Description
This pipeline is designed to extract entities that may be considered as risk factors from text.
In this pipeline, 3 NER models and 2 text matchers are used to extract the related clinical/medical entity labels.
How to use
from sparknlp.pretrained import PretrainedPipeline
ner_pipeline = PretrainedPipeline("explain_clinical_doc_risk_factors_light", "en", "clinical/models")
result = ner_pipeline.annotate("""A 65-year-old woman had a history of debulking surgery, bilateral oophorectomy with omentectomy,
total anterior hysterectomy with radical pelvic lymph nodes dissection due to ovarian carcinoma (mucinous-type carcinoma, stage Ic) 1 year ago.
The patient's medical compliance was poor and failed to complete her chemotherapy (cyclophosphamide 750 mg/m2, carboplatin 300 mg/m2).
Recently, she noted a palpable right breast mass, 15 cm in size which nearly occupied the whole right breast in 2 months.
Core needle biopsy revealed metaplastic carcinoma.
Neoadjuvant chemotherapy with the regimens of Taxotere (75 mg/m2), Epirubicin (75 mg/m2), and Cyclophosphamide (500 mg/m2) was given for 6 cycles with poor response,
followed by a modified radical mastectomy (MRM) with dissection of axillary lymph nodes and skin grafting.
Postoperatively, radiotherapy was done with 5000 cGy in 25 fractions.
The histopathologic examination revealed a metaplastic carcinoma with squamous differentiation associated with adenomyoepithelioma.
In response, his doctor prescribed a regimen tailored to his conditions:
Thiamine 100 mg q.day , Folic acid 1 mg q.day , multivitamins q.day , Calcium carbonate plus Vitamin D 250 mg t.i.d. , Heparin 5000 units subcutaneously b.i.d. , Prilosec 20 mg q.day , Senna two tabs qhs.
""")
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val ner_pipeline = PretrainedPipeline("explain_clinical_doc_risk_factors_light", "en", "clinical/models")
val result = ner_pipeline.annotate("""A 65-year-old woman had a history of debulking surgery, bilateral oophorectomy with omentectomy,
total anterior hysterectomy with radical pelvic lymph nodes dissection due to ovarian carcinoma (mucinous-type carcinoma, stage Ic) 1 year ago.
The patient's medical compliance was poor and failed to complete her chemotherapy (cyclophosphamide 750 mg/m2, carboplatin 300 mg/m2).
Recently, she noted a palpable right breast mass, 15 cm in size which nearly occupied the whole right breast in 2 months.
Core needle biopsy revealed metaplastic carcinoma.
Neoadjuvant chemotherapy with the regimens of Taxotere (75 mg/m2), Epirubicin (75 mg/m2), and Cyclophosphamide (500 mg/m2) was given for 6 cycles with poor response,
followed by a modified radical mastectomy (MRM) with dissection of axillary lymph nodes and skin grafting.
Postoperatively, radiotherapy was done with 5000 cGy in 25 fractions.
The histopathologic examination revealed a metaplastic carcinoma with squamous differentiation associated with adenomyoepithelioma.
In response, his doctor prescribed a regimen tailored to his conditions:
Thiamine 100 mg q.day , Folic acid 1 mg q.day , multivitamins q.day , Calcium carbonate plus Vitamin D 250 mg t.i.d. , Heparin 5000 units subcutaneously b.i.d. , Prilosec 20 mg q.day , Senna two tabs qhs.
""")
Results
| | chunks | begin | end | entities |
|---:|:--------------------------------------|--------:|------:|:--------------------------|
| 0 | debulking surgery | 37 | 53 | Procedure |
| 1 | bilateral oophorectomy | 56 | 77 | Cancer_Surgery |
| 2 | omentectomy | 84 | 94 | Procedure |
| 3 | total anterior hysterectomy | 98 | 124 | Procedure |
| 4 | radical pelvic lymph nodes dissection | 131 | 167 | Procedure |
| 5 | ovarian carcinoma | 176 | 192 | Cancer_dx |
| 6 | mucinous-type carcinoma | 195 | 217 | Disease_Syndrome_Disorder |
| 7 | chemotherapy | 312 | 323 | Chemotherapy |
| 8 | cyclophosphamide | 326 | 341 | Chemotherapy |
| 9 | carboplatin | 354 | 364 | Chemotherapy |
| 10 | breast mass | 416 | 426 | Disease_Syndrome_Disorder |
| 11 | 15 cm | 429 | 433 | Tumor_Size |
| 12 | Core needle biopsy | 502 | 519 | Procedure |
| 13 | metaplastic carcinoma | 530 | 550 | Disease_Syndrome_Disorder |
| 14 | Neoadjuvant chemotherapy | 554 | 577 | Chemotherapy |
| 15 | Taxotere | 600 | 607 | Chemotherapy |
| 16 | Epirubicin | 621 | 630 | Chemotherapy |
| 17 | Cyclophosphamide | 648 | 663 | Chemotherapy |
| 18 | modified radical mastectomy | 735 | 761 | Procedure |
| 19 | MRM | 764 | 766 | Cancer_Surgery |
| 20 | dissection of axillary lymph nodes | 774 | 807 | Procedure |
| 21 | skin grafting | 813 | 825 | Procedure |
| 22 | radiotherapy | 846 | 857 | Radiotherapy |
| 23 | metaplastic carcinoma | 943 | 963 | Disease_Syndrome_Disorder |
| 24 | squamous differentiation | 970 | 993 | Disease_Syndrome_Disorder |
| 25 | adenomyoepithelioma | 1011 | 1029 | Cancer_dx |
| 26 | Thiamine 100 mg | 1105 | 1119 | DRUG |
| 27 | Folic acid | 1129 | 1138 | Disease_Syndrome_Disorder |
| 28 | Calcium carbonate | 1175 | 1191 | DRUG |
| 29 | Heparin | 1224 | 1230 | DRUG |
| 30 | Prilosec 20 mg | 1267 | 1280 | DRUG |
Model Information
| Model Name: | explain_clinical_doc_risk_factors_light |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 6.0.2+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 1.8 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel
- MedicalNerModel
- NerConverterInternalModel
- TextMatcherInternalModel
- TextMatcherInternalModel
- MedicalNerModel
- NerConverterInternalModel
- ChunkMergeModel