sparknlp_jsl.annotator.AssertionFilterer#
- class sparknlp_jsl.annotator.AssertionFilterer(classname='com.johnsnowlabs.nlp.annotators.chunker.AssertionFilterer', java_model=None)[source]#
Bases:
AnnotatorModel
Filters entities coming from ASSERTION type annotations and returns the CHUNKS. Filters can be set via a white list on the extracted chunk, the assertion or a regular expression. White list for assertion is enabled by default. To use chunk white list,
criteria
has to be set toisin
. For regex,criteria
has to be set toregex
.Input Annotation types
Output Annotation type
DOCUMENT, CHUNK, ASSERTION
CHUNK
- Parameters:
- whiteList
If defined, list of entities to process. The rest will be ignored
- regex
If defined, list of entities to process. The rest will be ignored.
- criteria
- Tag representing what is the criteria to filter the chunks. possibles values (assertion|isIn|regex)
assertion: Filter by the assertion isIn : Filter by the chunk regex : Filter using a regex
- entitiesConfidence
Entity pairs to remove based on the confidence level
Examples
>>> import sparknlp >>> from sparknlp.base import * >>> from sparknlp.common import * >>> from sparknlp.annotator import * >>> from sparknlp.training import * >>> import sparknlp_jsl >>> from sparknlp_jsl.base import * >>> from sparknlp_jsl.annotator import * >>> from pyspark.ml import Pipeline To see how the assertions are extracted, see the example for AssertionDLModel. Define an extra step where the assertions are filtered >>> assertionFilterer = AssertionFilterer() \ ... .setInputCols(["sentence","ner_chunk","assertion"]) \ ... .setOutputCol("filtered") \ ... .setCriteria("assertion") \ ... .setWhiteList(["present"]) ... >>> assertionPipeline = Pipeline(stages=[ ... documentAssembler, ... sentenceDetector, ... tokenizer, ... embeddings, ... nerModel, ... nerConverter, ... clinicalAssertion, ... assertionFilterer ... ]) ... >>> assertionModel = assertionPipeline.fit(data) >>> result = assertionModel.transform(data)
>>> result.selectExpr("ner_chunk.result", "assertion.result").show(3, truncate=False) +--------------------------------+--------------------------------+ |result |result | +--------------------------------+--------------------------------+ |[severe fever, sore throat] |[present, present] | |[stomach pain] |[absent] | |[an epidural, PCA, pain control]|[present, present, hypothetical]| +--------------------------------+--------------------------------+
>>> result.select("filtered.result").show(3, truncate=False) +---------------------------+ |result | +---------------------------+ |[severe fever, sore throat]| |[] | |[an epidural, PCA] | +---------------------------+
Methods
__init__
([classname, java_model])Initialize this instance with a Java model object.
clear
(param)Clears a param from the param map if it has been explicitly set.
copy
([extra])Creates a copy of this instance with the same uid and some extra params.
explainParam
(param)Explains a single param and returns its name, doc, and optional default value and user-supplied value in a string.
Returns the documentation of all params with their optionally default values and user-supplied values.
extractParamMap
([extra])Extracts the embedded default param values and user-supplied values, and then merges them with extra values from input into a flat param map, where the latter value is used if there exist conflicts, i.e., with ordering: default param values < user-supplied values < extra.
Gets current column names of input annotations.
Gets whether Annotator should be evaluated lazily in a RecursivePipeline.
getOrDefault
(param)Gets the value of a param in the user-supplied param map or its default value.
Gets output column name of annotations.
getParam
(paramName)Gets a param by its name.
getParamValue
(paramName)Gets the value of a parameter.
hasDefault
(param)Checks whether a param has a default value.
hasParam
(paramName)Tests whether this instance contains a param with a given (string) name.
isDefined
(param)Checks whether a param is explicitly set by user or has a default value.
isSet
(param)Checks whether a param is explicitly set by user.
load
(path)Reads an ML instance from the input path, a shortcut of read().load(path).
read
()Returns an MLReader instance for this class.
save
(path)Save this ML instance to the given path, a shortcut of 'write().save(path)'.
set
(param, value)Sets a parameter in the embedded param map.
setCriteria
(s)Set tag representing what is the criteria to filter the chunks.
setInputCols
(*value)Sets column names of input annotations.
setLazyAnnotator
(value)Sets whether Annotator should be evaluated lazily in a RecursivePipeline.
setOutputCol
(value)Sets output column name of annotations.
setParamValue
(paramName)Sets the value of a parameter.
setParams
()setRegex
(value)Sets llist of regex to process.
setWhiteList
(value)Sets list of entities to process.
transform
(dataset[, params])Transforms the input dataset with optional parameters.
write
()Returns an MLWriter instance for this ML instance.
