Packages

package re

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Type Members

  1. case class BertREConfig(sentenceStartTokenId: Int = 102, sentenceEndTokenId: Int = 103, entity1StartTokenId: Int = 10, entity1EndTokenId: Int = 11, entity2StartTokenId: Int = 12, entity2EndTokenId: Int = 13, entity1StartTag: String = "e1b", entity1EndTag: String = "e1e", entity2StartTag: String = "e2b", entity2EndTag: String = "e2e") extends Product with Serializable
  2. case class DLRelationInstance(relationType: String, entity1: String, entity2: String, entity1_begin: Int, entity1_end: Int, entity2_begin: Int, entity2_end: Int, chunk1: String, chunk2: String, chunk1_conf: String, chunk2_conf: String, syntactic_distance: String, context: Sentence) extends Product with Serializable
  3. class GenericREModel extends RelationExtractionModel with HasStorageRef with ParamsAndFeaturesWritable with CheckLicense

    Instantiated RelationExtractionModel for extracting relationships between any entitites.

    Instantiated RelationExtractionModel for extracting relationships between any entitites. This class is not intended to be directly used, please use the RelationExtractionModel instead. Pairs of entitie should be specified using setRelationPairs Please see the Models Hub for available models.

    See also

    RelationExtractionModel to use the model

  4. class PosologyREModel extends GenericREModel

    Instantiated RelationExtractionModel for extracting relationships between different recognized drug entitites.

    Instantiated RelationExtractionModel for extracting relationships between different recognized drug entitites. This class is not intended to be directly used, please use the RelationExtractionModel instead. Possible values are "DRUG-DOSAGE", "DRUG-ADE", "DRUG-FORM", "DRUG-FREQUENCY", "DRUG-ROUTE", "DRUG-REASON", "DRUG-STRENGTH", "DRUG-DURATION". Please see the Models Hub for available models.

    See also

    RelationExtractionModel to use the model

  5. class REDataEncoder extends Serializable
  6. class RENerChunksFilter extends AnnotatorModel[RENerChunksFilter] with HasSimpleAnnotate[RENerChunksFilter] with CheckLicense

    Filters entities' dependency relations.

    Filters entities' dependency relations.

    The annotator filters desired relation pairs (defined by the parameter realtionPairs), and store those on the output column. Filtering the possible relations can be useful to perform additional analysis for a specific use case (e.g., checking adverse drug reactions and drug realations), which can be the input for further analysis using a pretrained RelationExtractionDLModel.

    For example, the ner_clinical NER model can identify PROBLEM, TEST, and TREATMENT entities. By using this annotator, one can filter (select) the relations between PROBLEM and TREATMENT entities only, removing any relation between the other entities, to further analyze the associations between clinical problems and treatments.

    Example

    Define pipeline stages to extract entities

    val documenter = new DocumentAssembler()
  .setInputCol("text")
  .setOutputCol("document")

val sentencer = new SentenceDetector()
  .setInputCols("document")
  .setOutputCol("sentences")

val tokenizer = new Tokenizer()
  .setInputCols("sentences")
  .setOutputCol("tokens")

val words_embedder = WordEmbeddingsModel.pretrained("embeddings_clinical", "en", "clinical/models")
  .setInputCols("sentences", "tokens")
  .setOutputCol("embeddings")

val pos_tagger = PerceptronModel.pretrained("pos_clinical", "en", "clinical/models")
  .setInputCols("sentences", "tokens")
  .setOutputCol("pos_tags")

val dependency_parser = DependencyParserModel.pretrained("dependency_conllu", "en")
  .setInputCols("sentences", "pos_tags", "tokens")
  .setOutputCol("dependencies")

val clinical_ner_tagger = MedicalNerModel.pretrained("jsl_ner_wip_greedy_clinical","en","clinical/models")
  .setInputCols("sentences", "tokens", "embeddings")
  .setOutputCol("ner_tags")

val ner_chunker = new NerConverter()
  .setInputCols("sentences", "tokens", "ner_tags")
  .setOutputCol("ner_chunks")

