Description
This model extracts entities related to cancer diagnosis, such as Metastasis, Histological_Type or Invasion.
Definitions of Predicted Entities:
Adenopathy
: Mentions of pathological findings of the lymph nodes.Cancer_Dx
: Mentions of cancer diagnoses (such as “breast cancer”) or pathological types that are usually used as synonyms for “cancer” (e.g. “carcinoma”). When anatomical references are present, they are included in the Cancer_Dx extraction.Cancer_Score
: Clinical or imaging scores that are specific for cancer settings (e.g. “BI-RADS” or “Allred score”).Grade
: All pathological grading of tumors (e.g. “grade 1”) or degrees of cellular differentiation (e.g. “well-differentiated”)Histological_Type
: Histological variants or cancer subtypes, such as “papillary”, “clear cell” or “medullary”.Invasion
: Mentions that refer to tumor invasion, such as “invasion” or “involvement”. Metastases or lymph node involvement are excluded from this category.Metastasis
: Terms that indicate a metastatic disease. Anatomical references are not included in these extractions.Pathology_Result
: The findings of a biopsy from the pathology report that is not covered by another entity (e.g. “malignant ductal cells”).Performance_Status
: Mentions of performance status scores, such as ECOG and Karnofsky. The name of the score is extracted together with the result (e.g. “ECOG performance status of 4”).Staging
: Mentions of cancer stage such as “stage 2b” or “T2N1M0”. It also includes words such as “in situ”, “early-stage” or “advanced”.Tumor_Finding
: All nonspecific terms that may be related to tumors, either malignant or benign (for example: “mass”, “tumor”, “lesion”, or “neoplasm”).Tumor_Size
: Size of the tumor, including numerical value and unit of measurement (e.g. “3 cm”).
Predicted Entities
Adenopathy
, Cancer_Dx
, Cancer_Score
, Grade
, Histological_Type
, Invasion
, Metastasis
, Pathology_Result
, Performance_Status
, Staging
, Tumor_Finding
, Tumor_Size
Live Demo Open in Colab Copy S3 URI
How to use
document_assembler = DocumentAssembler()\
.setInputCol("text")\
.setOutputCol("document")
sentence_detector = SentenceDetectorDLModel.pretrained("sentence_detector_dl_healthcare","en","clinical/models")\
.setInputCols(["document"])\
.setOutputCol("sentence")
tokenizer = Tokenizer() \
.setInputCols(["sentence"]) \
.setOutputCol("token")
word_embeddings = WordEmbeddingsModel().pretrained("embeddings_clinical", "en", "clinical/models")\
.setInputCols(["sentence", "token"]) \
.setOutputCol("embeddings")
ner = MedicalNerModel.pretrained("ner_oncology_diagnosis", "en", "clinical/models") \
.setInputCols(["sentence", "token", "embeddings"]) \
.setOutputCol("ner")
ner_converter = NerConverter() \
.setInputCols(["sentence", "token", "ner"]) \
.setOutputCol("ner_chunk")
pipeline = Pipeline(stages=[document_assembler,
sentence_detector,
tokenizer,
word_embeddings,
ner,
ner_converter])
data = spark.createDataFrame([["Two years ago, the patient presented with a tumor in her left breast and adenopathies. She was diagnosed with invasive ductal carcinoma.
Last week she was also found to have a lung metastasis."]]).toDF("text")
result = pipeline.fit(data).transform(data)
val document_assembler = new DocumentAssembler()
.setInputCol("text")
.setOutputCol("document")
val sentence_detector = SentenceDetectorDLModel.pretrained("sentence_detector_dl_healthcare","en","clinical/models")
.setInputCols("document")
.setOutputCol("sentence")
val tokenizer = new Tokenizer()
.setInputCols("sentence")
.setOutputCol("token")
val word_embeddings = WordEmbeddingsModel().pretrained("embeddings_clinical", "en", "clinical/models")
.setInputCols(Array("sentence", "token"))
.setOutputCol("embeddings")
val ner = MedicalNerModel.pretrained("ner_oncology_diagnosis", "en", "clinical/models")
.setInputCols(Array("sentence", "token", "embeddings"))
.setOutputCol("ner")
val ner_converter = new NerConverter()
.setInputCols(Array("sentence", "token", "ner"))
.setOutputCol("ner_chunk")
val pipeline = new Pipeline().setStages(Array(document_assembler,
sentence_detector,
tokenizer,
word_embeddings,
ner,
ner_converter))
val data = Seq("Two years ago, the patient presented with a tumor in her left breast and adenopathies. She was diagnosed with invasive ductal carcinoma.
Last week she was also found to have a lung metastasis.").toDS.toDF("text")
val result = pipeline.fit(data).transform(data)
import nlu
nlu.load("en.med_ner.oncology_diagnosis").predict("""Two years ago, the patient presented with a tumor in her left breast and adenopathies. She was diagnosed with invasive ductal carcinoma.
Last week she was also found to have a lung metastasis.""")
Results
| chunk | ner_label |
|:-------------|:------------------|
| tumor | Tumor_Finding |
| adenopathies | Adenopathy |
| invasive | Histological_Type |
| ductal | Histological_Type |
| carcinoma | Cancer_Dx |
| metastasis | Metastasis |
Model Information
Model Name: | ner_oncology_diagnosis |
Compatibility: | Healthcare NLP 4.2.2+ |
License: | Licensed |
Edition: | Official |
Input Labels: | [sentence, token, embeddings] |
Output Labels: | [ner] |
Language: | en |
Size: | 34.3 MB |
References
In-house annotated oncology case reports.
Benchmarking
label tp fp fn total precision recall f1
Histological_Type 354 63 99 453 0.85 0.78 0.81
Staging 234 27 24 258 0.90 0.91 0.90
Cancer_Score 36 15 26 62 0.71 0.58 0.64
Tumor_Finding 1121 83 136 1257 0.93 0.89 0.91
Invasion 154 27 27 181 0.85 0.85 0.85
Tumor_Size 1058 126 71 1129 0.89 0.94 0.91
Adenopathy 66 10 30 96 0.87 0.69 0.77
Performance_Status 116 15 19 135 0.89 0.86 0.87
Pathology_Result 852 686 290 1142 0.55 0.75 0.64
Metastasis 356 15 14 370 0.96 0.96 0.96
Cancer_Dx 1302 88 92 1394 0.94 0.93 0.94
Grade 201 23 35 236 0.90 0.85 0.87
macro_avg 5850 1178 863 6713 0.85 0.83 0.84
micro_avg 5850 1178 863 6713 0.85 0.87 0.86