Description
This pretrained pipeline is built on the top of ner_biomarker model.
Predicted Entities
How to use
from sparknlp.pretrained import PretrainedPipeline
pipeline = PretrainedPipeline("ner_biomarker_pipeline", "en", "clinical/models")
text = '''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 '''
result = pipeline.fullAnnotate(text)
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val pipeline = new PretrainedPipeline("ner_biomarker_pipeline", "en", "clinical/models")
val text = "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 result = pipeline.fullAnnotate(text)
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_chunks | begin | end | ner_label | confidence |
|---:|:-------------------------|--------:|------:|:----------------------|-------------:|
| 0 | intraductal | 38 | 48 | CancerModifier | 0.9998 |
| 1 | tubulopapillary | 50 | 64 | CancerModifier | 0.9995 |
| 2 | neoplasm of the pancreas | 66 | 89 | CancerDx | 0.7239 |
| 3 | clear cell | 96 | 105 | CancerModifier | 0.96745 |
| 4 | Immunohistochemistry | 120 | 139 | Test | 0.9768 |
| 5 | positivity | 150 | 159 | Biomarker_Measurement | 0.8704 |
| 6 | Pan-CK | 165 | 170 | Biomarker | 0.998 |
| 7 | CK7 | 174 | 176 | Biomarker | 0.9977 |
| 8 | CK8/18 | 180 | 185 | Biomarker | 0.9988 |
| 9 | MUC1 | 189 | 192 | Biomarker | 0.9965 |
| 10 | MUC6 | 196 | 199 | Biomarker | 0.9974 |
| 11 | carbonic anhydrase IX | 203 | 223 | Biomarker | 0.814033 |
| 12 | CD10 | 227 | 230 | Biomarker | 0.9975 |
| 13 | EMA | 234 | 236 | Biomarker | 0.9985 |
| 14 | β-catenin | 240 | 248 | Biomarker | 0.9948 |
| 15 | e-cadherin | 254 | 263 | Biomarker | 0.9952 |
Model Information
| Model Name: | ner_biomarker_pipeline |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 4.4.4+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 1.7 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel