🧬 Biomedical NER — Experimental Model (BC5CDR)

This model is a fine-tuned version of microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract on the bc5cdr dataset. It achieves the following results on the evaluation set:

Loss: 0.0835
Precision: 0.8582
Recall: 0.8977
F1: 0.8775
Accuracy: 0.9727

This repository hosts a testing version of a biomedical named entity recognition (NER) model fine-tuned on the BC5CDR dataset, which contains PubMed abstracts annotated for diseases and chemicals.

⚠️ Note: This model is shared for educational and testing purposes only. It is not intended for clinical or production use and may not generalize beyond the BC5CDR dataset.

Model overview

Base model: PubMedBERT (abstracts) (domain-specific transformer)
Task: Named Entity Recognition (token classification)
Entities:
- Chemical
- Disease
- O (non-entity tokens)

The model predicts entity spans following the standard BIO tagging scheme, e.g. B-Chemical, I-Disease, O.

Training notebook

The full training and preprocessing pipeline — including dataset preparation, sentence splitting, BIO tagging, and evaluation — is documented in this Kaggle notebook

Example usage

from transformers import AutoTokenizer, AutoModelForTokenClassification
from transformers import pipeline

tokenizer = AutoTokenizer.from_pretrained("Francesco-A/BiomedNLP-PubMedBERT-base-uncased-abstract-bc5cdr-ner-v1")
model = AutoModelForTokenClassification.from_pretrained("Francesco-A/BiomedNLP-PubMedBERT-base-uncased-abstract-bc5cdr-ner-v1")

ner = pipeline("token-classification", model=model, tokenizer=tokenizer, aggregation_strategy="first")

demo_texts = [
    "Aspirin is often used to treat inflammation, but may cause gastric bleeding.",
    "Naloxone reverses the antihypertensive effect of clonidine.",
]

for t in demo_texts:
    print("\nText:", t)
    preds = ner(t)
    for p in preds:
        print(f'  - {p["word"]}: {p["entity_group"]} (score {p["score"]:.2f})')

Training procedure

Training hyperparameters

The following hyperparameters were used during training:

learning_rate: 2e-5
train_batch_size: 64
eval_batch_size: 64
seed: 42
gradient_accumulation_steps: 4
total_train_batch_size: 256
optimizer: Adam with betas=(0.9,0.999) and epsilon=1e-08
lr_scheduler_type: linear
lr_scheduler_warmup_ratio: 0.1
num_epochs: 8
mixed_precision_training: Native AMP

Training results

Training Loss	Epoch	Step	Validation Loss	Precision	Recall	F1	Accuracy
No log	0.9836	15	0.5775	0.0299	0.0002	0.0004	0.8627
No log	1.9672	30	0.2332	0.7252	0.5753	0.6416	0.9284
No log	2.9508	45	0.1237	0.7610	0.8265	0.7924	0.9606
No log	4.0	61	0.0937	0.8364	0.8859	0.8605	0.9690
No log	4.9836	76	0.0860	0.8510	0.8927	0.8714	0.9714
No log	5.9672	91	0.0833	0.8502	0.8995	0.8741	0.9724
0.3513	6.9508	106	0.0859	0.8494	0.8992	0.8736	0.9714
0.3513	7.8689	120	0.0835	0.8582	0.8977	0.8775	0.9727