Description
Map clinical entities to UMLS CUI codes.
Predicted Entities
This model returns CUI (concept unique identifier) codes for Clinical Findings, Medical Devices, Anatomical Structures and Injuries & Poisoning terms
Live Demo Open in Colab Copy S3 URI
How to use
sbiobertresolve_umls_major_concepts resolver model must be used with sbiobert_base_cased_mli as embeddings ner_jsl as NER model. Cerebrovascular_Disease, Communicable_Disease, Diabetes, Disease_Syndrome_Disorder, Heart_Disease, Hyperlipidemia, Hypertension, Injury_or_Poisoning, Kidney_Disease, Medical-Device, Obesity, Oncological, Overweight, Psychological_Condition, Symptom, VS_Finding, ImagingFindings, EKG_Findings set in .setWhiteList().
...
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")
resolver = SentenceEntityResolverModel\
.pretrained("sbiobertresolve_umls_major_concepts", "en", "clinical/models") \
.setInputCols(["ner_chunk", "sbert_embeddings"]) \
.setOutputCol("resolution")\
.setDistanceFunction("EUCLIDEAN")
pipeline = Pipeline(stages = [document_assembler, sentence_detector, tokens, embeddings, ner, ner_converter, chunk2doc, sbert_embedder, resolver])
data = spark.createDataFrame([["""A 28-year-old female with a history of gestational diabetes mellitus diagnosed eight years prior to presentation and subsequent type two diabetes mellitus (T2DM), one prior episode of HTG-induced pancreatitis three years prior to presentation, associated with an acute hepatitis, and obesity with a body mass index (BMI) of 33.5 kg/m2, presented with a one-week history of polyuria, polydipsia, poor appetite, and vomiting."""]]).toDF("text")
results = pipeline.fit(data).transform(data)
import nlu
nlu.load("en.resolve.umls").predict("""A 28-year-old female with a history of gestational diabetes mellitus diagnosed eight years prior to presentation and subsequent type two diabetes mellitus (T2DM), one prior episode of HTG-induced pancreatitis three years prior to presentation, associated with an acute hepatitis, and obesity with a body mass index (BMI) of 33.5 kg/m2, presented with a one-week history of polyuria, polydipsia, poor appetite, and vomiting.""")
Results
| | ner_chunk | resolution |
|---:|:------------------------------|:-------------|
| 0 | 28-year-old | C1864118 |
| 1 | female | C3887375 |
| 2 | gestational diabetes mellitus | C2183115 |
| 3 | eight years prior | C5195266 |
| 4 | subsequent | C3844350 |
| 5 | type two diabetes mellitus | C4014362 |
| 6 | T2DM | C4014362 |
| 7 | HTG-induced pancreatitis | C4554179 |
| 8 | three years prior | C1866782 |
| 9 | acute | C1332147 |
| 10 | hepatitis | C1963279 |
| 11 | obesity | C1963185 |
| 12 | body mass index | C0578022 |
| 13 | 33.5 kg/m2 | C2911054 |
| 14 | one-week | C0420331 |
| 15 | polyuria | C3278312 |
| 16 | polydipsia | C3278316 |
| 17 | poor appetite | C0541799 |
| 18 | vomiting | C1963281 |
Model Information
| Model Name: | sbiobertresolve_umls_major_concepts |
| Compatibility: | Healthcare NLP 3.0.2+ |
| License: | Licensed |
| Edition: | Official |
| Input Labels: | [sentence_embeddings] |
| Output Labels: | [umls_code] |
| Language: | en |
Data Source
https://www.nlm.nih.gov/research/umls/index.html