    Define the relation pairs and the filter

    val relationPairs = Array("direction-external_body_part_or_region",
                      "external_body_part_or_region-direction",
                      "direction-internal_organ_or_component",
                      "internal_organ_or_component-direction")

val re_ner_chunk_filter = new RENerChunksFilter()
    .setInputCols("ner_chunks", "dependencies")
    .setOutputCol("re_ner_chunks")
    .setMaxSyntacticDistance(4)
    .setRelationPairs(Array("internal_organ_or_component-direction"))

val trained_pipeline = new Pipeline().setStages(Array(
  documenter,
  sentencer,
  tokenizer,
  words_embedder,
  pos_tagger,
  clinical_ner_tagger,
  ner_chunker,
  dependency_parser,
  re_ner_chunk_filter
))

val data = Seq("MRI demonstrated infarction in the upper brain stem , left cerebellum and  right basil ganglia").toDF("text")
val result = trained_pipeline.fit(data).transform(data)

    Show results

    result.selectExpr("explode(re_ner_chunks) as re_chunks")
  .selectExpr("re_chunks.begin", "re_chunks.result", "re_chunks.metadata.entity", "re_chunks.metadata.paired_to")
  .show(6, truncate=false)
+-----+-------------+---------------------------+---------+
|begin|result       |entity                     |paired_to|
+-----+-------------+---------------------------+---------+
|35   |upper        |Direction                  |41       |
|41   |brain stem   |Internal_organ_or_component|35       |
|35   |upper        |Direction                  |59       |
|59   |cerebellum   |Internal_organ_or_component|35       |
|35   |upper        |Direction                  |81       |
|81   |basil ganglia|Internal_organ_or_component|35       |
+-----+-------------+---------------------------+---------+
    See also

    RelationExtractionDLModel for BERT based extraction

  7. trait ReadRelationExtractionDLModelTensorflowModel extends ReadTensorflowModel
  8. trait ReadZeroShotRelationExtractionModel extends ReadTensorflowModel
  9. trait ReadablePretrainedRelationExtractionDLModel extends ParamsAndFeaturesReadable[RelationExtractionDLModel] with HasPretrained[RelationExtractionDLModel]
  10. trait ReadablePretrainedZeroShotRelationExtractionModel extends ParamsAndFeaturesReadable[ZeroShotRelationExtractionModel] with HasPretrained[ZeroShotRelationExtractionModel]
  11. trait RelationEncoding extends AnyRef
  12. class RelationExtractionApproach extends GenericClassifierApproach with HandleExceptionParams

    Trains a TensorFlow model for relation extraction.

    Trains a TensorFlow model for relation extraction.

    For pretrained models, see the documentation of RelationExtractionModel.

    To train a custom relation extraction model, you need to first create a Tensorflow graph using either the TfGraphBuilder annotator or the tf_graph module. Then, set the path to the Tensorflow graph using the method setModelFile.

    If the parameter relationDirectionCol is set, the model will be trained using the direction information (see the parameter decription for details). Otherwise, the model won't have direction between the relation of the entities. After training a model (using the .fit() method), the resulting object is of class RelationExtractionModel.

    Example

    Defining pipeline stages to extract entities first

    val documentAssembler = new DocumentAssembler()
  .setInputCol("text")
  .setOutputCol("document")

val tokenizer = new Tokenizer()
  .setInputCols(Array("document"))
  .setOutputCol("tokens")

val embedder = WordEmbeddingsModel
  .pretrained("embeddings_clinical", "en", "clinical/models")
  .setInputCols(Array("document", "tokens"))
  .setOutputCol("embeddings")

val posTagger = PerceptronModel
  .pretrained("pos_clinical", "en", "clinical/models")
  .setInputCols(Array("document", "tokens"))
  .setOutputCol("posTags")

val nerTagger = MedicalNerModel
  .pretrained("ner_events_clinical", "en", "clinical/models")
  .setInputCols(Array("document", "tokens", "embeddings"))
  .setOutputCol("ner_tags")

val nerConverter = new NerConverter()
  .setInputCols(Array("document", "tokens", "ner_tags"))
  .setOutputCol("nerChunks")

val depencyParser = DependencyParserModel
  .pretrained("dependency_conllu", "en")
  .setInputCols(Array("document", "posTags", "tokens"))
  .setOutputCol("dependencies")

