com.johnsnowlabs.nlp.annotators.assertion.context
ContextualAssertion
Companion object ContextualAssertion
class ContextualAssertion extends AnnotatorModel[ContextualAssertion] with HasSimpleAnnotate[ContextualAssertion] with HandleExceptionParams with HasSafeAnnotate[ContextualAssertion] with CheckLicense
An annotator model for contextual assertion analysis.
This model identifies contextual cues within text data, such as negation, uncertainty, and assertion. It is used clinical assertion detection, etc. It annotates text chunks with assertions based on configurable rules, prefix and suffix patterns, and exception patterns.
Example
Define pipeline stages to extract entities
val documentAssembler = new DocumentAssembler() .setInputCol("text") .setOutputCol("document") val sentenceDetector = new SentenceDetector() .setInputCols(Array("document")) .setOutputCol("sentences") val tokenizer = new Tokenizer() .setInputCols(Array("sentences")) .setOutputCol("tokens") val embedder = WordEmbeddingsModel .pretrained("embeddings_clinical", "en", "clinical/models") .setInputCols(Array("sentences", "tokens")) .setOutputCol("embeddings") val nerTagger = MedicalNerModel .pretrained("ner_clinical", "en", "clinical/models") .setInputCols(Array("sentences", "tokens", "embeddings")) .setOutputCol("nerTags") val nerConverter = new NerConverterInternal() .setInputCols(Array("sentences", "tokens", "nerTags")) .setOutputCol("nerChunks")
Define Contextual Assertion rules that are to be searched for in the text
val contextualAssertion = new ContextualAssertion() .setInputCols(Array("sentences", "tokens","nerChunks")) .setOutputCol("assertion") .setScopeWindow(2,2) .setPrefixRegexPatterns(Array("\\b(no|without|denies|never|none|free of|negative for|not include)\\b")) .setSuffixRegexPatterns(Array("\\b(free of|negative for|absence of|absence|not|neither|rule out)\\b")) .setPrefixPatterns(Array("not","never")) .setSuffixPatterns(Array("no","never")) .setCaseSensitive(false) .setAssertion("absent") val flattener = new Flattener() .setInputCols("assertion") .setExplodeSelectedFields(Map("assertion" -> Array("result", "metadata.ner_chunk as ner_chunk ", "metadata.ner_label as ner_label"))) val pipeline = new Pipeline() .setStages(Array(documentAssembler, sentenceDetector, tokenizer, embedder, nerTagger, nerConverter, contextualAssertion, flattener )).fit(testDataSet) val testText = "Patient resting in bed. Patient given azithromycin without any difficulty. Patient has audible wheezing, states chest tightness." + " No evidence of hypertension. Patient denies nausea at this time. zofran declined. Patient is also having intermittent sweating " + "associated with pneumonia. Patient refused pain but tylenol still given. Neither substance abuse nor alcohol use however cocaine " + "once used in the last year. Alcoholism unlikely. Patient has headache and fever. Patient is not diabetic. Not clearly of diarrhea. " + "Lab reports confirm lymphocytopenia. Cardaic rhythm is Sinus bradycardia. Patient also has a history of cardiac injury." + "No kidney injury reported. No abnormal rashes or ulcers. Patient might not have liver disease. Confirmed absence of hemoptysis." + "Although patient has severe pneumonia and fever, test reports are negative for COVID-19 infection. COVID-19 viral infection absent." val testDataSet = Seq(testText).toDS.toDF("text") val dataSetResult = pipeline.transform(testDataSet)
Show results
result.show(truncate=false) +----------------+------------------+---------+ |assertion_result| ner_chunk|ner_label| +----------------+------------------+---------+ | absent| any difficulty| PROBLEM| | absent| nausea| PROBLEM| | absent| diabetic| PROBLEM| | absent| kidney injury| PROBLEM| | absent| abnormal rashes| PROBLEM| | absent| liver disease| PROBLEM| | absent|COVID-19 infection| PROBLEM| +----------------+------------------+---------+
- Grouped
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- By Inheritance
