BioBERT Base Cased v1.2 Finetuned NER Open-Source Model - Efficiently Handle Named Entity Recognition in Biomedical Texts

Biobert Base Cased V1.2 Finetuned Ner

Developed by sciarrilli

Named entity recognition model fine-tuned on jnlpba dataset based on BioBERT v1.2, specializing in biomedical text processing

Sequence Labeling

Transformers

#Biomedical NER #High Recall #BERT Fine-tuning

Downloads 83

Release Time : 3/2/2022

Model Overview

This model is a BERT model optimized for named entity recognition tasks in the biomedical field, capable of identifying professional entities in biomedical literature

Model Features

Biomedical Domain Optimization

Based on the BioBERT pre-trained model, specifically optimized for biomedical texts

High-Performance Entity Recognition

Achieves an F1 score of 0.768 on the jnlpba dataset, demonstrating excellent performance

Multi-Entity Type Recognition

Capable of identifying various entity types in biomedical literature

Model Capabilities

Biomedical Named Entity Recognition

Text Token Classification

Biomedical Literature Analysis

Use Cases

Biomedical Research

Literature Entity Extraction

Automatically extracts key entities such as genes and proteins from biomedical research papers

Accuracy 90.5%, Recall 83.0%

Knowledge Graph Construction

Automatically identifies and labels entities for biomedical knowledge graphs

Medical Information Processing

Electronic Medical Record Analysis

Extracts key medical entities from medical records

Training Loss	Epoch	Step	Validation Loss	Precision	Recall	F1	Accuracy
0.257	1.0	1160	0.2889	0.7091	0.8222	0.7615	0.9021
0.1962	2.0	2320	0.3009	0.7154	0.8259	0.7667	0.9048
0.158	3.0	3480	0.3214	0.7098	0.8228	0.7621	0.9031
0.131	4.0	4640	0.3385	0.7174	0.8292	0.7692	0.9055
0.1081	5.0	5800	0.3655	0.7151	0.8301	0.7683	0.9050

Property	Details
Tags	generated_from_trainer
Datasets	jnlpba
Metrics	precision, recall, f1, accuracy
Model Name	biobert - base - cased - v1.2 - finetuned - ner
Task	Token Classification
Dataset Name	jnlpba
Precision	0.7150627220423177
Recall	0.8300729927007299
F1	0.7682875335686659
Accuracy	0.90497239665345

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Biobert Base Cased V1.2 Finetuned Ner

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