Healthcare NLP Annotators

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
# First, pipeline stages for pre-processing the dataset (containing columns for text and label) are defined.
document = DocumentAssembler() \
    .setInputCol("text") \
    .setOutputCol("document")
chunk = Doc2Chunk() \
    .setInputCols(["document"]) \
    .setOutputCol("chunk")
token = Tokenizer() \
    .setInputCols(["document"]) \
    .setOutputCol("token")
embeddings = WordEmbeddingsModel.pretrained("embeddings_clinical", "en", "clinical/models") \
    .setInputCols(["document", "token"]) \
    .setOutputCol("embeddings")

# Define AssertionDLApproach with parameters and start training
assertionStatus = AssertionDLApproach() \
    .setLabelCol("label") \
    .setInputCols(["document", "chunk", "embeddings"]) \
    .setOutputCol("assertion") \
    .setBatchSize(128) \
    .setDropout(0.012) \
    .setLearningRate(0.015) \
    .setEpochs(1) \
    .setStartCol("start") \
    .setEndCol("end") \
    .setMaxSentLen(250)

trainingPipeline = Pipeline().setStages([
    document,
    chunk,
    token,
    embeddings,
    assertionStatus
])

assertionModel = trainingPipeline.fit(data)
assertionResults = assertionModel.transform(data).cache()

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
# Training with Glove Embeddings
# First define pipeline stages to extract embeddings and text chunks
documentAssembler = DocumentAssembler() \
    .setInputCol("text") \
    .setOutputCol("document")

tokenizer = Tokenizer() \
    .setInputCols(["document"]) \
    .setOutputCol("token")

glove = WordEmbeddingsModel.pretrained("embeddings_clinical", "en", "clinical/models") \
    .setInputCols(["document", "token"]) \
    .setOutputCol("word_embeddings") \
    .setCaseSensitive(False)

chunkAssembler = Doc2Chunk() \
    .setInputCols(["document"]) \
    .setChunkCol("target") \
    .setOutputCol("chunk")

# Then the AssertionLogRegApproach model is defined. Label column is needed in the dataset for training.
assertion = AssertionLogRegApproach() \
    .setLabelCol("label") \
    .setInputCols(["document", "chunk", "word_embeddings"]) \
    .setOutputCol("assertion") \
    .setReg(0.01) \
    .setBefore(11) \
    .setAfter(13) \
    .setStartCol("start") \
    .setEndCol("end")

assertionPipeline = Pipeline(stages=[
    documentAssembler,
    sentenceDetector,
    tokenizer,
    embeddings,
    nerModel,
    nerConverter,
    assertion
])

assertionModel = assertionPipeline.fit(dataset)

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
# Training a SNOMED model
# Define pre-processing pipeline for training data. It needs consists of columns for the normalized training data
# and their labels.
document = DocumentAssembler() \
    .setInputCol("normalized_text") \
    .setOutputCol("document")

chunk = Doc2Chunk() \
    .setInputCols(["document"]) \
    .setOutputCol("chunk")

token = Tokenizer() \
    .setInputCols(["document"]) \
    .setOutputCol("token")

embeddings = WordEmbeddingsModel.pretrained("embeddings_healthcare_100d", "en", "clinical/models") \
    .setInputCols(["document", "token"]) \
    .setOutputCol("embeddings")

chunkEmb = ChunkEmbeddings() \
        .setInputCols(["chunk", "embeddings"]) \
        .setOutputCol("chunk_embeddings")

snomedTrainingPipeline = Pipeline().setStages([
    document,
    chunk,
    token,
    embeddings,
    chunkEmb
])

snomedTrainingModel = snomedTrainingPipeline.fit(data)

snomedData = snomedTrainingModel.transform(data).cache()

# Then the Resolver can be trained with
snomedExtractor = ChunkEntityResolverApproach() \
    .setInputCols(["token", "chunk_embeddings"]) \
    .setOutputCol("recognized") \
    .setNeighbours(1000) \
    .setAlternatives(25) \
    .setNormalizedCol("normalized_text") \
    .setLabelCol("label") \
    .setEnableWmd(True).setEnableTfidf(True).setEnableJaccard(True) \
    .setEnableSorensenDice(True).setEnableJaroWinkler(True).setEnableLevenshtein(True) \
    .setDistanceWeights([1, 2, 2, 1, 1, 1]) \
    .setAllDistancesMetadata(True) \
    .setPoolingStrategy("MAX") \
    .setThreshold(1e32)
model = snomedExtractor.fit(snomedData)

