Detect Cellular/Molecular Biology Entities

Description

Pretrained named entity recognition deep learning model for molecular biology related terms. The SparkNLP deep learning model (MedicalNerModel) is inspired by a former state of the art model for NER: Chiu & Nicols, Named Entity Recognition with Bidirectional LSTM-CNN.

Predicted Entities

DNA, Cell_type, Cell_line, RNA, Protein.

Live Demo Open in Colab Download

How to use

...
word_embeddings = WordEmbeddingsModel.pretrained("embeddings_clinical", "en", "clinical/models")\
.setInputCols(["sentence", "token"])\
.setOutputCol("embeddings")
cellular_ner = MedicalNerModel.pretrained("ner_cellular", "en", "clinical/models") \
.setInputCols(["sentence", "token", "embeddings"]) \
.setOutputCol("ner")
...
nlpPipeline = Pipeline(stages=[document_assembler, sentence_detector, tokenizer, word_embeddings, cellular_ner, ner_converter])

model = nlpPipeline.fit(spark.createDataFrame([[""]]).toDF("text"))

results = model.transform(spark.createDataFrame([['Detection of various other intracellular signaling proteins is also described. Genetic characterization of transactivation of the human T-cell leukemia virus type 1 promoter: Binding of Tax to Tax-responsive element 1 is mediated by the cyclic AMP-responsive members of the CREB/ATF family of transcription factors. To achieve a better understanding of the mechanism of transactivation by Tax of human T-cell leukemia virus type 1 Tax-responsive element 1 (TRE-1), we developed a genetic approach with Saccharomyces cerevisiae. We constructed a yeast reporter strain containing the lacZ gene under the control of the CYC1 promoter associated with three copies of TRE-1. Expression of either the cyclic AMP response element-binding protein (CREB) or CREB fused to the GAL4 activation domain (GAD) in this strain did not modify the expression of the reporter gene. Tax alone was also inactive. ']], ["text"]))
...
val word_embeddings = WordEmbeddingsModel.pretrained("embeddings_clinical", "en", "clinical/models")
.setInputCols(Array("sentence", "token"))
.setOutputCol("embeddings")
val celular_ner = MedicalNerModel.pretrained("ner_cellular", "en", "clinical/models")
.setInputCols("sentence", "token", "embeddings")
.setOutputCol("ner")
...
val pipeline = new Pipeline().setStages(Array(document_assembler, sentence_detector, tokenizer, word_embeddings, cellular_ner, ner_converter))

val data = Seq("Detection of various other intracellular signaling proteins is also described. Genetic characterization of transactivation of the human T-cell leukemia virus type 1 promoter: Binding of Tax to Tax-responsive element 1 is mediated by the cyclic AMP-responsive members of the CREB/ATF family of transcription factors. To achieve a better understanding of the mechanism of transactivation by Tax of human T-cell leukemia virus type 1 Tax-responsive element 1 (TRE-1), we developed a genetic approach with Saccharomyces cerevisiae. We constructed a yeast reporter strain containing the lacZ gene under the control of the CYC1 promoter associated with three copies of TRE-1. Expression of either the cyclic AMP response element-binding protein (CREB) or CREB fused to the GAL4 activation domain (GAD) in this strain did not modify the expression of the reporter gene. Tax alone was also inactive.").toDF("text")
val result = pipeline.fit(data).transform(data)
import nlu
nlu.load("en.med_ner.cellular").predict("""Detection of various other intracellular signaling proteins is also described. Genetic characterization of transactivation of the human T-cell leukemia virus type 1 promoter: Binding of Tax to Tax-responsive element 1 is mediated by the cyclic AMP-responsive members of the CREB/ATF family of transcription factors. To achieve a better understanding of the mechanism of transactivation by Tax of human T-cell leukemia virus type 1 Tax-responsive element 1 (TRE-1), we developed a genetic approach with Saccharomyces cerevisiae. We constructed a yeast reporter strain containing the lacZ gene under the control of the CYC1 promoter associated with three copies of TRE-1. Expression of either the cyclic AMP response element-binding protein (CREB) or CREB fused to the GAL4 activation domain (GAD) in this strain did not modify the expression of the reporter gene. Tax alone was also inactive. """)

Results

|chunk                                                      |ner      |
+-----------------------------------------------------------+---------+
|intracellular signaling proteins                           |protein  |
|human T-cell leukemia virus type 1 promoter                |DNA      |
|Tax                                                        |protein  |
|Tax-responsive element 1                                   |DNA      |
|cyclic AMP-responsive members                              |protein  |
|CREB/ATF family                                            |protein  |
|transcription factors                                      |protein  |
|Tax                                                        |protein  |
|human T-cell leukemia virus type 1 Tax-responsive element 1|DNA      |
|TRE-1),                                                    |DNA      |
|lacZ gene                                                  |DNA      |
|CYC1 promoter                                              |DNA      |
|TRE-1                                                      |DNA      |
|cyclic AMP response element-binding protein                |protein  |
|CREB                                                       |protein  |
|CREB                                                       |protein  |
|GAL4 activation domain                                     |protein  |
|GAD                                                        |protein  |
|reporter gene                                              |DNA      |
|Tax                                                        |protein  |
+-----------------------------------------------------------+---------+

Model Information

Model Name: ner_cellular
Compatibility: Spark NLP for Healthcare 3.0.0+
License: Licensed
Edition: Official
Input Labels: [sentence, token, embeddings]
Output Labels: [ner]
Language: en

Data Source

Trained on the JNLPBA corpus containing more than 2.404 publication abstracts with 'embeddings_clinical'. http://www.geniaproject.org/

Benchmarking

|    | label         |     tp |    fp |   fn |     prec |      rec |       f1 |
|---:|:--------------|-------:|------:|-----:|---------:|---------:|---------:|
|  0 | B-cell_line   |    377 |   203 |  123 | 0.65     | 0.754    | 0.698148 |
|  1 | I-DNA         |   1519 |   277 |  266 | 0.845768 | 0.85098  | 0.848366 |
|  2 | I-protein     |   3981 |   911 |  786 | 0.813778 | 0.835116 | 0.824309 |
|  3 | B-protein     |   4483 |  1433 |  579 | 0.757776 | 0.885618 | 0.816724 |
|  4 | I-cell_line   |    786 |   340 |  203 | 0.698046 | 0.794742 | 0.743262 |
|  5 | I-RNA         |    178 |    42 |    9 | 0.809091 | 0.951872 | 0.874693 |
|  6 | B-RNA         |     99 |    28 |   19 | 0.779528 | 0.838983 | 0.808163 |
|  7 | B-cell_type   |   1440 |   294 |  480 | 0.83045  | 0.75     | 0.788177 |
|  8 | I-cell_type   |   2431 |   377 |  559 | 0.865741 | 0.813044 | 0.838565 |
|  9 | B-DNA         |    814 |   267 |  240 | 0.753006 | 0.772296 | 0.762529 |
| 10 | Macro-average | 16108  | 4172  | 3264 | 0.780318 | 0.824665 | 0.801879 |
| 11 | Micro-average | 16108  | 4172  | 3264 | 0.79428  | 0.831509 | 0.812469 |