Description
This pipeline includes Named-Entity Recognition, Assertion Status, Relation Extraction and Entity Resolution models to extract information from oncology texts. This pipeline focuses on entities related to oncological diagnosis.
Live Demo Open in Colab Copy S3 URI
How to use
from sparknlp.pretrained import PretrainedPipeline
pipeline = PretrainedPipeline("oncology_diagnosis_pipeline", "en", "clinical/models")
pipeline.fullAnnotate("Two years ago, the patient presented with a 4-cm tumor in her left breast. She was diagnosed with ductal carcinoma. According to her last CT, she has no lung metastases.")[0]
import com.johnsnowlabs.nlp.pretrained.PretrainedPipeline
val pipeline = new PretrainedPipeline("oncology_diagnosis_pipeline", "en", "clinical/models")
val result = pipeline.fullAnnotate("""Two years ago, the patient presented with a 4-cm tumor in her left breast. She was diagnosed with ductal carcinoma. According to her last CT, she has no lung metastases.""")(0)
import nlu
nlu.load("en.oncology_diagnosis.pipeline").predict("""Two years ago, the patient presented with a 4-cm tumor in her left breast. She was diagnosed with ductal carcinoma. According to her last CT, she has no lung metastases.""")
Results
******************** ner_oncology_wip results ********************
| chunk | ner_label |
|:-----------|:------------------|
| 4-cm | Tumor_Size |
| tumor | Tumor_Finding |
| left | Direction |
| breast | Site_Breast |
| ductal | Histological_Type |
| carcinoma | Cancer_Dx |
| lung | Site_Lung |
| metastases | Metastasis |
******************** ner_oncology_diagnosis_wip results ********************
| chunk | ner_label |
|:-----------|:------------------|
| 4-cm | Tumor_Size |
| tumor | Tumor_Finding |
| ductal | Histological_Type |
| carcinoma | Cancer_Dx |
| metastases | Metastasis |
******************** ner_oncology_tnm_wip results ********************
| chunk | ner_label |
|:-----------|:------------------|
| 4-cm | Tumor_Description |
| tumor | Tumor |
| ductal | Tumor_Description |
| carcinoma | Cancer_Dx |
| metastases | Metastasis |
******************** assertion_oncology_wip results ********************
| chunk | ner_label | assertion |
|:-----------|:------------------|:------------|
| tumor | Tumor_Finding | Present |
| ductal | Histological_Type | Present |
| carcinoma | Cancer_Dx | Present |
| metastases | Metastasis | Absent |
******************** assertion_oncology_problem_wip results ********************
| chunk | ner_label | assertion |
|:-----------|:------------------|:-----------------------|
| tumor | Tumor_Finding | Medical_History |
| ductal | Histological_Type | Medical_History |
| carcinoma | Cancer_Dx | Medical_History |
| metastases | Metastasis | Hypothetical_Or_Absent |
******************** re_oncology_wip results ********************
| chunk1 | entity1 | chunk2 | entity2 | relation |
|:---------|:--------------|:-----------|:--------------|:--------------|
| 4-cm | Tumor_Size | tumor | Tumor_Finding | is_related_to |
| 4-cm | Tumor_Size | carcinoma | Cancer_Dx | O |
| tumor | Tumor_Finding | breast | Site_Breast | is_related_to |
| breast | Site_Breast | carcinoma | Cancer_Dx | O |
| lung | Site_Lung | metastases | Metastasis | is_related_to |
******************** re_oncology_granular_wip results ********************
| chunk1 | entity1 | chunk2 | entity2 | relation |
|:---------|:--------------|:-----------|:--------------|:---------------|
| 4-cm | Tumor_Size | tumor | Tumor_Finding | is_size_of |
| 4-cm | Tumor_Size | carcinoma | Cancer_Dx | O |
| tumor | Tumor_Finding | breast | Site_Breast | is_location_of |
| breast | Site_Breast | carcinoma | Cancer_Dx | O |
| lung | Site_Lung | metastases | Metastasis | is_location_of |
******************** re_oncology_size_wip results ********************
| chunk1 | entity1 | chunk2 | entity2 | relation |
|:---------|:-----------|:----------|:--------------|:-----------|
| 4-cm | Tumor_Size | tumor | Tumor_Finding | is_size_of |
| 4-cm | Tumor_Size | carcinoma | Cancer_Dx | O |
******************** ICD-O resolver results ********************
| chunk | ner_label | code | normalized_term |
|:-----------|:------------------|:-------|:------------------|
| tumor | Tumor_Finding | 8000/1 | tumor |
| breast | Site_Breast | C50 | breast |
| ductal | Histological_Type | 8500/2 | dcis |
| carcinoma | Cancer_Dx | 8010/3 | carcinoma |
| lung | Site_Lung | C34.9 | lung |
| metastases | Metastasis | 8000/6 | tumor, metastatic |
Model Information
| Model Name: | oncology_diagnosis_pipeline |
| Type: | pipeline |
| Compatibility: | Spark NLP for Healthcare 4.2.2+ |
| License: | Licensed |
| Edition: | Official |
| Language: | en |
| Size: | 2.3 GB |
Included Models
- DocumentAssembler
- SentenceDetectorDLModel
- TokenizerModel
- WordEmbeddingsModel
- MedicalNerModel
- NerConverter
- MedicalNerModel
- NerConverter
- MedicalNerModel
- NerConverter
- ChunkMergeModel
- ChunkMergeModel
- AssertionDLModel
- AssertionDLModel
- PerceptronModel
- DependencyParserModel
- RelationExtractionModel
- RelationExtractionModel
- RelationExtractionModel
- ChunkMergeModel
- Chunk2Doc
- BertSentenceEmbeddings
- SentenceEntityResolverModel