Extract relations between phenotypic abnormalities and diseases (ReDL)

Description

Extract relations to fully understand the origin of some phenotypic abnormalities and their associated diseases. 1 : Entities are related, 0 : Entities are not related.

Predicted Entities

0, 1

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How to use

...
documenter = DocumentAssembler()\
    .setInputCol("text")\
    .setOutputCol("document")

sentencer = SentenceDetector()\
    .setInputCols(["document"])\
    .setOutputCol("sentences")

tokenizer = sparknlp.annotators.Tokenizer()\
    .setInputCols(["sentences"])\
    .setOutputCol("tokens")

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

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

ner_tagger = MedicalNerModel.pretrained("ner_human_phenotype_gene_clinical", "en", "clinical/models")\
    .setInputCols("sentences", "tokens", "embeddings")\
    .setOutputCol("ner_tags") 

ner_converter = NerConverter() \
    .setInputCols(["sentences", "tokens", "ner_tags"]) \
    .setOutputCol("ner_chunks")

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

#Set a filter on pairs of named entities which will be treated as relation candidates
re_ner_chunk_filter = RENerChunksFilter() \
    .setInputCols(["ner_chunks", "dependencies"])\
    .setMaxSyntacticDistance(10)\
    .setOutputCol("re_ner_chunks")

# The dataset this model is trained to is sentence-wise. 
# This model can also be trained on document-level relations - in which case, while predicting, use "document" instead of "sentence" as input.
re_model = RelationExtractionDLModel()\
    .pretrained('redl_human_phenotype_gene_biobert', 'en', "clinical/models") \
    .setPredictionThreshold(0.5)\
    .setInputCols(["re_ner_chunks", "sentences"]) \
    .setOutputCol("relations")

pipeline = Pipeline(stages=[documenter, sentencer, tokenizer, pos_tagger, words_embedder, ner_tagger, ner_converter, dependency_parser, re_ner_chunk_filter, re_model])

text = """She has a retinal degeneration, hearing loss and renal failure, short stature, Mutations in the SH3PXD2B gene coding for the Tks4 protein are responsible for the autosomal recessive."""

data = spark.createDataFrame([[text]]).toDF("text")

p_model = pipeline.fit(data)

result = p_model.transform(data)
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 pos_tagger = PerceptronModel()
    .pretrained("pos_clinical", "en", "clinical/models") 
    .setInputCols(Array("sentences", "tokens"))
    .setOutputCol("pos_tags")

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

val ner_tagger = MedicalNerModel.pretrained("ner_human_phenotype_gene_clinical", "en", "clinical/models")
    .setInputCols(Array("sentences", "tokens", "embeddings"))
    .setOutputCol("ner_tags") 

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

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

// Set a filter on pairs of named entities which will be treated as relation candidates
val re_ner_chunk_filter = RENerChunksFilter()
    .setInputCols(Array("ner_chunks", "dependencies"))
    .setMaxSyntacticDistance(10)
    .setOutputCol("re_ner_chunks")

// The dataset this model is trained to is sentence-wise. 
// This model can also be trained on document-level relations - in which case, while predicting, use "document" instead of "sentence" as input.
val re_model = RelationExtractionDLModel()
    .pretrained("redl_human_phenotype_gene_biobert", "en", "clinical/models")
    .setPredictionThreshold(0.5)
    .setInputCols(Array("re_ner_chunks", "sentences"))
    .setOutputCol("relations")
    
val pipeline = new Pipeline().setStages(Array(documenter, sentencer, tokenizer, pos_tagger, words_embedder, ner_tagger, ner_converter, dependency_parser, re_ner_chunk_filter, re_model))

val data = Seq("""She has a retinal degeneration, hearing loss and renal failure, short stature, Mutations in the SH3PXD2B gene coding for the Tks4 protein are responsible for the autosomal recessive.""").toDS.toDF("text")

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

Results

|    |   relation | entity1   |   entity1_begin |   entity1_end | chunk1               | entity2   |   entity2_begin |   entity2_end | chunk2              |   confidence |
|---:|-----------:|:----------|----------------:|--------------:|:---------------------|:----------|----------------:|--------------:|:--------------------|-------------:|
|  0 |          0 | HP        |              10 |            29 | retinal degeneration | HP        |              32 |            43 | hearing loss        |     0.893809 |
|  1 |          0 | HP        |              10 |            29 | retinal degeneration | HP        |              49 |            61 | renal failure       |     0.958486 |
|  2 |          1 | HP        |              10 |            29 | retinal degeneration | HP        |             162 |           180 | autosomal recessive |     0.65584  |
|  3 |          0 | HP        |              32 |            43 | hearing loss         | HP        |              64 |            76 | short stature       |     0.707055 |
|  4 |          1 | HP        |              32 |            43 | hearing loss         | GENE      |              96 |           103 | SH3PXD2B            |     0.640802 |

Model Information

Model Name: redl_human_phenotype_gene_biobert
Compatibility: Spark NLP for Healthcare 3.0.3+
License: Licensed
Edition: Official
Language: en
Case sensitive: true

Data Source

Trained on a silver standard corpus of human phenotype and gene annotations and their relations.

Benchmarking

Relation           Recall Precision        F1   Support
0                   0.922     0.908     0.915       129
1                   0.831     0.855     0.843        71
Avg.                0.877     0.882     0.879         -