README.md

---
license: apache-2.0
datasets:
- HUMADEX/greek_ner_dataset
language:
- el
metrics:
- f1
- precision
- recall
- confusion_matrix
base_model:
- google-bert/bert-base-cased
pipeline_tag: token-classification
tags:
- NER
- medical
- symptom
- extraction
- greek
---
# Greek Medical NER

## Acknowledgement

This model had been created as part of joint research of HUMADEX research group (https://www.linkedin.com/company/101563689/) and has received funding by the European Union Horizon Europe Research and Innovation Program project SMILE (grant number 101080923) and Marie Skłodowska-Curie Actions (MSCA) Doctoral Networks, project BosomShield ((rant number 101073222). Responsibility for the information and views expressed herein lies entirely with the authors.
Authors:
dr. Izidor Mlakar, Rigon Sallauka, dr. Umut Arioz, dr. Matej Rojc

## Publication
The paper associated with this model has been published: [10.3390/app15105585](https://doi.org/10.3390/app15105585)

Please cite this paper as follows if you use this model or build upon this work. Your citation supports the authors and the continued development of this research.
```bibtex
@article{app15105585,
  author  = {Sallauka, Rigon and Arioz, Umut and Rojc, Matej and Mlakar, Izidor},
  title   = {Weakly-Supervised Multilingual Medical NER for Symptom Extraction for Low-Resource Languages},
  journal = {Applied Sciences},
  volume  = {15},
  year    = {2025},
  number  = {10},
  article-number = {5585},
  url     = {https://www.mdpi.com/2076-3417/15/10/5585},
  issn    = {2076-3417},
  doi     = {10.3390/app15105585}
}
```

## Use
- **Primary Use Case**: This model is designed to extract medical entities such as symptoms, diagnostic tests, and treatments from clinical text in the Greek language.
- **Applications**: Suitable for healthcare professionals, clinical data analysis, and research into medical text processing.
- **Supported Entity Types**:
  - `PROBLEM`: Diseases, symptoms, and medical conditions.
  - `TEST`: Diagnostic procedures and laboratory tests.
  - `TREATMENT`: Medications, therapies, and other medical interventions.

## Training Data
- **Data Sources**: Annotated datasets, including clinical data and translations of English medical text into Greek.
- **Data Augmentation**: The training dataset underwent data augmentation techniques to improve the model's ability to generalize to different text structures.
- **Dataset Split
**:
  - **Training Set**: 80%
  - **Validation Set**: 10%
  - **Test Set**: 10%

## Model Training
-
 **Training Configuration**:
  - **Optimizer**: AdamW
  - **Learning Rate**: 3e-5
  - **Batch Size**: 64
  - **Epochs**: 200
  - **Loss Function**: Focal Loss to handle class imbalance
- **Frameworks**: PyTorch, Hugging Face Transformers, SimpleTransformers

## Evaluation metrics
- eval_loss = 0.4112480320792267
- f1_score = 0.6910085729376871
- precision = 0.7068717096148518
- recall = 0.675841788751424

Visit [HUMADEX/Weekly-Supervised-NER-pipline](https://github.com/HUMADEX/Weekly-Supervised-NER-pipline) for more info.

## How to Use
You can easily use this model with the Hugging Face `transformers` library. Here's an example of how to load and use the model for inference:

```python
from transformers import AutoTokenizer, AutoModelForTokenClassification

model_name = "HUMADEX/greek_medical_ner"

# Load the tokenizer and model
tokenizer = AutoTokenizer.from_pretrained(model_name)
model = AutoModelForTokenClassification.from_pretrained(model_name)

# Sample text for inference
text = "Ο ασθενής παραπονέθηκε για έντονους πονοκεφάλους και ναυτία που διαρκούσαν δύο ημέρες. Για την ανακούφιση των συμπτωμάτων, του χορηγήθηκε παρακεταμόλη και του συστήθηκε να ξεκουραστεί και να πίνει πολλά υγρά."

# Tokenize the input text
inputs = tokenizer(text, return_tensors="pt")