Package TEES

Turku Event Extraction System.

Turku Event Extraction System is an NLP tool for event and relation extraction. For information on using TEES, see the documentation at https://github.com/jbjorne/TEES/wiki. The API documentation is generated with Epydoc.

Submodules

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TEES.Classifiers: Classifiers predict the class of an example.
- TEES.Classifiers.AllCorrectClassifier
- TEES.Classifiers.AllTrueClassifier
- TEES.Classifiers.Classifier: Base class for classifiers
- TEES.Classifiers.ExternalClassifier
- TEES.Classifiers.SVMMultiClassClassifier
- TEES.Classifiers.SVMMultiClassModelUtils
TEES.Core: Event Detector system central classes.
- TEES.Core.DivideCorpus: Pseudorandomly distributed subsets
- TEES.Core.DivideExamples: Pseudorandomly distributed subsets
- TEES.Core.ExampleUtils: Tools for writing and reading classifier example files
- TEES.Core.IdSet: Manages classification class and feature ids.
- TEES.Core.Model: For storing the results of TEES training.
- TEES.Core.RecallAdjust: Trade precision for recall
- TEES.Core.SentenceGraph: Main class for representing a sentence
- TEES.Core.SimpleGraph: For representing the event argument and dependency graphs.
- TEES.Core.Split: Functions for dividing data into random sets.
TEES.Detectors: A high-level, object oriented interface to TEES.
- TEES.Detectors.CODetector
- TEES.Detectors.Detector: The base class for the object oriented interface.
- TEES.Detectors.EdgeDetector
- TEES.Detectors.EntityDetector
- TEES.Detectors.EventDetector
- TEES.Detectors.ModifierDetector
- TEES.Detectors.Preprocessor
- TEES.Detectors.SingleStageDetector
- TEES.Detectors.StepSelector
- TEES.Detectors.ToolChain
- TEES.Detectors.UnmergingDetector
TEES.Evaluators: Evaluators for measuring classifier performance.
- TEES.Evaluators.AveragingMultiClassEvaluator: For multi-class classifications
- TEES.Evaluators.BinaryEvaluator: For two-class classification
- TEES.Evaluators.BioNLP11GeniaTools
- TEES.Evaluators.EvaluateInteractionXML: For comparing a predicted interaction XML against a gold standard
- TEES.Evaluators.Evaluator: Base class for Evaluators
TEES.ExampleBuilders: Turn input data into machine learning examples.
- TEES.ExampleBuilders.EdgeExampleBuilder: Edge Examples
- TEES.ExampleBuilders.EntityExampleBuilder: Trigger examples
- TEES.ExampleBuilders.ExampleBuilder: Base class for ExampleBuilders
- TEES.ExampleBuilders.ExampleStats
- TEES.ExampleBuilders.FeatureBuilders: Provide methods used by several ExampleBuilders
  - TEES.ExampleBuilders.FeatureBuilders.BacteriaRenamingFeatureBuilder
  - TEES.ExampleBuilders.FeatureBuilders.BioInferOntologyFeatureBuilder: BioInfer ontology based features
  - TEES.ExampleBuilders.FeatureBuilders.DrugFeatureBuilder
  - TEES.ExampleBuilders.FeatureBuilders.EVEXFeatureBuilder: EVEX Feature Builder
  - TEES.ExampleBuilders.FeatureBuilders.EdgeFeatureBuilder: Dependency edge features
  - TEES.ExampleBuilders.FeatureBuilders.EventFeatureBuilder
  - TEES.ExampleBuilders.FeatureBuilders.FeatureBuilder: Base class for FeatureBuilders
  - TEES.ExampleBuilders.FeatureBuilders.GiulianoFeatureBuilder: Giuliano Feature Builder
  - TEES.ExampleBuilders.FeatureBuilders.GraphKernelFeatureBuilder
  - TEES.ExampleBuilders.FeatureBuilders.MultiEdgeFeatureBuilder: Shortest path features
  - TEES.ExampleBuilders.FeatureBuilders.NameGazetteer
  - TEES.ExampleBuilders.FeatureBuilders.NodalidaFeatureBuilder
  - TEES.ExampleBuilders.FeatureBuilders.RELFeatureBuilder
  - TEES.ExampleBuilders.FeatureBuilders.RandomFeatureBuilder
  - TEES.ExampleBuilders.FeatureBuilders.TokenFeatureBuilder
  - TEES.ExampleBuilders.FeatureBuilders.TriggerFeatureBuilder
  - TEES.ExampleBuilders.FeatureBuilders.WordNetFeatureBuilder
- TEES.ExampleBuilders.ModifierExampleBuilder: Speculation and negation examples
- TEES.ExampleBuilders.PhraseTriggerExampleBuilder: Trigger examples
- TEES.ExampleBuilders.UnmergingExampleBuilder: Edge Examples
TEES.ExampleWriters: ExampleWriters convert machine learning examples back to interaction xml.
- TEES.ExampleWriters.BioTextExampleWriter: Wrapper for all interaction XML example writers
