Description
This pipeline extracts Procedure and Measurement entities and maps them to corresponding Current Procedural Terminology (CPT) codes using sbiobert_base_cased_mli Sentence Bert Embeddings.
How to use
from sparknlp.pretrained import PretrainedPipeline
ner_pipeline = PretrainedPipeline.from_disk("cpt_procedures_measurements_resolver_pipeline")
result = ner_pipeline.annotate("""She was admitted to the hospital with chest pain and found to have bilateral pleural effusion, the right greater than the left. CT scan of the chest also revealed a large mediastinal lymph node.
We reviewed the pathology obtained from the pericardectomy in March 2006, which was diagnostic of mesothelioma.
At this time, chest tube placement for drainage of the fluid occurred and thoracoscopy, which were performed, which revealed epithelioid malignant mesothelioma.""")
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val ner_pipeline = PretrainedPipeline.from_disk("cpt_procedures_measurements_resolver_pipeline")
val result = ner_pipeline.annotate("""She was admitted to the hospital with chest pain and found to have bilateral pleural effusion, the right greater than the left. CT scan of the chest also revealed a large mediastinal lymph node.
We reviewed the pathology obtained from the pericardectomy in March 2006, which was diagnostic of mesothelioma.
At this time, chest tube placement for drainage of the fluid occurred and thoracoscopy, which were performed, which revealed epithelioid malignant mesothelioma.""")
Results
+--------------------+-----+---+---------+--------+------------------------------------------------------------+------------------------------------------------------------+
| chunk|begin|end|ner_label|cpt_code| resolutions| all_k_codes|
+--------------------+-----+---+---------+--------+------------------------------------------------------------+------------------------------------------------------------+
| pericardectomy| 239|252|Procedure| 33030|Pericardectomy [Pericardiectomy, subtotal or complete; wi...|33030:::33020:::64746:::49250:::27350:::68520:::32310:::2...|
|chest tube placement| 321|340|Procedure| 39503|Insertion of chest tube [Repair, neonatal diaphragmatic h...|39503:::96440:::32553:::35820:::32100:::36226:::21899:::2...|
| thoracoscopy| 381|392|Procedure| 1020900|Thoracoscopy [Thoracoscopy]:::Thoracoscopy, surgical; wit...|1020900:::32654:::32668:::1006014:::35820:::32606:::32555...|
+--------------------+-----+---+---------+--------+------------------------------------------------------------+------------------------------------------------------------+
Model Information
| Model Name: | cpt_procedures_measurements_resolver_pipeline |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 5.2.1+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 2.5 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- NerConverterInternalModel
- ChunkMergeModel
- Chunk2Doc
- BertSentenceEmbeddings
- SentenceEntityResolverModel
References
CPT resolver models are removed from the Models Hub due to license restrictions and can only be shared with the users who already have a valid CPT license. If you possess one and wish to use this model, kindly contact us at support@johnsnowlabs.com.