ICD10CM Injuries Entity Resolver

Description

Entity Resolution model Based on KNN using Word Embeddings + Word Movers Distance

Predicted Entities

ICD10-CM Codes and their normalized definition with clinical_embeddings

Live Demo Open in Colab Download

How to use

...
injury_resolver = ChunkEntityResolverModel.pretrained("chunkresolve_icd10cm_injuries_clinical","en","clinical/models")\
	.setInputCols("token","chunk_embeddings")\
	.setOutputCol("entity")
pipeline_puerile = Pipeline(stages = [documentAssembler, sentenceDetector, tokenizer, word_embeddings, clinical_ner, ner_converter, chunk_embeddings, injury_resolver])

model = pipeline_puerile.fit(spark.createDataFrame([["""The patient is a 5-month-old infant who presented initially on Monday with a cold, cough, and runny nose for 2 days. Mom states she had no fever. Her appetite was good but she was spitting up a lot. She had no difficulty breathing and her cough was described as dry and hacky. At that time, physical exam showed a right TM, which was red. Left TM was okay. She was fairly congested but looked happy and playful. She was started on Amoxil and Aldex and we told to recheck in 2 weeks to recheck her ear. Mom returned to clinic again today because she got much worse overnight. She was having difficulty breathing. She was much more congested and her appetite had decreased significantly today. She also spiked a temperature yesterday of 102.6 and always having trouble sleeping secondary to congestion."""]]).toDF("text"))

results = model.transform(data)
...
val injury_resolver = ChunkEntityResolverModel.pretrained("chunkresolve_icd10cm_injuries_clinical","en","clinical/models")
	.setInputCols(Array("token","chunk_embeddings"))
	.setOutputCol("resolution")
val pipeline = new Pipeline().setStages(Array(documentAssembler, sentenceDetector, tokenizer, word_embeddings, clinical_ner, ner_converter, chunk_embeddings, injury_resolver))

val result = pipeline.fit(Seq.empty["The patient is a 5-month-old infant who presented initially on Monday with a cold, cough, and runny nose for 2 days. Mom states she had no fever. Her appetite was good but she was spitting up a lot. She had no difficulty breathing and her cough was described as dry and hacky. At that time, physical exam showed a right TM, which was red. Left TM was okay. She was fairly congested but looked happy and playful. She was started on Amoxil and Aldex and we told to recheck in 2 weeks to recheck her ear. Mom returned to clinic again today because she got much worse overnight. She was having difficulty breathing. She was much more congested and her appetite had decreased significantly today. She also spiked a temperature yesterday of 102.6 and always having trouble sleeping secondary to congestion."].toDS.toDF("text")).transform(data)

Results

                  chunk      entity                              icd10_inj_description  icd10_inj_code

0         a cold, cough     PROBLEM       Insect bite (nonvenomous) of throat, sequela  S1016XS
1            runny nose     PROBLEM                Abrasion of nose, initial encounter  S0031XA
2                 fever     PROBLEM  Blister (nonthermal) of abdominal wall, initia...  S30821A
3  difficulty breathing     PROBLEM  Concussion without loss of consciousness, init...  S060X0A
4             her cough     PROBLEM          Contusion of throat, subsequent encounter  S100XXD
5         physical exam        TEST  Concussion without loss of consciousness, init...  S060X0A
6      fairly congested     PROBLEM  Contusion and laceration of right cerebrum wit...  S06310A
7                Amoxil   TREATMENT  Insect bite (nonvenomous), unspecified ankle, ...  S90569S
8                 Aldex   TREATMENT  Insect bite (nonvenomous) of penis, initial en...  S30862A
9  difficulty breathing     PROBLEM  Concussion without loss of consciousness, init...  S060X0A
10       more congested     PROBLEM  Complete traumatic amputation of two or more r...  S98211S
11     trouble sleeping     PROBLEM  Concussion without loss of consciousness, sequela  S060X0S
12           congestion     PROBLEM  Unspecified injury of portal vein, initial enc...  S35319A

Model Information

Name: chunkresolve_icd10cm_injuries_clinical  
Type: ChunkEntityResolverModel  
Compatibility: Spark NLP 2.4.5+  
License: Licensed  
Edition: Official  
Input labels: [token, chunk_embeddings]  
Output labels: [entity]  
Language: en  
Case sensitive: True  
Dependencies: embeddings_clinical  

Data Source

Trained on ICD10CM Dataset Range: S0000XA-S98929S https://www.icd10data.com/ICD10CM/Codes/S00-T88