    Then define RelationExtractionApproach and training parameters

    val re = new RelationExtractionApproach()
  .setInputCols(Array("embeddings", "posTags", "train_ner_chunks", "dependencies"))
  .setOutputCol("relations_t")
  .setLabelColumn("target_rel")
  .setEpochsNumber(300)
  .setBatchSize(200)
  .setlearningRate(0.001f)
  .setModelFile("path/to/graph_file.pb")
  .setFixImbalance(true)
  .setValidationSplit(0.05f)
  .setFromEntity("from_begin", "from_end", "from_label")
  .setToEntity("to_begin", "to_end", "to_label")

val finisher = new Finisher()
  .setInputCols(Array("relations_t"))
  .setOutputCols(Array("relations"))
  .setCleanAnnotations(false)
  .setValueSplitSymbol(",")
  .setAnnotationSplitSymbol(",")
  .setOutputAsArray(false)

    Define complete pipeline and start training

    val pipeline = new Pipeline()
  .setStages(Array(
    documentAssembler,
    tokenizer,
    embedder,
    posTagger,
    nerTagger,
    nerConverter,
    depencyParser,
    re,
    finisher))

val model = pipeline.fit(trainData)
    See also

    RelationExtractionModel for pretrained models and how to use it

  13. class RelationExtractionDLModel extends AnnotatorModel[RelationExtractionDLModel] with WriteTensorflowModel with HasStorageRef with HasCaseSensitiveProperties with HasSimpleAnnotate[RelationExtractionDLModel] with RelationEncoding with HasEngine with HandleExceptionParams with HasSafeAnnotate[RelationExtractionDLModel] with CheckLicense

    Extracts and classifies instances of relations between named entities.

    Extracts and classifies instances of relations between named entities. In contrast with RelationExtractionModel, RelationExtractionDLModel is based on BERT. For pretrained models please see the Models Hub for available models.

    Example

    Relation Extraction between body parts

    This is a continuation of the RENerChunksFilter example. See that class on how to extract the relation chunks. Define the extraction model

    val re_ner_chunk_filter = new RENerChunksFilter()
 .setInputCols("ner_chunks", "dependencies")
 .setOutputCol("re_ner_chunks")
 .setMaxSyntacticDistance(4)
 .setRelationPairs(Array("internal_organ_or_component-direction"))

val re_model = RelationExtractionDLModel.pretrained("redl_bodypart_direction_biobert", "en", "clinical/models")
  .setPredictionThreshold(0.5f)
  .setInputCols("re_ner_chunks", "sentences")
  .setOutputCol("relations")

val trained_pipeline = new Pipeline().setStages(Array(
  documenter,
  sentencer,
  tokenizer,
  words_embedder,
  pos_tagger,
  clinical_ner_tagger,
  ner_chunker,
  dependency_parser,
  re_ner_chunk_filter,
  re_model
))

val data = Seq("MRI demonstrated infarction in the upper brain stem , left cerebellum and  right basil ganglia").toDF("text")
val result = trained_pipeline.fit(data).transform(data)

    Show results

    result.selectExpr("explode(relations) as relations")
 .select(
   "relations.metadata.chunk1",
   "relations.metadata.entity1",
   "relations.metadata.chunk2",
   "relations.metadata.entity2",
   "relations.result"
 )
 .where("result != 0")
 .show(truncate=false)
+------+---------+-------------+---------------------------+------+
|chunk1|entity1  |chunk2       |entity2                    |result|
+------+---------+-------------+---------------------------+------+
|upper |Direction|brain stem   |Internal_organ_or_component|1     |
|left  |Direction|cerebellum   |Internal_organ_or_component|1     |
|right |Direction|basil ganglia|Internal_organ_or_component|1     |
+------+---------+-------------+---------------------------+------+
    See also

    RelationExtractionModel for ML based extraction

    RENerChunksFilter on how to create inputs

  14. class RelationExtractionModel extends GenericClassifierModel with ParamsAndFeaturesWritable with HandleExceptionParams with HasSafeAnnotate[GenericClassifierModel]

    Extracts and classifies instances of relations between named entities.

    Extracts and classifies instances of relations between named entities. For this, relation pairs need to be defined with setRelationPairs, to specify between which entities the extraction should be done.

    For pretrained models please see the Models Hub for available models.

