Description
This model extracts anatomical entities using an unspecific label. It is the version of ner_oncology_anatomy_general model augmented with langtest library.
Definitions of Predicted Entities:
Anatomical_Site: Relevant anatomical terms mentioned in the text.Direction: Directional and laterality terms, such as “left”, “right”, “bilateral”, “upper” and “lower”.
Predicted Entities
Anatomical_Site, Direction
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_anatomy_general_langtest", "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([["The patient presented a mass in her left breast, and a possible metastasis in her lungs and in her liver."]]).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_anatomy_general_langtest", "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("The patient presented a mass in her left breast, and a possible metastasis in her lungs and in her liver.").toDS.toDF("text")
val result = pipeline.fit(data).transform(data)
Results
+------+---------------+
|chunk |ner_label |
+------+---------------+
|left |Direction |
|breast|Anatomical_Site|
|lungs |Anatomical_Site|
|liver |Anatomical_Site|
+------+---------------+
Model Information
| Model Name: | ner_oncology_anatomy_general_langtest |
| Compatibility: | Healthcare NLP 5.0.2+ |
| License: | Licensed |
| Edition: | Official |
| Input Labels: | [sentence, token, embeddings] |
| Output Labels: | [ner] |
| Language: | en |
| Size: | 14.7 MB |
References
In-house annotated oncology case reports.
Benchmarking
label precision recall f1-score support
B-Direction 0.89 0.91 0.90 872
B-Anatomical_Site 0.86 0.88 0.87 2361
I-Anatomical_Site 0.76 0.86 0.81 1272
I-Direction 0.79 0.81 0.80 83
micro-avg 0.84 0.88 0.86 4588
macro-avg 0.83 0.86 0.84 4588
weighted-avg 0.84 0.88 0.86 4588