- TEES.ExampleWriters.EdgeExampleWriter
- TEES.ExampleWriters.EntityExampleWriter
- TEES.ExampleWriters.ModifierExampleWriter
- TEES.ExampleWriters.PhraseTriggerExampleWriter
- TEES.ExampleWriters.SentenceExampleWriter: Base class for ExampleWriters working with interaction XML.
- TEES.ExampleWriters.UnmergingExampleWriter
TEES.Tools
- TEES.Tools.BANNER
- TEES.Tools.BLLIPParser
- TEES.Tools.GeniaEventsToSharedTask
- TEES.Tools.GeniaSentenceSplitter
- TEES.Tools.ProcessUtils
- TEES.Tools.SentenceSplitter
- TEES.Tools.StanfordParser
- TEES.Tools.Tool
TEES.Utils: Supporting event detector components.
- TEES.Utils.CompareExamples
- TEES.Utils.CompareFeatures
- TEES.Utils.Connection
  - TEES.Utils.Connection.ClusterConnection
  - TEES.Utils.Connection.Connection
  - TEES.Utils.Connection.LSFConnection
  - TEES.Utils.Connection.PBSConnection
  - TEES.Utils.Connection.SLURMConnection
  - TEES.Utils.Connection.UnixConnection
- TEES.Utils.Convert
  - TEES.Utils.Convert.DDITools
  - TEES.Utils.Convert.SubtiWiki
  - TEES.Utils.Convert.convertBioNLP
  - TEES.Utils.Convert.convertDDI
  - TEES.Utils.Convert.processLPSN
- TEES.Utils.DefaultSettings
- TEES.Utils.DetectHeads
- TEES.Utils.Download
- TEES.Utils.ElementTreeUtils: Functions for easier use of cElementTree.
- TEES.Utils.FindHeads
- TEES.Utils.InteractionXML: Tools for working with interaction (and analysis) XML.
  - TEES.Utils.InteractionXML.Catenate
  - TEES.Utils.InteractionXML.CompareParse
  - TEES.Utils.InteractionXML.ConvertPMC
  - TEES.Utils.InteractionXML.CopyParse
  - TEES.Utils.InteractionXML.CorpusElements
  - TEES.Utils.InteractionXML.DeleteAttributes
  - TEES.Utils.InteractionXML.DeleteElements
  - TEES.Utils.InteractionXML.DivideSets
  - TEES.Utils.InteractionXML.ExportParse
  - TEES.Utils.InteractionXML.ExtendTriggers
  - TEES.Utils.InteractionXML.FixAltOffsets
  - TEES.Utils.InteractionXML.IDUtils
  - TEES.Utils.InteractionXML.ListInteractors
  - TEES.Utils.InteractionXML.MakeSubset
  - TEES.Utils.InteractionXML.MapPhrases
  - TEES.Utils.InteractionXML.MergeDuplicateEntities
  - TEES.Utils.InteractionXML.MergeNamedEntityTypes
  - TEES.Utils.InteractionXML.MergeParse
  - TEES.Utils.InteractionXML.MixSets
  - TEES.Utils.InteractionXML.ParseGraph: Program: Classes for working with parse graphs Date: Jan.
  - TEES.Utils.InteractionXML.ParseStats
  - TEES.Utils.InteractionXML.RecalculateIds
  - TEES.Utils.InteractionXML.RemoveDuplicateDependencies
  - TEES.Utils.InteractionXML.RemoveUnconnectedEntities
  - TEES.Utils.InteractionXML.ResolveEPITriggerTypes
  - TEES.Utils.InteractionXML.ResolveIdentityChains
  - TEES.Utils.InteractionXML.SentenceElements
  - TEES.Utils.InteractionXML.SplitMergedElements
  - TEES.Utils.InteractionXML.Subset
- TEES.Utils.Libraries: External programs.
  - TEES.Utils.Libraries.PorterStemmer: Porter Stemming Algorithm This is the Porter stemming algorithm, ported to Python from the version coded up in ANSI C by the author.
  - TEES.Utils.Libraries.combine: Combinations from multiple sequences
  - TEES.Utils.Libraries.progressbar: Text progressbar library for python.
  - TEES.Utils.Libraries.pstat: pstat.py module
  - TEES.Utils.Libraries.stats: stats.py module
- TEES.Utils.Menu
- TEES.Utils.Parameters
- TEES.Utils.ProgressCounter
- TEES.Utils.ProteinNameSplitter
- TEES.Utils.Range: Character offset tools.
- TEES.Utils.Release
- TEES.Utils.STFormat
  - TEES.Utils.STFormat.Analyze
  - TEES.Utils.STFormat.Compare
  - TEES.Utils.STFormat.ConvertXML
  - TEES.Utils.STFormat.Equiv
  - TEES.Utils.STFormat.RoundTrip
  - TEES.Utils.STFormat.STTools
  - TEES.Utils.STFormat.Scores
  - TEES.Utils.STFormat.Validate
- TEES.Utils.Settings
- TEES.Utils.Stream: Capture stdout or stderr messages to a log file
- TEES.Utils.TableUtils
- TEES.Utils.Timer
TEES.batch: Process a large number of input files
TEES.classify: Detect events or relations from text.
TEES.configure: Configure TEES by installing data files and external components.
TEES.setup
TEES.train: Train a new model for event or relation detection.

Variables

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__package__ = None