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
# Define a pipeline with 2 different NER models with a ChunkMergeApproach at the end
data = spark.createDataFrame([["A 63-year-old man presents to the hospital ..."]]).toDF("text")
pipeline = Pipeline(stages=[
 DocumentAssembler().setInputCol("text").setOutputCol("document"),
 SentenceDetector().setInputCols(["document"]).setOutputCol("sentence"),
 Tokenizer().setInputCols(["sentence"]).setOutputCol("token"),
  WordEmbeddingsModel.pretrained("embeddings_clinical", "en", "clinical/models").setOutputCol("embs"),
  MedicalNerModel.pretrained("ner_jsl", "en", "clinical/models") \
    .setInputCols(["sentence", "token", "embs"]).setOutputCol("jsl_ner"),
 NerConverter().setInputCols(["sentence", "token", "jsl_ner"]).setOutputCol("jsl_ner_chunk"),
  MedicalNerModel.pretrained("ner_bionlp", "en", "clinical/models") \
    .setInputCols(["sentence", "token", "embs"]).setOutputCol("bionlp_ner"),
 NerConverter().setInputCols(["sentence", "token", "bionlp_ner"]) \
    .setOutputCol("bionlp_ner_chunk"),
 ChunkMergeApproach().setInputCols(["jsl_ner_chunk", "bionlp_ner_chunk"]).setOutputCol("merged_chunk")
])

# Show results
result = pipeline.fit(data).transform(data).cache()
result.selectExpr("explode(merged_chunk) as a") \
  .selectExpr("a.begin","a.end","a.result as chunk","a.metadata.entity as entity") \
  .show(5, False)
+-----+---+-----------+---------+
|begin|end|chunk      |entity   |
+-----+---+-----------+---------+
|5    |15 |63-year-old|Age      |
|17   |19 |man        |Gender   |
|64   |72 |recurrent  |Modifier |
|98   |107|cellulitis |Diagnosis|
|110  |119|pneumonias |Diagnosis|
+-----+---+-----------+---------+

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
# An example JSON file `regex_token.json` can look like this:
#
# {
#    "entity": "Stage",
#    "ruleScope": "sentence",
#    "regex": "[cpyrau]?[T][0-9X?][a-z^cpyrau]",
#    "matchScope": "token"
#  }
#
# Which means to extract the stage code on a sentence level.
# An example pipeline could then be defined like this
# Pipeline could then be defined like this
documentAssembler = DocumentAssembler() \
  .setInputCol("text") \
  .setOutputCol("document")

sentenceDetector = SentenceDetector() \
  .setInputCols(["document"]) \
  .setOutputCol("sentence")

tokenizer = Tokenizer() \
  .setInputCols(["sentence"]) \
  .setOutputCol("token")

# Define the parser (json file needs to be provided)
data = spark.createDataFrame([["A patient has liver metastases pT1bN0M0 and the T5 primary site may be colon or... "]]).toDF("text")

contextualParser = ContextualParserApproach() \
  .setInputCols(["sentence", "token"]) \
  .setOutputCol("entity") \
  .setJsonPath("/path/to/regex_token.json") \
  .setCaseSensitive(True) \
  .setContextMatch(False)

pipeline = Pipeline(stages=[
    documentAssembler,
    sentenceDetector,
    tokenizer,
    contextualParser
  ])

result = pipeline.fit(data).transform(data)

# Show Results
result.selectExpr("explode(entity)").show(5, truncate=False)
+-------------------------------------------------------------------------------------------------------------------------+
|col                                                                                                                      |
+-------------------------------------------------------------------------------------------------------------------------+
|{chunk, 32, 39, pT1bN0M0, {field -> Stage, normalized -> , confidenceValue -> 0.13, hits -> regex, sentence -> 0}, []}   |
|{chunk, 49, 50, T5, {field -> Stage, normalized -> , confidenceValue -> 0.13, hits -> regex, sentence -> 0}, []}         |
|{chunk, 148, 156, cT4bcN2M1, {field -> Stage, normalized -> , confidenceValue -> 0.13, hits -> regex, sentence -> 1}, []}|
|{chunk, 189, 194, T?N3M1, {field -> Stage, normalized -> , confidenceValue -> 0.13, hits -> regex, sentence -> 2}, []}   |
|{chunk, 316, 323, pT1bN0M0, {field -> Stage, normalized -> , confidenceValue -> 0.13, hits -> regex, sentence -> 3}, []} |
+-------------------------------------------------------------------------------------------------------------------------+

