| --- |
| 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 |
| |