    Example

    Relation Extraction between body parts

    Define pipeline stages to extract entities

    val documenter = new DocumentAssembler()
  .setInputCol("text")
  .setOutputCol("document")

val sentencer = new SentenceDetector()
  .setInputCols("document")
  .setOutputCol("sentences")

val tokenizer = new Tokenizer()
  .setInputCols("sentences")
  .setOutputCol("tokens")

val words_embedder = WordEmbeddingsModel.pretrained("embeddings_clinical", "en", "clinical/models")
  .setInputCols("sentences", "tokens")
  .setOutputCol("embeddings")

val pos_tagger = PerceptronModel.pretrained("pos_clinical", "en", "clinical/models")
  .setInputCols("sentences", "tokens")
  .setOutputCol("pos_tags")

val dependency_parser = DependencyParserModel.pretrained("dependency_conllu", "en")
  .setInputCols("sentences", "pos_tags", "tokens")
  .setOutputCol("dependencies")

val clinical_ner_tagger = MedicalNerModel.pretrained("jsl_ner_wip_greedy_clinical","en","clinical/models")
  .setInputCols("sentences", "tokens", "embeddings")
  .setOutputCol("ner_tags")

val ner_chunker = new NerConverter()
  .setInputCols("sentences", "tokens", "ner_tags")
  .setOutputCol("ner_chunks")

    Define the relations that are to be extracted

    val relationPairs = Array("direction-external_body_part_or_region",
                      "external_body_part_or_region-direction",
                      "direction-internal_organ_or_component",
                      "internal_organ_or_component-direction")

val re_model = RelationExtractionModel.pretrained("re_bodypart_directions", "en", "clinical/models")
  .setInputCols("embeddings", "pos_tags", "ner_chunks", "dependencies")
  .setOutputCol("relations")
  .setRelationPairs(relationPairs)
  .setMaxSyntacticDistance(4)
  .setPredictionThreshold(0.9f)

val pipeline = new Pipeline().setStages(Array(
  documenter,
  sentencer,
  tokenizer,
  words_embedder,
  pos_tagger,
  clinical_ner_tagger,
  ner_chunker,
  dependency_parser,
  re_model
))

val data = Seq("MRI demonstrated infarction in the upper brain stem , left cerebellum and  right basil ganglia").toDF("text")
val result = pipeline.fit(data).transform(data)

    Show results

    result.selectExpr("explode(relations) as relations")
 .select(
   "relations.metadata.chunk1",
   "relations.metadata.entity1",
   "relations.metadata.chunk2",
   "relations.metadata.entity2",
   "relations.result"
 )
 .where("result != 0")
 .show(truncate=false)
+------+---------+-------------+---------------------------+------+
|chunk1|entity1  |chunk2       |entity2                    |result|
+------+---------+-------------+---------------------------+------+
|upper |Direction|brain stem   |Internal_organ_or_component|1     |
|left  |Direction|cerebellum   |Internal_organ_or_component|1     |
|right |Direction|basil ganglia|Internal_organ_or_component|1     |
+------+---------+-------------+---------------------------+------+
    See also

    RelationExtractionApproach to train your own model.

    RelationExtractionDLModel for BERT based extraction

  15. case class RelationInstance(relationType: String, entity1: String, entity2: String, entity1_begin: Int, entity1_end: Int, entity2_begin: Int, entity2_end: Int, chunk1: String, chunk2: String, chunk1_conf: String, chunk2_conf: String, vector: Array[Float], description: String, sentence: Int = 0) extends Product with Serializable
  16. class ZeroShotRelationExtractionModel extends MedicalBertForSequenceClassification with RelationEncoding with HasEngine

    ZeroShotRelationExtractionModel implements zero shot binary relations extraction by utilizing BERT transformer models trained on the NLI (Natural Language Inference) task.

    ZeroShotRelationExtractionModel implements zero shot binary relations extraction by utilizing BERT transformer models trained on the NLI (Natural Language Inference) task. The model inputs consists of documents/sentences and paired NER chunks, usually obtained by RENerChunksFilter. The definitions of relations which are extracted is given by a dictionary structures, specifying a set of statements regarding the relationship of named entities. These statements are automatically appended to each document in the dataset and the NLI model is used to determine whether a particular relationship between entities.

    Pretrained models can be loaded with pretrained of the companion object:

    val zeroShotRE = ZeroShotRelationExtractionModel.pretrained()
  .setInputCols("token", "document")
  .setOutputCol("label")

    For available pretrained models please see the Models Hub.

