human-mpra-gosai-2024-model

Model Description

This model is a multi-class classifier trained to classify genomic DNA sequences into one of 16 classes. It was trained by fine-tuning the Enformer model using the grelu library using the MPRA dataset from Gosai et al. 2024 (https://www.nature.com/articles/s41586-024-08070-z).

• Architecture: Fine-tuned Enformer
• Input: 200 bp DNA sequences
• Output: Probability across 16 class labels.

Repository Content

1. model.ckpt: The trained model weights and hyperparameters (PyTorch Lightning checkpoint).
2. 1_model.ipynb: Jupyter notebook containing the training logic, architecture definition, and evaluation loops.
3. output.log: Training logs.

How to use

To load this model for inference or fine-tuning, use the grelu interface:

from grelu.lightning import LightningModel
from huggingface_hub import hf_hub_download

ckpt_path = hf_hub_download(
    repo_id="Genentech/human-mpra-gosai-2024-model", 
    filename="model.ckpt"
)

model = LightningModel.load_from_checkpoint(ckpt_path)
model.eval()