Description
This model maps clinical entities and concepts (like drugs/ingredients) to RxNorm codes using mpnet_embeddings_biolord_2023_c embeddings. It trained on the augmented version of the dataset used in previous RxNorm resolver models. Additionally, this model returns concept classes of the drugs in the all_k_aux_labels column.
Predicted Entities
RxNorm Codes, Concept Classes
How to use
document_assembler = DocumentAssembler()\
.setInputCol("text")\
.setOutputCol("document")
sentenceDetectorDL = SentenceDetectorDLModel.pretrained("sentence_detector_dl_healthcare", "en", "clinical/models")\
.setInputCols(["document"])\
.setOutputCol("sentence")
tokenizer = Tokenizer()\
.setInputCols(["sentence"])\
.setOutputCol("token")
word_embeddings = WordEmbeddingsModel.pretrained("embeddings_clinical", "en", "clinical/models")\
.setInputCols(["sentence", "token"])\
.setOutputCol("word_embeddings")
ner = MedicalNerModel.pretrained("ner_posology_greedy", "en", "clinical/models")\
.setInputCols(["sentence", "token", "word_embeddings"])\
.setOutputCol("ner")\
ner_converter = NerConverterInternal()\
.setInputCols(["sentence", "token", "ner"])\
.setOutputCol("ner_chunk")\
.setWhiteList(["DRUG"])
c2doc = Chunk2Doc()\
.setInputCols("ner_chunk")\
.setOutputCol("ner_chunk_doc")
biolord_embedding = MPNetEmbeddings.pretrained("mpnet_embeddings_biolord_2023_c", "en")\
.setInputCols(["ner_chunk_doc"])\
.setOutputCol("embeddings")
rxnorm_resolver = SentenceEntityResolverModel.pretrained("biolordresolve_rxnorm_augmented", "en", "clinical/models")\
.setInputCols(["embeddings"]) \
.setOutputCol("rxnorm_code")\
.setDistanceFunction("EUCLIDEAN")
resolver_pipeline = Pipeline(stages = [document_assembler,
sentenceDetectorDL,
tokenizer,
word_embeddings,
ner,
ner_converter,
c2doc,
biolord_embedding,
rxnorm_resolver])
text= "The patient was prescribed aspirin and and Albuterol inhaler, two puffs every 4 hours as needed for asthma. She was seen by the endocrinology service and was discharged on avandia 4 mg at night , Coumadin 5 mg with meals , and metformin 1000 mg two times a day and Lisinopril 10 mg daily"
data = spark.createDataFrame([[text]]).toDF("text")
result = resolver_pipeline.fit(data).transform(data)
val document_assembler = new DocumentAssembler()
.setInputCol("text")
.setOutputCol("document")
val sentence_detector = SentenceDetectorDLModel.pretrained("sentence_detector_dl_healthcare","en","clinical/models")
.setInputCols("document")
.setOutputCol("sentence")
val tokenizer = new Tokenizer()
.setInputCols("sentence")
.setOutputCol("token")
val word_embeddings = WordEmbeddingsModel.pretrained("embeddings_clinical", "en", "clinical/models")
.setInputCols(Array("sentence","token"))
.setOutputCol("embeddings")
val ner = MedicalNerModel.pretrained("ner_posology_greedy", "en", "clinical/models")
.setInputCols(Array("sentence","token","embeddings"))
.setOutputCol("ner")
val ner_converter = new NerConverter()
.setInputCols(Array("sentence","token","ner"))
.setOutputCol("ner_chunk")
.setWhiteList("DRUG")
val chunk2doc = new Chunk2Doc()
.setInputCols("ner_chunk")
.setOutputCol("ner_chunk_doc")
val biolord_embedding = MPNetEmbeddings.pretrained("mpnet_embeddings_biolord_2023_c", "en")\
.setInputCols(["ner_chunk_doc"])\
.setOutputCol("embeddings")
val rxnorm_resolver = SentenceEntityResolverModel.pretrained("biolordresolve_rxnorm_augmented", "en", "clinical/models")
.setInputCols("embeddings")
.setOutputCol("rxnorm_code")
.setDistanceFunction("EUCLIDEAN")