- ContextualAssertion
- CheckLicense
- HasSafeAnnotate
- HandleExceptionParams
- HasSimpleAnnotate
- AnnotatorModel
- CanBeLazy
- RawAnnotator
- HasOutputAnnotationCol
- HasInputAnnotationCols
- HasOutputAnnotatorType
- ParamsAndFeaturesWritable
- HasFeatures
- DefaultParamsWritable
- MLWritable
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final
def
!=(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
final
def
##(): Int
- Definition Classes
- AnyRef → Any
-
final
def
$[T](param: Param[T]): T
- Attributes
- protected
- Definition Classes
- Params
-
def
$$[T](feature: StructFeature[T]): T
- Attributes
- protected
- Definition Classes
- HasFeatures
-
def
$$[K, V](feature: MapFeature[K, V]): Map[K, V]
- Attributes
- protected
- Definition Classes
- HasFeatures
-
def
$$[T](feature: SetFeature[T]): Set[T]
- Attributes
- protected
- Definition Classes
- HasFeatures
-
def
$$[T](feature: ArrayFeature[T]): Array[T]
- Attributes
- protected
- Definition Classes
- HasFeatures
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final
def
==(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
def
_transform(dataset: Dataset[_], recursivePipeline: Option[PipelineModel]): DataFrame
- Attributes
- protected
- Definition Classes
- AnnotatorModel
-
def
addPrefixKeywords(values: Array[String]): ContextualAssertion.this.type
add prefix keywords in addition to the existing ones
-
def
addSuffixKeywords(values: Array[String]): ContextualAssertion.this.type
add suffix keywords in addition to the existing ones
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def
afterAnnotate(dataset: DataFrame): DataFrame
- Attributes
- protected
- Definition Classes
- AnnotatorModel
-
final
def
annotate(annotations: Seq[Annotation]): Seq[Annotation]
- Definition Classes
- ContextualAssertion → HasSimpleAnnotate
-
final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
-
def
beforeAnnotate(dataset: Dataset[_]): Dataset[_]
- Attributes
- protected
- Definition Classes
- AnnotatorModel
-
final
def
checkSchema(schema: StructType, inputAnnotatorType: String): Boolean
- Attributes
- protected
- Definition Classes
- HasInputAnnotationCols
-
def
checkValidEnvironment(spark: Option[SparkSession], scopes: Seq[String]): Unit
- Definition Classes
- CheckLicense
-
def
checkValidScope(scope: String): Unit
- Definition Classes
- CheckLicense
-
def
checkValidScopeAndEnvironment(scope: String, spark: Option[SparkSession], checkLp: Boolean): Unit
- Definition Classes
- CheckLicense
-
def
checkValidScopesAndEnvironment(scopes: Seq[String], spark: Option[SparkSession], checkLp: Boolean): Unit
- Definition Classes
- CheckLicense
-
final
def
clear(param: Param[_]): ContextualAssertion.this.type
- Definition Classes
- Params
-
def
clone(): AnyRef
- Attributes
- protected[lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( ... ) @native()
-
val
confidenceCalculationDirection: Param[String]
Direction of confidence calculation.
Direction of confidence calculation. If
left
, the confidence is calculated based on the distance of the found regex or keyword in left side of the sentence from a chunk. Ifright
, the confidence is calculated based on the distance of the found regex or keyword in right side of the sentence from a chunk. Ifboth
, the confidence is calculated based on the distance of the found regex or keyword in both sides of the sentence from a chunk.Default is "left"
-
def
copy(extra: ParamMap): ContextualAssertion
- Definition Classes
- RawAnnotator → Model → Transformer → PipelineStage → Params
-
def
copyValues[T <: Params](to: T, extra: ParamMap): T
- Attributes
- protected
- Definition Classes
- Params
-
final
def
defaultCopy[T <: Params](extra: ParamMap): T
- Attributes
- protected
- Definition Classes
- Params
-
def
dfAnnotate: UserDefinedFunction
- Definition Classes
- HasSimpleAnnotate
-
val
doExceptionHandling: BooleanParam
If true, exceptions are handled.