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") \
    .setUseAbbreviations(True)

tokenizer = Tokenizer() \
    .setInputCols(["sentence"]) \
    .setOutputCol("token")

embeddings = WordEmbeddingsModel \
    .pretrained("embeddings_clinical", "en", "clinical/models") \
    .setInputCols(["sentence", "token"]) \
    .setOutputCol("embeddings")

# Ner entities
clinical_sensitive_entities = MedicalNerModel \
    .pretrained("ner_deid_enriched", "en", "clinical/models") \
    .setInputCols(["sentence", "token", "embeddings"]).setOutputCol("ner")

nerConverter = NerConverter() \
    .setInputCols(["sentence", "token", "ner"]) \
    .setOutputCol("ner_con")

# Deidentification
deIdentification = DeIdentification() \
    .setInputCols(["ner_chunk", "token", "sentence"]) \
    .setOutputCol("dei") \
    # file with custom regex pattern for custom entities
    .setRegexPatternsDictionary("path/to/dic_regex_patterns_main_categories.txt") \
    # file with custom obfuscator names for the entities
    .setObfuscateRefFile("path/to/obfuscate_fixed_entities.txt") \
    .setRefFileFormat("csv") \
    .setRefSep("#") \
    .setMode("obfuscate") \
    .setDateFormats(Array("MM/dd/yy","yyyy-MM-dd")) \
    .setObfuscateDate(True) \
    .setDateTag("DATE") \
    .setDays(5) \
    .setObfuscateRefSource("file")

# Pipeline
data = spark.createDataFrame([
    ["# 7194334 Date : 01/13/93 PCP : Oliveira , 25 years-old , Record date : 2079-11-09."]
]).toDF("text")

pipeline = Pipeline(stages=[
    documentAssembler,
    sentenceDetector,
    tokenizer,
    embeddings,
    clinical_sensitive_entities,
    nerConverter,
    deIdentification
])
result = pipeline.fit(data).transform(data)

# Show Results
result.select("dei.result").show(truncate = False)
+--------------------------------------------------------------------------------------------------+
|result                                                                                            |
+--------------------------------------------------------------------------------------------------+
|[# 01010101 Date : 01/18/93 PCP : Dr. Gregory House , <AGE> years-old , Record date : 2079-11-14.]|
+--------------------------------------------------------------------------------------------------+

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
# Define pipeline stages to prepare the data
document_assembler = DocumentAssembler() \
  .setInputCol("text") \
  .setOutputCol("document")

tokenizer = Tokenizer() \
  .setInputCols(["document"]) \
  .setOutputCol("token")

normalizer = Normalizer() \
  .setInputCols(["token"]) \
  .setOutputCol("normalized")

stopwords_cleaner = StopWordsCleaner() \
  .setInputCols(["normalized"]) \
  .setOutputCol("cleanTokens") \
  .setCaseSensitive(False)

stemmer = Stemmer() \
  .setInputCols(["cleanTokens"]) \
  .setOutputCol("stem")

# Define the document classifier and fit training data to it
logreg = DocumentLogRegClassifierApproach() \
  .setInputCols(["stem"]) \
  .setLabelCol("category") \
  .setOutputCol("prediction")

pipeline = Pipeline(stages=[
  document_assembler,
  tokenizer,
  normalizer,
  stopwords_cleaner,
  stemmer,
  logreg
])

model = pipeline.fit(trainingData)

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
features_asm = FeaturesAssembler() \
    .setInputCols(["feature_1", "feature_2", "...", "feature_n"]) \
    .setOutputCol("features")

gen_clf = GenericClassifierApproach() \
    .setLabelColumn("target") \
    .setInputCols(["features"]) \
    .setOutputCol("prediction") \
    .setModelFile("/path/to/graph_file.pb") \
    .setEpochsNumber(50) \
    .setBatchSize(100) \
    .setFeatureScaling("zscore") \
    .setlearningRate(0.001) \
    .setFixImbalance(True) \
    .setOutputLogsPath("logs") \
    .setValidationSplit(0.2) # keep 20% of the data for validation purposes

pipeline = Pipeline().setStages([
    features_asm,
    gen_clf
])

clf_model = pipeline.fit(data)