Description
This pipeline can be used to extracts symptom or sign information in medical text.
Predicted Entities
SYMPTOM_OR_SIGN
How to use
from sparknlp.pretrained import PretrainedPipeline
ner_pipeline = PretrainedPipeline("ner_symptom_or_sign_benchmark_pipeline", "en", "clinical/models")
text = """IDENTIFYING DATA AND CHIEF COMPLAINT :
Mrs. Saujule T. Neathe is a 73 year old Gravida 6 Para 4 abortions 2 with a background history of stage IIIC papillary serous adenocarcinoma of the ovary who presents on 5/30/94 for failure to thrive , right lower lobe pneumonia and obstructive uropathy .
This course of chemotherapy was complicated only by persistent diarrhea and some nausea and vomiting .
An abdominopelvic computerized tomography scan during that admission showed recurrent disease in the pelvis with bilateral hydronephrosis .
Two days following discharge , however , the patient was admitted to Sephsandpot Center because of a decreased urinary output and persistent nausea and vomiting and anorexia .
PHYSICAL EXAMINATION :
( on admission ) showed the patient to be low-grade febrile with temperature of 99.6. She was noted to be a thin , cachectic woman in no apparent distress . Head and neck examination remarkable only for extreme dry mucous membranes consistent with dehydration .
Abdomen :
showed well healed midline scar , non-distended , non-tender , bowel sounds were good , multiple small nodules were palpated subcutaneously in the upper abdomen which was non-tender , there was no costovertebral angle tenderness .
Pelvic and rectal examinations confirmed recurrence of tumor mass in the pelvis .
The patient was occult blood negative .
Extremities : showed no evidence of acute deep venous thrombosis . However , left leg had two plus pitting edema to the knee whereas the right leg had minimal edema .
"""
result = ner_pipeline.fullAnnotate(text)
from sparknlp.pretrained import PretrainedPipeline
ner_pipeline = nlp.PretrainedPipeline("ner_symptom_or_sign_benchmark_pipeline", "en", "clinical/models")
text = """IDENTIFYING DATA AND CHIEF COMPLAINT :
Mrs. Saujule T. Neathe is a 73 year old Gravida 6 Para 4 abortions 2 with a background history of stage IIIC papillary serous adenocarcinoma of the ovary who presents on 5/30/94 for failure to thrive , right lower lobe pneumonia and obstructive uropathy .
This course of chemotherapy was complicated only by persistent diarrhea and some nausea and vomiting .
An abdominopelvic computerized tomography scan during that admission showed recurrent disease in the pelvis with bilateral hydronephrosis .
Two days following discharge , however , the patient was admitted to Sephsandpot Center because of a decreased urinary output and persistent nausea and vomiting and anorexia .
PHYSICAL EXAMINATION :
( on admission ) showed the patient to be low-grade febrile with temperature of 99.6. She was noted to be a thin , cachectic woman in no apparent distress . Head and neck examination remarkable only for extreme dry mucous membranes consistent with dehydration .
Abdomen :
showed well healed midline scar , non-distended , non-tender , bowel sounds were good , multiple small nodules were palpated subcutaneously in the upper abdomen which was non-tender , there was no costovertebral angle tenderness .
Pelvic and rectal examinations confirmed recurrence of tumor mass in the pelvis .
The patient was occult blood negative .
Extremities : showed no evidence of acute deep venous thrombosis . However , left leg had two plus pitting edema to the knee whereas the right leg had minimal edema .
"""
result = ner_pipeline.fullAnnotate(text)
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val ner_pipeline = PretrainedPipeline("ner_symptom_or_sign_benchmark_pipeline", "en", "clinical/models")
val text = """IDENTIFYING DATA AND CHIEF COMPLAINT :
Mrs. Saujule T. Neathe is a 73 year old Gravida 6 Para 4 abortions 2 with a background history of stage IIIC papillary serous adenocarcinoma of the ovary who presents on 5/30/94 for failure to thrive , right lower lobe pneumonia and obstructive uropathy .
This course of chemotherapy was complicated only by persistent diarrhea and some nausea and vomiting .
An abdominopelvic computerized tomography scan during that admission showed recurrent disease in the pelvis with bilateral hydronephrosis .
Two days following discharge , however , the patient was admitted to Sephsandpot Center because of a decreased urinary output and persistent nausea and vomiting and anorexia .
PHYSICAL EXAMINATION :
( on admission ) showed the patient to be low-grade febrile with temperature of 99.6. She was noted to be a thin , cachectic woman in no apparent distress . Head and neck examination remarkable only for extreme dry mucous membranes consistent with dehydration .
Abdomen :
showed well healed midline scar , non-distended , non-tender , bowel sounds were good , multiple small nodules were palpated subcutaneously in the upper abdomen which was non-tender , there was no costovertebral angle tenderness .
Pelvic and rectal examinations confirmed recurrence of tumor mass in the pelvis .
The patient was occult blood negative .
Extremities : showed no evidence of acute deep venous thrombosis . However , left leg had two plus pitting edema to the knee whereas the right leg had minimal edema .
"""
val result = ner_pipeline.fullAnnotate(text)
Results
| | chunk | begin | end | ner_label |
|---:|:--------------------------------|--------:|------:|:----------------|
| 0 | failure to thrive | 221 | 237 | SYMPTOM_OR_SIGN |
| 1 | nausea | 376 | 381 | SYMPTOM_OR_SIGN |
| 2 | vomiting | 387 | 394 | SYMPTOM_OR_SIGN |
| 3 | decreased urinary output | 639 | 662 | SYMPTOM_OR_SIGN |
| 4 | nausea | 679 | 684 | SYMPTOM_OR_SIGN |
| 5 | vomiting | 690 | 697 | SYMPTOM_OR_SIGN |
| 6 | febrile | 789 | 795 | SYMPTOM_OR_SIGN |
| 7 | thin | 845 | 848 | SYMPTOM_OR_SIGN |
| 8 | cachectic | 852 | 860 | SYMPTOM_OR_SIGN |
| 9 | dry mucous membranes | 948 | 967 | SYMPTOM_OR_SIGN |
| 10 | scar | 1036 | 1039 | SYMPTOM_OR_SIGN |
| 11 | non-tender | 1059 | 1068 | SYMPTOM_OR_SIGN |
| 12 | nodules | 1112 | 1118 | SYMPTOM_OR_SIGN |
| 13 | non-tender | 1180 | 1189 | SYMPTOM_OR_SIGN |
| 14 | costovertebral angle tenderness | 1206 | 1236 | SYMPTOM_OR_SIGN |
| 15 | mass | 1301 | 1304 | SYMPTOM_OR_SIGN |
| 16 | pitting edema | 1461 | 1473 | SYMPTOM_OR_SIGN |
| 17 | edema | 1521 | 1525 | SYMPTOM_OR_SIGN |
Model Information
| Model Name: | ner_symptom_or_sign_benchmark_pipeline |
| Type: | pipeline |
| Compatibility: | Healthcare NLP 5.5.3+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 1.7 GB |
Included Models
- DocumentAssembler
- SentenceDetector
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverterInternalModel
- TextMatcherInternalModel
- TextMatcherInternalModel
- MedicalNerModel
- NerConverterInternalModel
- ChunkMergeModel
- ChunkMergeModel
Benchmarking
label precision recall f1-score support
O 0.993 0.995 0.994 79865
SYMPTOM_OR_SIGN 0.848 0.787 0.816 2706
accuracy - - 0.988 82571
macro-avg 0.920 0.891 0.905 82571
weighted-avg 0.988 0.988 0.988 82571