README.md

---
language: en
tags:
- medembed
- medical-embedding
- clinical-embedding
- information-retrieval
- sentence-transformers
license: apache-2.0
datasets:
- MedicalQARetrieval
- NFCorpus
- PublicHealthQA
- TRECCOVID
- ArguAna
metrics:
- nDCG
- MAP
- Recall
- Precision
- MRR
base_model:
- BAAI/bge-base-en-v1.5
---

# MedEmbed: Specialized Embedding Model for Medical and Clinical Information Retrieval

![benchmark-scores](https://cdn-uploads.huggingface.co/production/uploads/60c8619d95d852a24572b025/gTx5-m68LQ3eyNd6fLki2.png)

## Model Description

MedEmbed is a family of embedding models fine-tuned specifically for medical and clinical data, designed to enhance performance in healthcare-related natural language processing (NLP) tasks, particularly information retrieval.

**GitHub Repo:** [https://github.com/abhinand5/MedEmbed](https://github.com/abhinand5/MedEmbed)

**Technical Blog Post:** [https://huggingface.co./blog/abhinand/medembed-finetuned-embedding-models-for-medical-ir](https://huggingface.co./blog/abhinand/medembed-finetuned-embedding-models-for-medical-ir)

## Intended Use

This model is intended for use in medical and clinical contexts to improve information retrieval, question answering, and semantic search tasks. It can be integrated into healthcare systems, research tools, and medical literature databases to enhance search capabilities and information access.

## Training Data

![synthetic-datagen-flow](https://cdn-uploads.huggingface.co/production/uploads/60c8619d95d852a24572b025/asaA5QDO_j0PWFQV9NXCu.png)

The model was trained using a novel synthetic data generation pipeline:
1. Source: Clinical notes from PubMed Central (PMC)
2. Processing: LLaMA 2 70B model used to generate query-response pairs
3. Augmentation: Negative sampling for challenging examples
4. Format: Triplets (query, positive response, negative response) for contrastive learning

## Performance

MedEmbed consistently outperforms general-purpose embedding models across various medical NLP benchmarks:

- ArguAna
- MedicalQARetrieval
- NFCorpus
- PublicHealthQA
- TRECCOVID

Specific performance metrics (nDCG, MAP, Recall, Precision, MRR) are available in the full documentation.

## Limitations

While highly effective for medical and clinical data, this model may not generalize well to non-medical domains. It should be used with caution in general-purpose NLP tasks.

## Ethical Considerations

Users should be aware of potential biases in medical data and the ethical implications of AI in healthcare. This model should be used as a tool to assist, not replace, human expertise in medical decision-making.

## Citation

If you use this model in your research, please cite:

```bibtex
@software{balachandran2024medembed,
  author = {Balachandran, Abhinand},
  title = {MedEmbed: Medical-Focused Embedding Models},
  year = {2024},
  url = {https://github.com/abhinand5/MedEmbed}
}
```

For more detailed information, visit our GitHub repository.