Description
This pipeline extracts Procedure entities from clinical texts and map them to their corresponding ICD-10-PCS codes using sbiobert_base_cased_mli Sentence Bert Embeddings.
How to use
from sparknlp.pretrained import PretrainedPipeline
ner_pipeline = PretrainedPipeline("icd10pcs_resolver_pipeline", "en", "clinical/models")
result = ner_pipeline.annotate("""[['Given the severity of her abdominal examination and her persistence of her symptoms,\n it is detected that need for laparoscopic appendectomy and possible jejunectomy\n as well as pyeloplasty. We recommend performing a mediastinoscopy']]""")
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val ner_pipeline = PretrainedPipeline("icd10pcs_resolver_pipeline", "en", "clinical/models")
val result = ner_pipeline.annotate("""[['Given the severity of her abdominal examination and her persistence of her symptoms,\n it is detected that need for laparoscopic appendectomy and possible jejunectomy\n as well as pyeloplasty. We recommend performing a mediastinoscopy']]""")
Results
+-------------------------+---------+-------------+----------------------------------------------------------------------+----------------------------------------------------------------------+----------------------------------------------------------------------+
| chunk| label|icd10pcs_code| resolution| all_codes| all_resolutions|
+-------------------------+---------+-------------+----------------------------------------------------------------------+----------------------------------------------------------------------+----------------------------------------------------------------------+
|laparoscopic appendectomy|Procedure| 0DTJ8ZZ| resection of appendix, endo [resection of appendix, endo]|0DTJ8ZZ:::0DT84ZZ:::0DTJ4ZZ:::0WBH4ZZ:::0DTR4ZZ:::0DBJ8ZZ:::0DTG4ZZ...|resection of appendix, endo [resection of appendix, endo]:::resecti...|
| jejunectomy|Procedure| 0DBA8ZZ| excision of jejunum, endo [excision of jejunum, endo]|0DBA8ZZ:::0DTA8ZZ:::0D5A8ZZ:::0DLA8ZZ:::0DBA8ZX:::0DT88ZZ:::0DCA8ZZ...|excision of jejunum, endo [excision of jejunum, endo]:::resection o...|
| pyeloplasty|Procedure| 0TS84ZZ|reposition bilateral ureters, perc endo approach [reposition bilate...|0TS84ZZ:::0TS74ZZ:::069B3ZZ:::06SB3ZZ:::0TR74JZ:::0TQ43ZZ:::049A3ZZ...|reposition bilateral ureters, perc endo approach [reposition bilate...|
| mediastinoscopy|Procedure| BB1CZZZ| fluoroscopy of mediastinum [fluoroscopy of mediastinum]|BB1CZZZ:::0WJC4ZZ:::BB4CZZZ:::0WJC3ZZ:::0WHC33Z:::0WHC43Z:::0WHC3YZ...|fluoroscopy of mediastinum [fluoroscopy of mediastinum]:::inspectio...|
+-------------------------+---------+-------------+----------------------------------------------------------------------+----------------------------------------------------------------------+----------------------------------------------------------------------+
Model Information
| Model Name: | icd10pcs_resolver_pipeline |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 5.2.1+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 2.8 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- NerConverterInternalModel
- ChunkMergeModel
- Chunk2Doc
- BertSentenceEmbeddings
- SentenceEntityResolverModel