val pipeline = new Pipeline().setStages(Array(
document_assembler,
sentence_detector,
tokenizer,
word_embeddings,
ner,
ner_converter,
chunk2doc,
biolord_embedding,
rxnorm_resolver))
val data = Seq("The patient was prescribed aspirin and and Albuterol inhaler, two puffs every 4 hours as needed for asthma. He was seen by the endocrinology service and she was discharged on Coumadin 5 mg with meals , and metformin 1000 mg two times a day and Lisinopril 10 mg daily").toDS().toDF("text")
val result = pipeline.fit(data).transform(data)
Results
| | ner_chunk | entity | rxnorm_code | resolution | all_k_results | all_k_distances | all_k_cosine_distances | all_k_resolutions | all_k_aux_labels |
|---:|:------------------|:---------|--------------:|:----------------------------------------------------------------|:--------------------------------------------...|:---------------------------------------------|:---------------------------------------------|:-----------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------|
| 0 | aspirin | DRUG | 1191 | aspirin [aspirin] | 1191:::1154070:::1537020:::1295740:::1299851...| 0.2747:::0.4428:::0.4512:::0.4900:::0.5305...| 0.0377:::0.0980:::0.1018:::0.1200:::0.1407...| aspirin [aspirin]:::aspirin pill [aspirin pill]:::aspirin effervescent oral tablet:::aspirin oral powder...| Ingredient:::Clinical Dose Group:::Clinical Drug Form:::Clinical Dose Group:::B...|
| 1 | Albuterol inhaler | DRUG | 745678 | albuterol metered dose inhaler [albuterol metered dose inhaler] | 745678:::1649559:::745790:::307779:::745679:...| 0.4336:::0.4758:::0.5416:::0.5701:::0.5863...| 0.0940:::0.1132:::0.1466:::0.1625:::0.1719...| albuterol metered dose inhaler [albuterol metered dose inhaler]:::albuterol dry powder inhaler [albutero...| Clinical Drug Form:::Clinical Drug Form:::Clinical Drug Form:::Clinical Drug:::...|
| 2 | Coumadin 5 mg | DRUG | 855333 | warfarin sodium 5 mg [coumadin] | 855333:::432467:::438740:::451604:::855345::...| 0.3421:::0.4407:::0.4601:::0.4798:::0.5002...| 0.0585:::0.0971:::0.1058:::0.1151:::0.1251...| warfarin sodium 5 mg [coumadin]:::coumarin 5 mg oral tablet:::coumarin 5 mg [coumarin 5 mg]:::coumarin 0...| Branded Drug Comp:::Clinical Drug:::Clinical Drug Comp:::Clinical Drug Comp:::B...|
| 3 | metformin 1000 mg | DRUG | 316255 | metformin 1000 mg [metformin 1000 mg] | 316255:::860995:::860999:::861004:::316256::...| 0.3468:::0.4492:::0.4492:::0.5133:::0.5497...| 0.0601:::0.1009:::0.1009:::0.1317:::0.1511...| metformin 1000 mg [metformin 1000 mg]:::metformin hydrochloride 1000 mg [metformin hydrochloride 1000 mg...| Clinical Drug Comp:::Clinical Drug Comp:::Clinical Drug:::Clinical Drug:::Clini...|
| 4 | Lisinopril 10 mg | DRUG | 314076 | lisinopril 10 mg oral tablet | 314076:::316151:::197885:::567576:::316153::...| 0.4704:::0.4845:::0.6129:::0.6281:::0.6384...| 0.1106:::0.1174:::0.1878:::0.1973:::0.2038...| lisinopril 10 mg oral tablet:::lisinopril 10 mg [lisinopril 10 mg]:::hydrochlorothiazide 12.5 mg / lisin...| Clinical Drug:::Clinical Drug Comp:::Clinical Drug:::Branded Drug Comp:::Clinic...|
Model Information
| Model Name: | biolordresolve_rxnorm_augmented |
| Compatibility: | Healthcare NLP 5.3.1+ |
| License: | Licensed |
| Edition: | Official |
| Input Labels: | [mpnet_embeddings] |
| Output Labels: | [rxnorm_code] |
| Language: | en |
| Size: | 1.3 GB |
| Case sensitive: | false |
References
In this model, RxNorm version 5.0 was used for the training.