    Example

    val documentAssembler = new DocumentAssembler()
  .setInputCol("text")
  .setOutputCol("document")

val tokenizer = new Tokenizer()
  .setInputCols(Array("document"))
  .setOutputCol("tokens")

val sentencer = new SentenceDetector()
  .setInputCols(Array("document"))
  .setOutputCol("sentences")

val embeddings = WordEmbeddingsModel
  .pretrained("embeddings_clinical", "en", "clinical/models")
  .setInputCols(Array("sentences", "tokens"))
  .setOutputCol("embeddings")

val posTagger = PerceptronModel
  .pretrained("pos_clinical", "en", "clinical/models")
  .setInputCols(Array("sentences", "tokens"))
  .setOutputCol("posTags")

val nerTagger = MedicalNerModel
  .pretrained("ner_clinical", "en", "clinical/models")
  .setInputCols(Array("sentences", "tokens", "embeddings"))
  .setOutputCol("nerTags")

val nerConverter = new NerConverter()
  .setInputCols(Array("sentences", "tokens", "nerTags"))
  .setOutputCol("nerChunks")

val dependencyParser = DependencyParserModel
  .pretrained("dependency_conllu", "en")
  .setInputCols(Array("document", "posTags", "tokens"))
  .setOutputCol("dependencies")

val reNerFilter = new RENerChunksFilter()
  .setRelationPairs(Array("problem-test","problem-treatment"))
  .setMaxSyntacticDistance(4)
  .setDocLevelRelations(false)
  .setInputCols(Array("nerChunks", "dependencies"))
  .setOutputCol("RENerChunks")

val re = ZeroShotRelationExtractionModel
  .load("/tmp/spark_sbert_zero_shot")
  .setRelationalCategories(
    Map(
      "CURE" -> Array("{TREATMENT} cures {PROBLEM}."),
      "IMPROVE" -> Array("{TREATMENT} improves {PROBLEM}.", "{TREATMENT} cures {PROBLEM}."),
      "REVEAL" -> Array("{TEST} reveals {PROBLEM}.")
      ))
  .setPredictionThreshold(0.9f)
  .setMultiLabel(false)
  .setInputCols(Array("sentences", "RENerChunks"))
  .setOutputCol("relations)

val pipeline = new Pipeline()
  .setStages(Array(
    documentAssembler,
    sentencer,
    tokenizer,
    embeddings,
    posTagger,
    nerTagger,
    nerConverter,
    dependencyParser,
    reNerFilter,
    re))

val model = pipeline.fit(Seq("").toDS.toDF("text"))
val results = model.transform(
  Seq("Paracetamol can alleviate headache or sickness. An MRI test can be used to find cancer.").toDS.toDF("text"))

results
  .selectExpr("EXPLODE(relations) as relation")
  .selectExpr("relation.result", "relation.metadata.confidence")
  .show(truncate = false)

+-------+----------+
|result |confidence|
+-------+----------+
|REVEAL |0.9760039 |
|IMPROVE|0.98819494|
|IMPROVE|0.9929625 |
+-------+----------+
    See also

    http://jmlr.org/papers/v21/20-074.html for details about using NLI models for zero shot categorization

    RENerChunksFilter on how to generate paired named entity chunks for relation extraction

Value Members

  1. object REFeatureGenerator
  2. object RENerChunksFilter extends RENerChunksFilter with ParamsAndFeaturesReadable[RENerChunksFilter]
  3. object RelationDirection
  4. object RelationExtractionApproach extends RelationExtractionApproach
  5. object RelationExtractionDLModel extends ReadablePretrainedRelationExtractionDLModel with ReadRelationExtractionDLModelTensorflowModel with Serializable
  6. object RelationExtractionModel extends ReadsGenericClassifierGraph[RelationExtractionModel] with ReadablePretrainedGenericClassifier[RelationExtractionModel] with Serializable
  7. object ZeroShotRelationExtractionModel extends ReadablePretrainedZeroShotRelationExtractionModel with ReadZeroShotRelationExtractionModel with Serializable

    This is the companion object of MedicalBertForSequenceClassification.

    This is the companion object of MedicalBertForSequenceClassification. Please refer to that class for the documentation.

Ungrouped