If true, exceptions are handled. If exception causing data is passed to the model, a error annotation is emitted which has the exception message. Processing continues with the next one. This comes with a performance penalty.
- Definition Classes
- HandleExceptionParams
-
final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
def
equals(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
def
explainParam(param: Param[_]): String
- Definition Classes
- Params
-
def
explainParams(): String
- Definition Classes
- Params
-
def
extraValidate(structType: StructType): Boolean
- Attributes
- protected
- Definition Classes
- RawAnnotator
-
def
extraValidateMsg: String
- Attributes
- protected
- Definition Classes
- RawAnnotator
-
final
def
extractParamMap(): ParamMap
- Definition Classes
- Params
-
final
def
extractParamMap(extra: ParamMap): ParamMap
- Definition Classes
- Params
-
val
features: ArrayBuffer[Feature[_, _, _]]
- Definition Classes
- HasFeatures
-
def
finalize(): Unit
- Attributes
- protected[lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( classOf[java.lang.Throwable] )
-
def
get[T](feature: StructFeature[T]): Option[T]
- Attributes
- protected
- Definition Classes
- HasFeatures
-
def
get[K, V](feature: MapFeature[K, V]): Option[Map[K, V]]
- Attributes
- protected
- Definition Classes
- HasFeatures
-
def
get[T](feature: SetFeature[T]): Option[Set[T]]
- Attributes
- protected
- Definition Classes
- HasFeatures
-
def
get[T](feature: ArrayFeature[T]): Option[Array[T]]
- Attributes
- protected
- Definition Classes
- HasFeatures
-
final
def
get[T](param: Param[T]): Option[T]
- Definition Classes
- Params
-
def
getAssertion: String
Gets assertion parameter value.
-
final
def
getClass(): Class[_]
- Definition Classes
- AnyRef → Any
- Annotations
- @native()
-
final
def
getDefault[T](param: Param[T]): Option[T]
- Definition Classes
- Params
-
def
getInputCols: Array[String]
- Definition Classes
- HasInputAnnotationCols
-
def
getLazyAnnotator: Boolean
- Definition Classes
- CanBeLazy
-
final
def
getOrDefault[T](param: Param[T]): T
- Definition Classes
- Params
-
final
def
getOutputCol: String
- Definition Classes
- HasOutputAnnotationCol
-
def
getParam(paramName: String): Param[Any]
- Definition Classes
- Params
-
def
getScopeWindow: (Int, Int)
Get scope window
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final
def
hasDefault[T](param: Param[T]): Boolean
- Definition Classes
- Params
-
def
hasParam(paramName: String): Boolean
- Definition Classes
- Params
-
def
hasParent: Boolean
- Definition Classes
- Model
-
def
hashCode(): Int
- Definition Classes
- AnyRef → Any
- Annotations
- @native()
-
val
inExceptionMode: Boolean
- Attributes
- protected
- Definition Classes
- HasSafeAnnotate
-
def
initializeLogIfNecessary(isInterpreter: Boolean, silent: Boolean): Boolean
- Attributes
- protected
- Definition Classes
- Logging
-
def
initializeLogIfNecessary(isInterpreter: Boolean): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
val
inputAnnotatorTypes: Array[String]
DOCUMENT, CHUNK, TOKEN
DOCUMENT, CHUNK, TOKEN
- Definition Classes
- ContextualAssertion → HasInputAnnotationCols
-
final
val
inputCols: StringArrayParam
- Attributes
- protected
- Definition Classes
- HasInputAnnotationCols
-
final
def
isDefined(param: Param[_]): Boolean
- Definition Classes
- Params
-
final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
-
final
def
isSet(param: Param[_]): Boolean
- Definition Classes
- Params
-
def
isTraceEnabled(): Boolean
- Attributes
- protected
- Definition Classes
- Logging
-
val
lazyAnnotator: BooleanParam
- Definition Classes
- CanBeLazy
-
def
log: Logger
- Attributes
- protected
- Definition Classes
- Logging
-
def