Attributes
criteria
entitiesConfidence
getter_attrs
inputCols
lazyAnnotator
name
outputCol
Returns all params ordered by name.
regex
whiteList
- clear(param)#
Clears a param from the param map if it has been explicitly set.
- copy(extra=None)#
Creates a copy of this instance with the same uid and some extra params. This implementation first calls Params.copy and then make a copy of the companion Java pipeline component with extra params. So both the Python wrapper and the Java pipeline component get copied.
- Parameters:
extra – Extra parameters to copy to the new instance
- Returns:
Copy of this instance
- explainParam(param)#
Explains a single param and returns its name, doc, and optional default value and user-supplied value in a string.
- explainParams()#
Returns the documentation of all params with their optionally default values and user-supplied values.
- extractParamMap(extra=None)#
Extracts the embedded default param values and user-supplied values, and then merges them with extra values from input into a flat param map, where the latter value is used if there exist conflicts, i.e., with ordering: default param values < user-supplied values < extra.
- Parameters:
extra – extra param values
- Returns:
merged param map
- getInputCols()#
Gets current column names of input annotations.
- getLazyAnnotator()#
Gets whether Annotator should be evaluated lazily in a RecursivePipeline.
- getOrDefault(param)#
Gets the value of a param in the user-supplied param map or its default value. Raises an error if neither is set.
- getOutputCol()#
Gets output column name of annotations.
- getParam(paramName)#
Gets a param by its name.
- getParamValue(paramName)#
Gets the value of a parameter.
- Parameters:
- paramNamestr
Name of the parameter
- hasDefault(param)#
Checks whether a param has a default value.
- hasParam(paramName)#
Tests whether this instance contains a param with a given (string) name.
- isDefined(param)#
Checks whether a param is explicitly set by user or has a default value.
- isSet(param)#
Checks whether a param is explicitly set by user.
- classmethod load(path)#
Reads an ML instance from the input path, a shortcut of read().load(path).
- property params#
Returns all params ordered by name. The default implementation uses
dir()
to get all attributes of typeParam
.
- classmethod read()#
Returns an MLReader instance for this class.
- save(path)#
Save this ML instance to the given path, a shortcut of ‘write().save(path)’.
- set(param, value)#
Sets a parameter in the embedded param map.
- setCriteria(s)[source]#
Set tag representing what is the criteria to filter the chunks. possibles values (assertion|isIn|regex)
- Parameters:
- pairslist
List of dash-separated pairs of named entities
- setInputCols(*value)#
Sets column names of input annotations.
- Parameters:
- *valuestr
Input columns for the annotator
- setLazyAnnotator(value)#
Sets whether Annotator should be evaluated lazily in a RecursivePipeline.
- Parameters:
- valuebool
Whether Annotator should be evaluated lazily in a RecursivePipeline
- setOutputCol(value)#
Sets output column name of annotations.
- Parameters:
- valuestr
Name of output column
- setParamValue(paramName)#
Sets the value of a parameter.
- Parameters:
- paramNamestr
Name of the parameter
- setRegex(value)[source]#
Sets llist of regex to process. The rest will be ignored.
- Parameters:
- valuelist
List of dash-separated pairs of named entities
- setWhiteList(value)[source]#
Sets list of entities to process. The rest will be ignored.
- Parameters:
- valuelist
If defined, list of entities to process. The rest will be ignored.
- transform(dataset, params=None)#
Transforms the input dataset with optional parameters.
- Parameters:
dataset – input dataset, which is an instance of
pyspark.sql.DataFrame
params – an optional param map that overrides embedded params.
- Returns:
transformed dataset
New in version 1.3.0.
- uid#
A unique id for the object.
- write()#
Returns an MLWriter instance for this ML instance.