Detect Drugs and Posology Entities (ner_posology_greedy)

Description

This model detects drugs, dosage, form, frequency, duration, route, and drug strength in text. It differs from ner_posology in the sense that it chunks together drugs, dosage, form, strength, and route when they appear together, resulting in a bigger chunk. It is trained using embeddings_clinical so please use the same embeddings in the pipeline.

Predicted Entities

DRUG, STRENGTH, DURATION, FREQUENCY, FORM, DOSAGE, ROUTE.

Live Demo Open in Colab Download

How to use

Use as part of an nlp pipeline with the following stages: DocumentAssembler, SentenceDetector, Tokenizer, WordEmbeddingsModel, NerDLModel. Add the NerConverter to the end of the pipeline to convert entity tokens into full entity chunks.

...
word_embeddings = WordEmbeddingsModel.pretrained("embeddings_clinical", "en", "clinical/models")\
   .setInputCols(["sentence", "token"])\
   .setOutputCol("embeddings")
clinical_ner = NerDLModel.pretrained("ner_posology_greedy", "en", "clinical/models") \
   .setInputCols(["sentence", "token", "embeddings"]) \
   .setOutputCol("ner")
...
nlp_pipeline = Pipeline(stages=[document_assembler, sentence_detector, tokenizer, word_embeddings, clinical_ner, ner_converter])
model = nlp_pipeline.fit(spark.createDataFrame([[""]]).toDF("text"))
results = model.transform(spark.createDataFrame([["The patient was prescribed 1 capsule of Advil 10 mg for 5 days and magnesium hydroxide 100mg/1ml suspension PO. He was seen by the endocrinology service and she was discharged on 40 units of insulin glargine at night, 12 units of insulin lispro with meals, and metformin 1000 mg two times a day."]]).toDF("text"))
...
val word_embeddings = WordEmbeddingsModel.pretrained("embeddings_clinical", "en", "clinical/models")
   .setInputCols(Array("sentence", "token"))
   .setOutputCol("embeddings")
val clinical_ner = NerDLModel.pretrained("ner_posology_greedy", "en", "clinical/models")
    .setInputCols(Array("sentence", "token", "embeddings"))
    .setOutputCol("ner")
...
val pipeline = new Pipeline().setStages(Array(document_assembler, sentence_detector, tokenizer, word_embeddings, clinical_ner, ner_converter))
val data = Seq("The patient was prescribed 1 capsule of Advil 10 mg for 5 days and magnesium hydroxide 100mg/1ml suspension PO. He was seen by the endocrinology service and she was discharged on 40 units of insulin glargine at night, 12 units of insulin lispro with meals, and metformin 1000 mg two times a day.").toDF("text")
val result = pipeline.fit(data).transform(data)

Results

+----+----------------------------------+---------+-------+------------+
|    | chunks                           |   begin |   end | entities   |
|---:|---------------------------------:|--------:|------:|-----------:|
|  0 | 1 capsule of Advil 10 mg         |      27 |    50 | DRUG       |
|  1 | magnesium hydroxide 100mg/1ml PO |      67 |    98 | DRUG       |
|  2 | for 5 days                       |      52 |    61 | DURATION   |
|  3 | 40 units of insulin glargine     |     168 |   195 | DRUG       |
|  4 | at night                         |     197 |   204 | FREQUENCY  |
|  5 | 12 units of insulin lispro       |     207 |   232 | DRUG       |
|  6 | with meals                       |     234 |   243 | FREQUENCY  |
|  7 | metformin 1000 mg                |     250 |   266 | DRUG       |
|  8 | two times a day                  |     268 |   282 | FREQUENCY  |
+----+----------------------------------+---------+-------+------------+

Model Information

Model Name: ner_posology_greedy
Type: ner
Compatibility: Spark NLP 2.6.5+
License: Licensed
Edition: Official
Input Labels: [sentence, token, embeddings]
Output Labels: [ner]
Language: en
Dependencies: embeddings_clinical

Data Source

Trained on augmented i2b2_med7 + FDA dataset with embeddings_clinical, https://www.i2b2.org/NLP/Medication.

Benchmarking

label tp fp fn prec rec f1
B-DRUG 29362 1679 1985 0.9459103 0.93667656 0.94127077
B-STRENGTH 14018 1172 864 0.922844 0.9419433 0.9322958
I-DURATION 6404 935 476 0.87259847 0.93081397 0.9007666
I-STRENGTH 16686 1991 1292 0.8933983 0.9281344 0.9104351
I-FREQUENCY 19743 1088 1081 0.9477702 0.94808877 0.9479294
B-FORM 2733 526 780 0.8386008 0.7779676 0.80714715
B-DOSAGE 2774 474 688 0.85406405 0.80127096 0.8268257
I-DOSAGE 1357 490 844 0.7347049 0.6165379 0.67045456
I-DRUG 37846 4103 3386 0.90219074 0.91787934 0.9099674
I-ROUTE 208 30 62 0.8739496 0.77037036 0.8188976
B-ROUTE 3061 340 451 0.9000294 0.87158316 0.88557786
B-DURATION 2491 388 276 0.865231 0.900253 0.8823946
B-FREQUENCY 13065 608 436 0.9555328 0.9677061 0.9615809
I-FORM 154 69 386 0.69058293 0.2851852 0.40366974
             
Macro-average 149902 13893 13007 0.8712434 0.82817215 0.849162
Micro-average 149902 13893 13007 0.91518056 0.92015785 0.9176625