logDebug(msg: ⇒ String, throwable: Throwable): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
logDebug(msg: ⇒ String): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
logError(msg: ⇒ String, throwable: Throwable): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
logError(msg: ⇒ String): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
logInfo(msg: ⇒ String, throwable: Throwable): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
logInfo(msg: ⇒ String): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
logName: String
- Attributes
- protected
- Definition Classes
- Logging
-
def
logTrace(msg: ⇒ String, throwable: Throwable): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
logTrace(msg: ⇒ String): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
logWarning(msg: ⇒ String, throwable: Throwable): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
logWarning(msg: ⇒ String): Unit
- Attributes
- protected
- Definition Classes
- Logging
-
def
msgHelper(schema: StructType): String
- Attributes
- protected
- Definition Classes
- HasInputAnnotationCols
-
final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
final
def
notify(): Unit
- Definition Classes
- AnyRef
- Annotations
- @native()
-
final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
- Annotations
- @native()
-
def
onWrite(path: String, spark: SparkSession): Unit
- Attributes
- protected
- Definition Classes
- ParamsAndFeaturesWritable
-
val
optionalInputAnnotatorTypes: Array[String]
- Definition Classes
- HasInputAnnotationCols
-
val
outputAnnotatorType: AnnotatorType
ASSERTION
ASSERTION
- Definition Classes
- ContextualAssertion → HasOutputAnnotatorType
-
final
val
outputCol: Param[String]
- Attributes
- protected
- Definition Classes
- HasOutputAnnotationCol
-
lazy val
params: Array[Param[_]]
- Definition Classes
- Params
-
var
parent: Estimator[ContextualAssertion]
- Definition Classes
- Model
-
def
safeAnnotate(annotations: Seq[Annotation]): Seq[Annotation]
A protected method designed to safely annotate a sequence of Annotation objects by handling exceptions.
A protected method designed to safely annotate a sequence of Annotation objects by handling exceptions.
- annotations
A sequence of Annotation.
- returns
A sequence of Annotation objects after processing, potentially containing error annotations.
- Attributes
- protected
- Definition Classes
- HasSafeAnnotate
-
def
save(path: String): Unit
- Definition Classes
- MLWritable
- Annotations
- @Since( "1.6.0" ) @throws( ... )
-
def
set[T](feature: StructFeature[T], value: T): ContextualAssertion.this.type
- Attributes
- protected
- Definition Classes
- HasFeatures
-
def
set[K, V](feature: MapFeature[K, V], value: Map[K, V]): ContextualAssertion.this.type
- Attributes
- protected
- Definition Classes
- HasFeatures
-
def
set[T](feature: SetFeature[T], value: Set[T]): ContextualAssertion.this.type
- Attributes
- protected
- Definition Classes
- HasFeatures
-
def
set[T](feature: ArrayFeature[T], value: Array[T]): ContextualAssertion.this.type
- Attributes
- protected
- Definition Classes
- HasFeatures
-
final
def
set(paramPair: ParamPair[_]): ContextualAssertion.this.type
- Attributes
- protected
- Definition Classes
- Params
-
final
def
set(param: String, value: Any): ContextualAssertion.this.type
- Attributes
- protected
- Definition Classes
- Params
-
final
def
set[T](param: Param[T], value: T): ContextualAssertion.this.type
- Definition Classes
- Params
-
def
setAssertion(value: String): ContextualAssertion.this.type
Set the assertion to be tagged.
Set the assertion to be tagged. Default is "assertion"
-
def
setCaseSensitive(value: Boolean): ContextualAssertion.this.type
Whether to use case sensitive when matching values.
