Compare event distribution |
| ConvertXML.py | Utils/STFormat | Conversion between BioNLP ST format and Interaction XML |
| Equiv.py | Utils/STFormat | Resolve annotated equivalences |
| RoundTrip.py | Utils/STFormat | Convert ST format to interaction XML and back |
| STTools.py | Utils/STFormat | ST format input and output |
| Scores.py | Utils/STFormat | Analyze confidence scores |
| Validate.py | Utils/STFormat | Validate BioNLP'11 event constraints |