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
How to use
...
puerile_resolver = ChunkEntityResolverModel.pretrained("chunkresolve_icd10cm_puerile_clinical","en","clinical/models")\
.setInputCols("token","chunk_embeddings")\
.setOutputCol("resolution")
pipeline_puerile = Pipeline(stages = [documentAssembler, sentenceDetector, tokenizer, word_embeddings, clinical_ner, ner_converter, chunk_embeddings, puerile_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 puerile_resolver = ChunkEntityResolverModel.pretrained("chunkresolve_icd10cm_puerile_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, puerile_resolver))
val data = Seq("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")
val result = pipeline.fit(data).transform(data)
Results
chunk entity icd10Puerile_description icd10Puerile_code
0 cold Symptom_Name Prolonged pregnancy O481
1 cough Symptom_Name Diseases of the respiratory system complicatin... O9953
2 runny nose Symptom_Name Other specified pregnancy related conditions, ... O26899
3 Mom Gender Classical hydatidiform mole O010
4 she Gender Other vomiting complicating pregnancy O218
5 no Negated Continuing pregnancy after spontaneous abortio... O3111X0
6 fever Symptom_Name Puerperal sepsis O85
7 Her Gender Obesity complicating the puerperium O99215
8 she Gender Other vomiting complicating pregnancy O218
9 spitting up a lot Symptom_Name Eclampsia, unspecified as to time period O159
10 She Gender Other vomiting complicating pregnancy O218
11 no Negated Continuing pregnancy after spontaneous abortio... O3111X0
12 difficulty breathing Symptom_Name Other disorders of lactation O9279
13 her Gender Diseases of the nervous system complicating th... O99355
14 cough Symptom_Name Diseases of the respiratory system complicatin... O9953
15 dry Modifier Cracked nipple associated with lactation O9213
16 hacky Modifier Severe pre-eclampsia, unspecified trimester O1410
17 She Gender Other vomiting complicating pregnancy O218
18 fairly Modifier Maternal care for high head at term, not appli... O324XX0
19 congested Symptom_Name Postpartum thyroiditis O905
20 She Gender Other vomiting complicating pregnancy O218
21 Amoxil Drug_Name Suppressed lactation O925
22 Aldex Drug_Name Severe pre-eclampsia, unspecified trimester O1410
23 her Gender Diseases of the nervous system complicating th... O99355
24 Mom Gender Classical hydatidiform mole O010
25 she Gender Other vomiting complicating pregnancy O218
26 She Gender Other vomiting complicating pregnancy O218
27 difficulty breathing Symptom_Name Other disorders of lactation O9279
28 She Gender Other vomiting complicating pregnancy O218
29 congested and her appetite had decreased Symptom_Name Decreased fetal movements, second trimester, n... O368120
30 She Gender Other vomiting complicating pregnancy O218
31 102.6 Temperature Postpartum coagulation defects O723
32 trouble sleeping Symptom_Name Other disorders of lactation O9279
33 secondary to Modifier Unspecified pre-existing hypertension complica... O10919
34 congestion Symptom_Name Viral hepatitis complicating childbirth O9842
Model Information
| Name: | chunkresolve_icd10cm_puerile_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: O0000-O9989 https://www.icd10data.com/ICD10CM/Codes/O00-O9A