---
license: mit
language:
  - en
tags:
  - peft
  - lora
  - biogpt
  - biomedical
  - clinvar
base_model: microsoft/biogpt
---
**Year:** 2024–2025  
**License:** MIT  
**Author:** Sepideh Moafi 

# PathogenAgentAI-BioGPT LoRA Adapter

## Model Description

A parameter-efficient LoRA adapter for BioGPT, developed as part of the PathogenAgentAI research software project. Fine-tuned on ClinVar-derived instruction data for biomedical language-model applications.

## Model Details

- Model type: LoRA adapter (PEFT-compatible)
- Base model: microsoft/biogpt
- Framework: PEFT 0.19.1
- Adapter size: ~12.6 MB
- Precision: BF16
- Format: Safetensors
- License: MIT

## LoRA Configuration

- Rank (r): 16
- LoRA alpha: 32
- LoRA dropout: 0.05
- Target modules: q_proj, k_proj, v_proj, o_proj
- Task type: CAUSAL_LM

## Intended Use

- Parameter-efficient adaptation of BioGPT for biomedical text generation
- Research on biomedical language models
- Experimentation with ClinVar-derived variant information
- Reproducible research and model adaptation experiments

Not intended for clinical diagnosis, treatment decisions, or direct clinical use.

## How to Get Started

```python
from peft import PeftModel
from transformers import AutoModelForCausalLM

base_model = AutoModelForCausalLM.from_pretrained("microsoft/biogpt")
model = PeftModel.from_pretrained(base_model, "Sepideh2027/PathogenAgentAI-BioGPT-LoRA")
Training Details

· Training data: ~20,000 ClinVar-derived instruction-style examples (16k/2k/2k train/validation/test split)
· Training procedure: LoRA, BF16 mixed precision
· Hardware: NVIDIA T4 GPU

Limitations

· Inherits all limitations of the base BioGPT model.
· Not validated for clinical use.
· Generated outputs should be independently verified against authoritative biomedical sources.

Related Resources

· Fine-tuned model: Sepideh2027/biogpt-clinvar-finetuned
· Instruction-tuning dataset: Sepideh2027/Agent

Citation

@software{Moafi2025pathogenagent,
  author = {Moafi, Sepideh},
  title = {PathogenAgentAI-BioGPT LoRA Adapter},
  year = {2025},
  url = {https://huggingface.co/Sepideh2027/PathogenAgentAI-BioGPT-LoRA}
}

BioGPT-ClinVar: Parameter-Efficient Fine-Tuning of a Biomedical Foundation Model. Research Square, 2026. DOI: 10.21203/rs.3.rs-10196893/v1

Contact

Sepideh Moafi
GitHub: AIResearcher20
Hugging Face: Sepideh2027