Description
This model contains a pre-trained weights of BioBERT, a language representation model for biomedical domain, especially designed for biomedical text mining tasks such as biomedical named entity recognition, relation extraction, question answering, etc. The details are described in the paper “BioBERT: a pre-trained biomedical language representation model for biomedical text mining”.
How to use
...
embeddings = BertSentenceEmbeddings.pretrained("sent_biobert_pmc_base_cased", "en") \
.setInputCols("sentence") \
.setOutputCol("sentence_embeddings")
nlp_pipeline = Pipeline(stages=[document_assembler, sentence_detector, embeddings])
pipeline_model = nlp_pipeline.fit(spark.createDataFrame([[""]]).toDF("text"))
result = pipeline_model.transform(spark.createDataFrame([['I hate cancer', "Antibiotics aren't painkiller"]], ["text"]))
...
val embeddings = BertSentenceEmbeddings.pretrained("sent_biobert_pmc_base_cased", "en")
.setInputCols("sentence")
.setOutputCol("sentence_embeddings")
val pipeline = new Pipeline().setStages(Array(document_assembler, sentence_detector, embeddings))
val data = Seq("I hate cancer, "Antibiotics aren't painkiller").toDF("text")
val result = pipeline.fit(data).transform(data)
import nlu
text = ["I hate cancer", "Antibiotics aren't painkiller"]
embeddings_df = nlu.load('en.embed_sentence.biobert.pmc_base_cased').predict(text, output_level='sentence')
embeddings_df
Results
sentence en_embed_sentence_biobert_pmc_base_cased_embeddings
I hate cancer [0.34035101532936096, 0.04413360357284546, -0....
Antibiotics aren't painkiller [0.4397204518318176, 0.066007100045681, -0.114...
Model Information
| Model Name: | sent_biobert_pmc_base_cased |
| Type: | embeddings |
| Compatibility: | Spark NLP 2.6.2 |
| License: | Open Source |
| Edition: | Official |
| Input Labels: | [sentence] |
| Output Labels: | [sentence_embeddings] |
| Language: | [en] |
| Dimension: | 768 |
| Case sensitive: | true |
Data Source
The model is imported from https://github.com/dmis-lab/biobert