Whether to use case sensitive when matching values. Default is false
-
def
setConfidenceCalculationDirection(value: String): ContextualAssertion.this.type
If
left
, the confidence is calculated based on the distance of the found regex or keyword in left side of the sentence from a chunk.If
left
, the confidence is calculated based on the distance of the found regex or keyword in left side of the sentence from a chunk. Ifright
, the confidence is calculated based on the distance of the found regex or keyword in right side of the sentence from a chunk. Ifboth
, the confidence is calculated based on the distance of the found regex or keyword in both sides of the sentence from a chunk. Default is "left" -
def
setDefault[T](feature: StructFeature[T], value: () ⇒ T): ContextualAssertion.this.type
- Attributes
- protected
- Definition Classes
- HasFeatures
-
def
setDefault[K, V](feature: MapFeature[K, V], value: () ⇒ Map[K, V]): ContextualAssertion.this.type
- Attributes
- protected
- Definition Classes
- HasFeatures
-
def
setDefault[T](feature: SetFeature[T], value: () ⇒ Set[T]): ContextualAssertion.this.type
- Attributes
- protected
- Definition Classes
- HasFeatures
-
def
setDefault[T](feature: ArrayFeature[T], value: () ⇒ Array[T]): ContextualAssertion.this.type
- Attributes
- protected
- Definition Classes
- HasFeatures
-
final
def
setDefault(paramPairs: ParamPair[_]*): ContextualAssertion.this.type
- Attributes
- protected
- Definition Classes
- Params
-
final
def
setDefault[T](param: Param[T], value: T): ContextualAssertion.this.type
- Attributes
- protected[org.apache.spark.ml]
- Definition Classes
- Params
-
def
setDoExceptionHandling(value: Boolean): ContextualAssertion.this.type
If true, exceptions are handled.
If true, exceptions are handled. If exception causing data is passed to the model, a error annotation is emitted which has the exception message. Processing continues with the next one. This comes with a performance penalty.
- Definition Classes
- HandleExceptionParams
- def setExceptionKeywords(value: ArrayList[String]): ContextualAssertion.this.type
-
def
setExceptionKeywords(value: Array[String]): ContextualAssertion.this.type
Set the exception patterns not to be searched for Defaults are "not only", "not necessarily", "not need", "not certain if", "not clearly", "not likely", "not cause", "not extend", "not always", "not only", "not yet", "not otherwise", "not exclude"
- def setExceptionRegexPatterns(value: ArrayList[String]): ContextualAssertion.this.type
- def setExceptionRegexPatterns(value: Array[String]): ContextualAssertion.this.type
-
def
setIncludeChunkToScope(value: Boolean): ContextualAssertion.this.type
Whether to include chunk to scope when matching values Default is false
-
final
def
setInputCols(value: String*): ContextualAssertion.this.type
- Definition Classes
- HasInputAnnotationCols
-
def
setInputCols(value: Array[String]): ContextualAssertion.this.type
- Definition Classes
- HasInputAnnotationCols
-
def
setLazyAnnotator(value: Boolean): ContextualAssertion.this.type
- Definition Classes
- CanBeLazy
-
final
def
setOutputCol(value: String): ContextualAssertion.this.type
- Definition Classes
- HasOutputAnnotationCol
-
def
setParent(parent: Estimator[ContextualAssertion]): ContextualAssertion
- Definition Classes
- Model
-
def
setPrefixAndSuffixMatch(value: Boolean): ContextualAssertion.this.type
Whether to match both prefix and suffix to annotate the hit.
Whether to match both prefix and suffix to annotate the hit. Default is false
- def setPrefixKeywords(value: ArrayList[String]): ContextualAssertion.this.type
-
def
setPrefixKeywords(value: Array[String]): ContextualAssertion.this.type
Set the prefix keywords to look for before chunk Defaults are "no", "not", "never", "without", "absent", "neither", "nor", "denies", "free of", "lack of", "unremarkable for", "ruled out", "rule out", "declined", "denied"
- def setPrefixRegexPatterns(value: ArrayList[String]): ContextualAssertion.this.type
-
def
setPrefixRegexPatterns(value: Array[String]): ContextualAssertion.this.type
Set the prefix patterns to look for before chunk.
