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--- |
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license: mit |
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library_name: pytorch-lightning |
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pipeline_tag: tabular-regression |
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tags: |
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- biology |
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- genomics |
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datasets: |
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- Genentech/borzoi-data |
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--- |
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# Borzoi Model (Linder et al. 2025) |
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## Model Description |
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This repository contains the weights for the Borzoi model, a model designed to predict functional genomic tracks from genomic DNA sequences. |
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- **Architecture:** Convolutions followed by Transformer and U-net layers. |
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- **Input:** 524,288 bp of genomic DNA sequence. |
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- **Output Resolution:** 32 bp bins. |
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- **Source:** [Linder, J. et al. Nature Genetics (2025)](https://www.nature.com/articles/s41588-024-02053-6) |
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## Repository Content |
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The repository includes both full PyTorch Lightning checkpoints and raw state dictionaries for the human and mouse versions of the model. Each model has 4 independent replicates. Note that the weights are derived from the publication but the model has been converted into the PyTorch Lightning format used by gReLU (https://github.com/Genentech/gReLU). |
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| File | Type | Description | |
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| :--- | :--- | :--- | |
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| `human_rep0.ckpt` | PyTorch Lightning | Full checkpoint including base model and human head, replicate 0. | |
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| `human_rep1.ckpt` | PyTorch Lightning | Full checkpoint including base model and human head, replicate 1. | |
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| `human_rep2.ckpt` | PyTorch Lightning | Full checkpoint including base model and human head, replicate 2. | |
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| `human_rep3.ckpt` | PyTorch Lightning | Full checkpoint including base model and human head, replicate 3. | |
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| `mouse_rep0.ckpt` | PyTorch Lightning | Full checkpoint including base model and mouse head, replicate 0. | |
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| `mouse_rep1.ckpt` | PyTorch Lightning | Full checkpoint including base model and mouse head, replicate 1. | |
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| `mouse_rep2.ckpt` | PyTorch Lightning | Full checkpoint including base model and mouse head, replicate 2. | |
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| `mouse_rep3.ckpt` | PyTorch Lightning | Full checkpoint including base model and mouse head, replicate 3. | |
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| `human_state_dict_rep0.h5` | HDF5 | Weights-only state dictionary for the human model, replicate 0. | |
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| `human_state_dict_rep1.h5` | HDF5 | Weights-only state dictionary for the human model, replicate 1. | |
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| `human_state_dict_rep2.h5` | HDF5 | Weights-only state dictionary for the human model, replicate 2. | |
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| `human_state_dict_rep3.h5` | HDF5 | Weights-only state dictionary for the human model, replicate 3. | |
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| `mouse_state_dict_rep0.h5` | HDF5 | Weights-only state dictionary for the mouse model, replicate 0. | |
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| `mouse_state_dict_rep1.h5` | HDF5 | Weights-only state dictionary for the mouse model, replicate 1. | |
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| `mouse_state_dict_rep2.h5` | HDF5 | Weights-only state dictionary for the mouse model, replicate 2. | |
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| `mouse_state_dict_rep3.h5` | HDF5 | Weights-only state dictionary for the mouse model, replicate 3. | |
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| `save_wandb_borzoi_human.ipynb` | Jupyter Notebook | Code used to create human checkpoints | |
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| `save_wandb_borzoi_mouse.ipynb` | Jupyter Notebook | Code used to create mouse checkpoints | |
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## Model Heads & Output Tracks |
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The uman and mouse `.ckpt` files for the same replicate utilize the same core transformer trunk but differ in their species-specific output heads. |
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### Outputs |
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Human Head: 7,611 total tracks |
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Mouse Head: 2,608 total tracks |
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## Usage |
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The models are intended for use with the `grelu` library. |
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```python |
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from grelu.lightning import LightningModel |
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from huggingface_hub import hf_hub_download |
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# Download the desired checkpoint |
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ckpt_path = hf_hub_download( |
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repo_id="Genentech/borzoi-model", |
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filename="human_rep0.ckpt" |
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) |
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# Load the model |
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model = LightningModel.load_from_checkpoint(ckpt_path) |
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model.eval() |
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``` |
