Healthcare NLP v3.4.2 Release Notes

 

3.4.2

We are glad to announce that Spark NLP Healthcare 3.4.2 has been released!

Highlights

  • New RCT Classifier, NER models and pipeline (Deidentification)
  • Setting the scope window (target area) dynamically in Assertion Status detection models
  • Reading JSON files (exported from ALAB) from HDFS with AnnotationJsonReader
  • Allow users to write Tensorflow graphs to HDFS
  • Serving Spark NLP on APIs
  • Updated documentation on installing Spark NLP for Healthcare in AWS EMR (Jupyter, Livy, Yarn, Hadoop)
  • New series of notebooks to reproduce the academic papers published by our colleagues
  • PySpark tutorial notebooks to let non-Spark users get started with Apache Spark ecosystem in Python
  • New & updated notebooks
  • List of recently updated or added models

New RCT Classifier, NER Models and Pipeline (Deidentification)

We are releasing a new bert_sequence_classifier_rct_biobert model, four new Spanish deidentification NER models (ner_deid_generic_augmented, ner_deid_subentity_augmented, ner_deid_generic_roberta_augmented, ner_deid_subentity_roberta_augmented) and a pipeline (clinical_deidentification_augmented).

  • bert_sequence_classifier_rct_biobert: This model can classify the sections within abstract of scientific articles regarding randomized clinical trials (RCT) (BACKGROUND, CONCLUSIONS, METHODS, OBJECTIVE, RESULTS).

Example :

...
sequenceClassifier_model = MedicalBertForSequenceClassification.pretrained("bert_sequence_classifier_rct_biobert", "en", "clinical/models")\
  .setInputCols(["document",'token'])\
  .setOutputCol("class")
...

sample_text = "Previous attempts to prevent all the unwanted postoperative responses to major surgery with an epidural hydrophilic opioid , morphine , have not succeeded . The authors ' hypothesis was that the lipophilic opioid fentanyl , infused epidurally close to the spinal-cord opioid receptors corresponding to the dermatome of the surgical incision , gives equal pain relief but attenuates postoperative hormonal and metabolic responses more effectively than does systemic fentanyl ."

result = sequence_clf_model.transform(spark.createDataFrame([[sample_text]]).toDF("text"))

>> class: 'BACKGROUND'

  • ner_deid_generic_augmented, ner_deid_subentity_augmented, ner_deid_generic_roberta_augmented, ner_deid_subentity_roberta_augmented models and clinical_deidentification_augmented pipeline : You can use either sciwi-embeddings (300 dimensions) or the Roberta Clinical Embeddings (infix _roberta_) with these NER models. These models and pipeline are different to their non-augmented versions in the following:

    • They are trained with more data, now including an in-house annotated deidentification dataset;
    • New SEX tag is available for all of them. This tag is now included in the NER and has been improved with more rules in the ContextualParsers of the pipeline, resulting in having a bigger recall to detect the sex of the patient.
    • New STREET, CITY and COUNTRY entities are added to subentity versions.

For more details and examples, please check Clinical Deidentification in Spanish notebook.

Example :

...
embeddings = WordEmbeddingsModel.pretrained("embeddings_sciwiki_300d","es","clinical/models")\
    .setInputCols(["sentence", "token"])\
    .setOutputCol("embeddings")

deid_ner = MedicalNerModel.pretrained("ner_deid_generic_augmented", "es", "clinical/models")\
    .setInputCols(["sentence", "token", "embeddings"])\
    .setOutputCol("ner")

deid_sub_entity_ner = MedicalNerModel.pretrained("ner_deid_subentity_augmented", "es", "clinical/models")\
    .setInputCols(["sentence", "token", "embeddings"])\
    .setOutputCol("ner_sub_entity")
...

Results :

chunk                    entity_subentity    entity_generic
-----------------------  ------------------  ----------------
Antonio Miguel Martínez  PATIENT             NAME
un varón                 SEX                 SEX
35                       AGE                 AGE
auxiliar de enfermería   PROFESSION          PROFESSION
Cadiz                    CITY                LOCATION
España                   COUNTRY             LOCATION
Clinica San Carlos       HOSPITAL            LOCATION

Setting the Scope Window (Target Area) Dynamically in Assertion Status Detection Models

This parameter allows you to train the Assertion Status Models to focus on specific context windows when resolving the status of a NER chunk. The window is in format [X,Y] being X the number of tokens to consider on the left of the chunk, and Y the max number of tokens to consider on the right. Let’s take a look at what different windows mean:

  • By default, the window is [-1,-1] which means that the Assertion Status will look at all of the tokens in the sentence/document (up to a maximum of tokens set in setMaxSentLen()).
  • [0,0] means “don’t pay attention to any token except the ner_chunk”, what basically is not considering any context for the Assertion resolution.
  • [9,15] is what empirically seems to be the best baseline, meaning that we look up to 9 tokens on the left and 15 on the right of the ner chunk to understand the context and resolve the status.

