Description
This advanced pipeline extracts clinical conditions from clinical texts and utilizes the sbiobert_base_cased_mli Sentence Bert Embeddings to map these entities to their corresponding Hierarchical Condition Categories (HCC) codes.
How to use
from sparknlp.pretrained import PretrainedPipeline
ner_pipeline = PretrainedPipeline("hcc_resolver_pipeline", "en", "clinical/models")
result = ner_pipeline.annotate("""The patient's medical record indicates a diagnosis of Diabetes and Chronic Obstructive Pulmonary Disease, requiring comprehensive care and management.""")
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val ner_pipeline = PretrainedPipeline("hcc_resolver_pipeline", "en", "clinical/models")
val result = ner_pipeline.annotate("""The patient's medical record indicates a diagnosis of Diabetes and Chronic Obstructive Pulmonary Disease, requiring comprehensive care and management.""")
Results
| | chunks | begin | end | entities | hcc_code | resolutions | all_codes |
|---:|:--------------------------------------|--------:|------:|:-----------|-----------:|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------------------|
| 0 | Diabetes | 54 | 61 | PROBLEM | 19 | diabetes monitored [type 2 diabetes mellitus without complications]:::anaemia of diabetes [anemia, unspecified]:::anemia of diabetes (disorder) [type 2 diabetes mellitus with other specified complication] | 19:::0:::18 |
| 1 | Chronic Obstructive Pulmonary Disease | 67 | 103 | PROBLEM | 111 | chronic obstructive pulmonary disease [chronic obstructive pulmonary disease, unspecified]:::chronic lung disease [pneumoconiosis due to other dust containing silica]:::chronic pulmonary heart disease [pulmonary heart disease, unspecified]:::other chronic obstructive pulmonary disease [other chronic obstructive pulmonary disease] | 111:::112:::85:::0 |
Model Information
| Model Name: | hcc_resolver_pipeline |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 5.2.1+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 3.5 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel
- Chunk2Doc
- BertSentenceEmbeddings
- SentenceEntityResolverModel