Set the prefix patterns to look for before chunk. Default is Array.empty[String]
-
def
setScopeWindow(window: (Int, Int)): ContextualAssertion.this.type
Set the scope window of the assertion.
Set the scope window of the assertion. The scope window is defined by two non-negative integers except (-1,-1). The first integer is the number of tokens to the left of the chunk, and the second integer is the number of tokens to the right of the chunk. Default is (-1, -1) which means the whole sentence
-
def
setScopeWindowDelimiters(value: Array[String]): ContextualAssertion.this.type
Set delimiters used to limit the scope window.
- def setSuffixKeywords(value: ArrayList[String]): ContextualAssertion.this.type
-
def
setSuffixKeywords(value: Array[String]): ContextualAssertion.this.type
Set the suffix keywords to look for after chunk Defaults are "not detected", "not demonstrate", "not appear", "not had", "was ruled out", "were ruled out", "are ruled out", "is ruled out", "unlikely", "not developed", "not present", "not associated with", "not had", "free from", "resolved"
- def setSuffixRegexPatterns(value: ArrayList[String]): ContextualAssertion.this.type
-
def
setSuffixRegexPatterns(value: Array[String]): ContextualAssertion.this.type
Set the suffix patterns to look for after chunk.
Set the suffix patterns to look for after chunk. Default is Array.empty[String]
-
final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
- AnyRef
-
def
toString(): String
- Definition Classes
- Identifiable → AnyRef → Any
-
final
def
transform(dataset: Dataset[_]): DataFrame
- Definition Classes
- AnnotatorModel → Transformer
-
def
transform(dataset: Dataset[_], paramMap: ParamMap): DataFrame
- Definition Classes
- Transformer
- Annotations
- @Since( "2.0.0" )
-
def
transform(dataset: Dataset[_], firstParamPair: ParamPair[_], otherParamPairs: ParamPair[_]*): DataFrame
- Definition Classes
- Transformer
- Annotations
- @Since( "2.0.0" ) @varargs()
-
final
def
transformSchema(schema: StructType): StructType
- Definition Classes
- RawAnnotator → PipelineStage
-
def
transformSchema(schema: StructType, logging: Boolean): StructType
- Attributes
- protected
- Definition Classes
- PipelineStage
- Annotations
- @DeveloperApi()
-
val
uid: String
- Definition Classes
- ContextualAssertion → Identifiable
-
def
validate(schema: StructType): Boolean
- Attributes
- protected
- Definition Classes
- RawAnnotator
-
final
def
wait(): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... ) @native()
-
def
wrapColumnMetadata(col: Column): Column
- Attributes
- protected
- Definition Classes
- RawAnnotator
-
def
write: MLWriter
- Definition Classes
- ParamsAndFeaturesWritable → DefaultParamsWritable → MLWritable
Inherited from CheckLicense
Inherited from HasSafeAnnotate[ContextualAssertion]
Inherited from HandleExceptionParams
Inherited from HasSimpleAnnotate[ContextualAssertion]
Inherited from AnnotatorModel[ContextualAssertion]
Inherited from CanBeLazy
Inherited from RawAnnotator[ContextualAssertion]
Inherited from HasOutputAnnotationCol
Inherited from HasInputAnnotationCols
Inherited from HasOutputAnnotatorType
Inherited from ParamsAndFeaturesWritable
Inherited from HasFeatures
Inherited from DefaultParamsWritable
Inherited from MLWritable
Inherited from Model[ContextualAssertion]
Inherited from Transformer
Inherited from PipelineStage
Inherited from Logging
Inherited from Params
Inherited from Serializable
Inherited from Serializable
Inherited from Identifiable
Inherited from AnyRef
Inherited from Any
Parameters
Annotator types
Required input and expected output annotator types