Description
This pretrained pipeline is built on the top of ner_biomarker model.
How to use
pipeline = PretrainedPipeline("ner_biomarker_pipeline", "en", "clinical/models")
pipeline.annotate("Here , we report the first case of an intraductal tubulopapillary neoplasm of the pancreas with clear cell morphology . Immunohistochemistry revealed positivity for Pan-CK , CK7 , CK8/18 , MUC1 , MUC6 , carbonic anhydrase IX , CD10 , EMA , β-catenin and e-cadherin ")
val pipeline = new PretrainedPipeline("ner_biomarker_pipeline", "en", "clinical/models")
pipeline.annotate("Here , we report the first case of an intraductal tubulopapillary neoplasm of the pancreas with clear cell morphology . Immunohistochemistry revealed positivity for Pan-CK , CK7 , CK8/18 , MUC1 , MUC6 , carbonic anhydrase IX , CD10 , EMA , β-catenin and e-cadherin ")
import nlu
nlu.load("en.med_ner.biomarker.pipeline").predict("""Here , we report the first case of an intraductal tubulopapillary neoplasm of the pancreas with clear cell morphology . Immunohistochemistry revealed positivity for Pan-CK , CK7 , CK8/18 , MUC1 , MUC6 , carbonic anhydrase IX , CD10 , EMA , β-catenin and e-cadherin """)
Results
| | ner_chunk | entity | confidence |
|---:|:-------------------------|:----------------------|-------------:|
| 0 | intraductal | CancerModifier | 0.9934 |
| 1 | tubulopapillary | CancerModifier | 0.6403 |
| 2 | neoplasm of the pancreas | CancerDx | 0.758825 |
| 3 | clear cell | CancerModifier | 0.9633 |
| 4 | Immunohistochemistry | Test | 0.9534 |
| 5 | positivity | Biomarker_Measurement | 0.8795 |
| 6 | Pan-CK | Biomarker | 0.9975 |
| 7 | CK7 | Biomarker | 0.9975 |
| 8 | CK8/18 | Biomarker | 0.9987 |
| 9 | MUC1 | Biomarker | 0.9967 |
| 10 | MUC6 | Biomarker | 0.9972 |
| 11 | carbonic anhydrase IX | Biomarker | 0.937567 |
| 12 | CD10 | Biomarker | 0.9974 |
| 13 | EMA | Biomarker | 0.9899 |
| 14 | β-catenin | Biomarker | 0.8059 |
| 15 | e-cadherin | Biomarker | 0.9806 |
Model Information
| Model Name: | ner_biomarker_pipeline |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 3.4.1+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 1.7 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverter