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SciBERT finetuned on JNLPA for NER downstream task

Language Model

SciBERT is a pretrained language model based on BERT and trained by the Allen Institute for AI on papers from the corpus of Semantic Scholar. Corpus size is 1.14M papers, 3.1B tokens. SciBERT has its own vocabulary (scivocab) that's built to best match the training corpus.

Downstream task

allenai/scibert_scivocab_cased has been finetuned for Named Entity Recognition (NER) dowstream task. The code to train the NER can be found here.


The corpus used to fine-tune the NER is BioNLP / JNLPBA shared task.

  • Training data consist of 2,000 PubMed abstracts with term/word annotation. This corresponds to 18,546 samples (senteces).
  • Evaluation data consist of 404 PubMed abstracts with term/word annotation. This corresponds to 3,856 samples (sentences).

The classes (at word level) and its distribution (number of examples for each class) for training and evaluation datasets are shown below:

Class Label # training examples # evaluation examples
O 382,963 81,647
B-protein 30,269 5,067
I-protein 24,848 4,774
B-cell_type 6,718 1,921
I-cell_type 8,748 2,991
B-DNA 9,533 1,056
I-DNA 15,774 1,789
B-cell_line 3,830 500
I-cell_line 7,387 9,89
B-RNA 951 118
I-RNA 1,530 187


An exhaustive hyperparameter search was done. The hyperparameters that provided the best results are:

  • Max length sequence: 128
  • Number of epochs: 6
  • Batch size: 32
  • Dropout: 0.3
  • Optimizer: Adam

The used learning rate was 5e-5 with a decreasing linear schedule. A warmup was used at the beggining of the training with a ratio of steps equal to 0.1 from the total training steps.

The model from the epoch with the best F1-score was selected, in this case, the model from epoch 5.


The following table shows the evaluation metrics calculated at span/entity level:

precision recall f1-score
cell_line 0.5205 0.7100 0.6007
cell_type 0.7736 0.7422 0.7576
protein 0.6953 0.8459 0.7633
DNA 0.6997 0.7894 0.7419
RNA 0.6985 0.8051 0.7480
micro avg 0.6984 0.8076 0.7490
macro avg 0.7032 0.8076 0.7498

The macro F1-score is equal to 0.7498, compared to the value provided by the Allen Institute for AI in their paper, which is equal to 0.7728. This drop in performance could be due to several reasons, but one hypothesis could be the fact that the authors used an additional conditional random field, while this model uses a regular classification layer with softmax activation on top of SciBERT model.

At word level, this model achieves a precision of 0.7742, a recall of 0.8536 and a F1-score of 0.8093.

Model usage in inference

Use the pipeline:

from transformers import pipeline

text = "Mouse thymus was used as a source of glucocorticoid receptor from normal CS lymphocytes."

nlp_ner = pipeline("ner",


{'word': 'glucocorticoid', 
'score': 0.9894881248474121, 
'entity': 'B-protein'}, 
{'word': 'receptor', 
'score': 0.989505410194397, 
'entity': 'I-protein'}, 

{'word': 'normal', 
'score': 0.7680378556251526, 
'entity': 'B-cell_type'}, 

{'word': 'cs', 
'score': 0.5176806449890137, 
'entity': 'I-cell_type'}, 

{'word': 'lymphocytes', 
'score': 0.9898491501808167, 
'entity': 'I-cell_type'}

Or load model and tokenizer as follows:

import torch
from transformers import AutoTokenizer, AutoModelForTokenClassification

# Example
text = "Mouse thymus was used as a source of glucocorticoid receptor from normal CS lymphocytes."

# Load model
tokenizer = AutoTokenizer.from_pretrained("fran-martinez/scibert_scivocab_cased_ner_jnlpba")
model = AutoModelForTokenClassification.from_pretrained("fran-martinez/scibert_scivocab_cased_ner_jnlpba")

# Get input for BERT
input_ids = torch.tensor(tokenizer.encode(text)).unsqueeze(0)

# Predict
with torch.no_grad():
  outputs = model(input_ids)

# From the output let's take the first element of the tuple.
# Then, let's get rid of [CLS] and [SEP] tokens (first and last)
predictions = outputs[0].argmax(axis=-1)[0][1:-1]

# Map label class indexes to string labels.
for token, pred in zip(tokenizer.tokenize(text), predictions):
  print(token, '->', model.config.id2label[pred.numpy().item()])

mouse -> O
thymus -> O
was -> O
used -> O
as -> O
a -> O
source -> O
of -> O
glucocorticoid -> B-protein
receptor -> I-protein
from -> O
normal -> B-cell_type
cs -> I-cell_type
lymphocytes -> I-cell_type
. -> O
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Token Classification
This model can be loaded on the Inference API on-demand.

Datasets used to train sschet/scibert_scivocab_cased_ner_jnlpba