Check this scope window tuning assertion status detection notebook that illustrates the effect of the different windows and how to properly fine-tune your AssertionDLModels to get the best of them.

Example :

assertion_status = AssertionDLApproach() \
          .setGraphFolder("assertion_dl/") \
          .setInputCols("sentence", "chunk", "embeddings") \
          .setOutputCol("assertion") \
          ...
          ...
          .setScopeWindow([9, 15])     # NEW! Scope Window!

Reading JSON Files (Exported from ALAB) From HDFS with AnnotationJsonReader

Now we can read the dataframe from a HDFS that we read the files from in our cluster.

Example :

filename = "hdfs:///user/livy/import.json"
reader = AnnotationToolJsonReader(assertion_labels = ['AsPresent', 'AsAbsent', 'AsConditional', 'AsHypothetical', 'Family', 'AsPossible', 'AsElse'])
df = reader.readDataset(spark, filename)

Allow Users Write Tensorflow Graphs to HDFS

Now we can save custom Tensorflow graphs to the HDFS that mainly being used in a cluster environment.

tf_graph.build("ner_dl", build_params={"embeddings_dim": 200, "nchars": 128, "ntags": 12, "is_medical": 1}, model_location="hdfs:///user/livy", model_filename="auto")

Serving Spark NLP on APIs

Two new notebooks and a series of blog posts / Medium articles have been created to guide Spark NLP users to serve Spark NLP on a RestAPI.

The difference between both approaches are the following:

  • SynapseML is a Microsoft Azure Open Source library used to carry out ML at scale. In this case, we use the Spark Serving feature, that leverages Spark Streaming and adds a web server with a Load Balancer, allowing concurrent processing of Spark NLP calls. Best approach if you look for scalability with Load Balancing.
  • FastAPI + LightPipelines: A solution to run Spark NLP using a FastAPI webserver. It uses LightPipelines, what means having a very good performance but not leveraging Spark Clusters. Also, no Load Balancer is available in the suggestion, but you can create your own. Best approach if you look for performance.
  • Databricks and MLFlow: Using MLFlow Serve or Databricks Jobs APIs to serve for inference Spark NLP pipelines from within Databricks. Best approach if you look for scalability within Databricks.

Updated Documentation on Installing Spark NLP For Healthcare in AWS EMR (Jupyter, Livy, Yarn, Hadoop)

Ready-to-go Spark NLP for Healthcare environment in AWS EMR. Full instructions are here.

New Series of Notebooks to Reproduce the Academic Papers Published by Our Colleagues

You can find all these notebooks here

PySpark Tutorial Notebooks to Let Non-Spark Users to Get Started with Apache Spark Ecosystem in Python

John Snow Labs has created a series of 8 notebooks to go over PySpark from zero to hero. Notebooks cover PySpark essentials, DataFrame creation, querying, importing data from different formats, functions / udfs, Spark MLLib examples (regression, classification, clustering) and Spark NLP best practises (usage of parquet, repartition, coalesce, custom annotators, etc).

You can find all these notebooks here.

New & Updated Notebooks

  • Series of academic notebooks : A new series of academic paper notebooks, available here
  • Clinical_Deidentification_in_Spanish.ipynb: A notebook showcasing Clinical Deidentification in Spanish, available here.
  • Clinical_Deidentification_Comparison.ipynb: A new series of comparisons between different Deidentification libraries. So far, it contains Spark NLP for Healthcare and ScrubaDub with Spacy Transformers. Available here.
  • Scope_window_tuning_assertion_status_detection.ipynb: How to finetune Assertion Status using the Scope Window. Available here
  • Clinical_Longformer_vs_BertSentence_&_USE.ipynb: A Comparison of how Clinical Longformer embeddings, averaged by the Sentence Embeddings annotator, performs compared to BioBert and UniversalSentenceEncoding. Link here.
  • Serving_SparkNLP_with_Synapse.ipynb: Serving SparkNLP for production purposes using Synapse ML. Available here
  • Serving_SparkNLP_with_FastAPI_and_LP.ipynb: Serving SparkNLP for production purposes using FastAPI, RestAPI and LightPipelines. Available here
  • Series of PySpark tutorial notebooks: Available here

List of Recently Updated or Added Models

  • sbiobertresolve_hcpcs
  • bert_sequence_classifier_rct_biobert
  • ner_deid_generic_augmented_es
  • ner_deid_subentity_augmented_es
  • ner_deid_generic_roberta_augmented_es
  • ner_deid_subentity_roberta_augmented_es
  • clinical_deidentification_augmented_es

For all Spark NLP for healthcare models, please check : Models Hub Page

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