sparknlp_jsl.annotator.SentenceEntityResolverModel#
- class sparknlp_jsl.annotator.SentenceEntityResolverModel(classname='com.johnsnowlabs.nlp.annotators.resolution.SentenceEntityResolverModel', java_model=None)[source]#
Bases:
AnnotatorModel
,HasEmbeddingsProperties
,HasStorageModel
,SentenceResolverParams
Thius class contains all the parameters and methods to train a SentenceEntityResolverModel. The model transforms a dataset with Input Annotation type SENTENCE_EMBEDDINGS, coming from e.g. [BertSentenceEmbeddings](/docs/en/transformers#bertsentenceembeddings) and returns the normalized entity for a particular trained ontology / curated dataset. (e.g. ICD-10, RxNorm, SNOMED etc.)
Input Annotation types
Output Annotation type
SENTENCE_EMBEDDINGS
ENTITY
- Parameters:
- returnCosineDistances
Extract Cosine Distances. TRUE or False
- aux_label_col
Auxiliary label which maps resolved entities to additional labels
- useAuxLabel
Use AuxLabel Col or not
- searchTree
Search tree for resolution
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 >>> documentAssembler = DocumentAssembler().setInputCol("text").setOutputCol("document") >>> sentenceDetector = SentenceDetector().setInputCols(["document"]).setOutputCol("sentence") >>> tokenizer = Tokenizer().setInputCols(["sentence"]).setOutputCol("token") >>> bertEmbeddings = BertSentenceEmbeddings.pretrained("sent_biobert_pubmed_base_cased") \ ... .setInputCols(["sentence"]) \ ... .setOutputCol("embeddings") >>> snomedTrainingPipeline = Pipeline(stages=[ ... documentAssembler, ... sentenceDetector, ... bertEmbeddings, ... ]) >>> snomedTrainingModel = snomedTrainingPipeline.fit(data) >>> snomedData = snomedTrainingModel.transform(data).cache() >>> assertionModel = assertionPipeline.fit(data) >>> assertionModel = assertionPipeline.fit(data)
>>> bertExtractor = SentenceEntityResolverApproach() \ ... .setNeighbours(25) \ ... .setThreshold(1000) \ ... .setInputCols(["bert_embeddings"]) \ ... .setNormalizedCol("normalized_text") \ ... .setLabelCol("label") \ ... .setOutputCol("snomed_code") \ ... .setDistanceFunction("EUCLIDIAN") \ ... .setCaseSensitive(False)
>>> snomedModel = bertExtractor.fit(snomedData)
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 whether to ignore case in tokens for embeddings matching.
Gets embeddings dimension.
Gets whether to include indexed storage in trained model.
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.
Gets unique reference name for identification.
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).
loadStorage
(path, spark, storage_ref)loadStorages
(path, spark, storage_ref, databases)pretrained
(name[, lang, remote_loc])read
()Returns an MLReader instance for this class.
save
(path)Save this ML instance to the given path, a shortcut of 'write().save(path)'.
saveStorage
(path, spark)Saves the current model to storage.
set
(param, value)Sets a parameter in the embedded param map.
setAuxLabelCol
(name)Sets auxiliary label which maps resolved entities to additional labels
setCaseSensitive
(value)Sets whether to ignore case in tokens for embeddings matching.
What function to use to calculate confidence: INVERSE or SOFTMAX.
setDimension
(value)Sets embeddings dimension.
setDistanceFunction
(dist)Sets distance function to use for WMD: 'EUCLIDEAN' or 'COSINE'.
setIncludeStorage
(value)Sets whether to include indexed storage in trained model.
setInputCols
(*value)Sets column names of input annotations.
setLazyAnnotator
(value)Sets whether Annotator should be evaluated lazily in a RecursivePipeline.
setMissAsEmpty
(value)Sets whether or not to return an empty annotation on unmatched chunks.
Sets number of neighbours to consider in the KNN query to calculate WMD.
setOutputCol
(value)Sets output column name of annotations.
setParamValue
(paramName)Sets the value of a parameter.
setParams
()Sets auxiliary label which maps resolved entities to additional labels
setStorageRef
(value)Sets unique reference name for identification.
setThreshold
(thres)Sets Threshold value for the last distance calculated.
setUseAuxLabel
(name)Sets Use AuxLabel Col or not.
transform
(dataset[, params])Transforms the input dataset with optional parameters.
write
()Returns an MLWriter instance for this ML instance.
Attributes
aux_label_col
caseSensitive
confidenceFunction
dimension
distanceFunction
getter_attrs
includeStorage
inputCols
lazyAnnotator
missAsEmpty
name
neighbours
outputCol
Returns all params ordered by name.
returnCosineDistances
searchTree
storageRef
threshold
useAuxLabel
- 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
- getCaseSensitive()#
Gets whether to ignore case in tokens for embeddings matching.
- Returns:
- bool
Whether to ignore case in tokens for embeddings matching
- getDimension()#
Gets embeddings dimension.
- getIncludeStorage()#
Gets whether to include indexed storage in trained model.
- Returns:
- bool
Whether to include indexed storage in trained model
- 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
- getStorageRef()#
Gets unique reference name for identification.
- Returns:
- str
Unique reference name for identification
- 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)’.
- saveStorage(path, spark)#
Saves the current model to storage.
- Parameters:
- pathstr
Path for saving the model.
- spark
pyspark.sql.SparkSession
The current SparkSession
- set(param, value)#
Sets a parameter in the embedded param map.
- setAuxLabelCol(name)[source]#
Sets auxiliary label which maps resolved entities to additional labels
- Parameters:
- namestr
Auxiliary label which maps resolved entities to additional labels
- setCaseSensitive(value)#
Sets whether to ignore case in tokens for embeddings matching.
- Parameters:
- valuebool
Whether to ignore case in tokens for embeddings matching
- setConfidenceFunction(s)#
What function to use to calculate confidence: INVERSE or SOFTMAX.
- Parameters:
- sstr
What function to use to calculate confidence: INVERSE or SOFTMAX.
- setDimension(value)#
Sets embeddings dimension.
- Parameters:
- valueint
Embeddings dimension
- setDistanceFunction(dist)#
Sets distance function to use for WMD: ‘EUCLIDEAN’ or ‘COSINE’.
- Parameters:
- diststr
Value that selects what distance function to use for WMD: ‘EUCLIDEAN’ or ‘COSINE’.
- setIncludeStorage(value)#
Sets whether to include indexed storage in trained model.
- Parameters:
- valuebool
Whether to include indexed storage in trained model
- 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
- setMissAsEmpty(value)#
Sets whether or not to return an empty annotation on unmatched chunks.
- Parameters:
- valuebool
whether or not to return an empty annotation on unmatched chunks.
- setNeighbours(k)#
Sets number of neighbours to consider in the KNN query to calculate WMD.
- Parameters:
- kint
Number of neighbours to consider in the KNN query to calculate WMD.
- 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
- setSearchTree(s)[source]#
Sets auxiliary label which maps resolved entities to additional labels
- Parameters:
- namestr
Auxiliary label which maps resolved entities to additional labels
- setStorageRef(value)#
Sets unique reference name for identification.
- Parameters:
- valuestr
Unique reference name for identification
- setThreshold(thres)#
Sets Threshold value for the last distance calculated.
- Parameters:
- thresfloat
Threshold value for the last distance calculated.
- setUseAuxLabel(name)[source]#
Sets Use AuxLabel Col or not.
- Parameters:
- namebool
Use AuxLabel Col or not.
- 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.