Description
This model maps extracted medical entities to Snomed codes (with Morph Abnormality, Procedure, Substance, Physical Object, Body Structure concepts from INT version) using chunk embeddings.
Predicted Entities
Snomed Codes and their normalized definition with sbiobert_base_cased_mli embeddings.
How to use
...
chunk2doc = Chunk2Doc().setInputCols("ner_chunk").setOutputCol("ner_chunk_doc")
sbert_embedder = BertSentenceEmbeddings\
.pretrained("sbiobert_base_cased_mli","en","clinical/models")\
.setInputCols(["ner_chunk_doc"])\
.setOutputCol("sbert_embeddings")
snomed_aux_int_resolver = SentenceEntityResolverModel.pretrained("sbiobertresolve_snomed_auxConcepts_int","en", "clinical/models") \
.setInputCols(["sbert_embeddings"]) \
.setOutputCol("resolution")\
.setDistanceFunction("EUCLIDEAN")
nlpPipeline = Pipeline(stages=[document_assembler, sentence_detector, tokenizer, word_embeddings, clinical_ner, ner_converter, chunk2doc, sbert_embedder, snomed_aux_int_resolver])
data = spark.createDataFrame([["This is an 82 - year-old male with a history of prior tobacco use , hypertension , chronic renal insufficiency , COPD , gastritis , and TIA who initially presented to Braintree with a non-ST elevation MI and Guaiac positive stools , transferred to St . Margaret\'s Center for Women & Infants for cardiac catheterization with PTCA to mid LAD lesion complicated by hypotension and bradycardia requiring Atropine , IV fluids and transient dopamine possibly secondary to vagal reaction , subsequently transferred to CCU for close monitoring , hemodynamically stable at the time of admission to the CCU ."]]).toDF("text")
results = nlpPipeline.fit(data).transform(data)
...
chunk2doc = Chunk2Doc().setInputCols("ner_chunk").setOutputCol("ner_chunk_doc")
val sbert_embedder = BertSentenceEmbeddings
.pretrained("sbiobert_base_cased_mli","en","clinical/models")
.setInputCols(Array("ner_chunk_doc"))
.setOutputCol("sbert_embeddings")
val snomed_aux_int_resolver = SentenceEntityResolverModel
.pretrained("sbiobertresolve_snomed_auxConcepts_int","en", "clinical/models")
.setInputCols(Array("ner_chunk", "sbert_embeddings"))
.setOutputCol("resolution")
.setDistanceFunction("EUCLIDEAN")
val pipeline = new Pipeline().setStages(Array(document_assembler, sentence_detector, tokenizer, word_embeddings, clinical_ner, ner_converter, chunk2doc, sbert_embedder, snomed_aux_int_resolver))
val data = Seq("This is an 82 - year-old male with a history of prior tobacco use , hypertension , chronic renal insufficiency , COPD , gastritis , and TIA who initially presented to Braintree with a non-ST elevation MI and Guaiac positive stools , transferred to St . Margaret\'s Center for Women & Infants for cardiac catheterization with PTCA to mid LAD lesion complicated by hypotension and bradycardia requiring Atropine , IV fluids and transient dopamine possibly secondary to vagal reaction , subsequently transferred to CCU for close monitoring , hemodynamically stable at the time of admission to the CCU .").toDF("text")
val result = pipeline.fit(data).transform(data)
Results
+--------------------+-----+---+---------+---------------+----------+--------------------+--------------------+
| chunk|begin|end| entity| code|confidence| resolutions| codes|
+--------------------+-----+---+---------+---------------+----------+--------------------+--------------------+
| hypertension| 68| 79| PROBLEM| 148439002| 0.2138|risk factors pres...|148439002:::42595...|
|chronic renal ins...| 83|109| PROBLEM| 722403003| 0.8517|gastrointestinal ...|722403003:::13781...|
| COPD| 113|116| PROBLEM|845101000000100| 0.0962|management of chr...|845101000000100::...|
| gastritis| 120|128| PROBLEM| 711498001| 0.3398|magnetic resonanc...|711498001:::71771...|
| TIA| 136|138| PROBLEM| 449758002| 0.1927|traumatic infarct...|449758002:::85844...|
|a non-ST elevatio...| 182|202| PROBLEM| 1411000087101| 0.0823|ct of left knee::...|1411000087101:::3...|
|Guaiac positive s...| 208|229| PROBLEM| 388507006| 0.0555|asparagus rast:::...|388507006:::71771...|
|cardiac catheteri...| 295|317| TEST| 41976001| 0.9790|cardiac catheteri...|41976001:::705921...|
| PTCA| 324|327|TREATMENT| 312644004| 0.0616|angioplasty of po...|312644004:::41507...|
| mid LAD lesion| 332|345| PROBLEM| 91749005| 0.1399|structure of firs...|91749005:::917470...|
+--------------------+-----+---+---------+---------------+----------+--------------------+--------------------+
Model Information
| Name: | sbiobertresolve_snomed_auxConcepts_int |
| Type: | SentenceEntityResolverModel |
| Compatibility: | Spark NLP 2.6.4 + |
| License: | Licensed |
| Edition: | Official |
| Input labels: | [ner_chunk, chunk_embeddings] |
| Output labels: | [resolution] |
| Language: | en |
| Dependencies: | sbiobert_base_cased_mli |
Data Source
Trained on SNOMED (INT version) Findings with sbiobert_base_cased_mli sentence embeddings.
https://www.snomed.org/