transformers pytorch bert text-classification en arxiv:2409.19581 base_model:microsoft/BiomedNLP-BiomedBERT-base-uncased-abstract-fulltext base_model:finetune:microsoft/BiomedNLP-BiomedBERT-base-uncased-abstract-fulltext license:apache-2.0 endpoints_compatible region:us
---
base_model:
- microsoft/BiomedNLP-BiomedBERT-base-uncased-abstract-fulltext
language:
- en
library_name: transformers
license: apache-2.0
metrics:
- precision
- recall
- f1
pipeline_tag: text-classification
---

# Fine-tuned RE Model for DiMB-RE

## Model Description
This is a fine-tuned **Relation Extraction (RE)** model based on the [BiomedNLP-BiomedBERT-base-uncased](https://huggingface.co/microsoft/BiomedNLP-BiomedBERT-base-uncased-abstract-fulltext) model, specifically designed for sentence classification task to extract relations between extract entities for diet, human metabolism and microbiome field. The model has been trained on the DiMB-RE dataset and is optimized to infer relationship with 13 relation types.

<!-- ### Key Features:
- **Language**: English
- **Task**: Token classification for Named Entity Recognition (NER)
- **Base Model**: BiomedNLP-BiomedBERT-base-uncased-abstract-fulltext
- **Domains**: Biomedical, Clinical, Scientific -->

## Performance
The model has been evaluated on the DiMB-RE using the following metrics:
- **RE (w/ GOLD entities and triggers)** - P: 0.799, R: 0.772, F1: 0.785
- **RE (Strict, w/ predicted entities and triggers)** - P: 0.416, R: 0.336, F1: 0.371
- **RE (Relaxed, w/ predicted entities and triggers)** - P: 0.448, R: 0.370, F1: 0.409

## Citation
If you use this model, please cite like below:

```bibtex
@misc{hong2024dimbreminingscientificliterature,
      title={DiMB-RE: Mining the Scientific Literature for Diet-Microbiome Associations}, 
      author={Gibong Hong and Veronica Hindle and Nadine M. Veasley and Hannah D. Holscher and Halil Kilicoglu},
      year={2024},
      eprint={2409.19581},
      archivePrefix={arXiv},
      primaryClass={cs.CL},
      url={https://arxiv.org/abs/2409.19581}, 
}
```