| --- |
| license: bsd-3-clause |
| library_name: pytorch |
| tags: |
| - biology |
| - dna |
| - dna-shape |
| - genomics |
| --- |
| |
| # Deep DNAshape — PyTorch weights |
|
|
| PyTorch (`.pt`) conversions of the pretrained [Deep DNAshape](https://github.com/JinsenLi/deepDNAshape) |
| TensorFlow checkpoints, for use with [pyaptamer](https://github.com/gc-os-ai/pyaptamer). |
|
|
| These are **not** newly trained models. Every tensor is a bit-exact copy of the |
| corresponding variable in the upstream TensorFlow checkpoint, with the Conv1D |
| kernel transposed from TensorFlow's `(kernel, in, out)` layout to PyTorch's |
| `(out, in, kernel)`. All credit for the models belongs to the original authors. |
|
|
| ## Contents |
|
|
| One `state_dict` per DNA shape feature, 27 in total. |
|
|
| Intra-base pair features (4 input channels, one value per base): |
| `Buckle`, `EP`, `MGW`, `Opening`, `ProT`, `Shear`, `Stagger`, `Stretch` |
|
|
| Inter-base pair features (16 input channels, one value per base step): |
| `HelT`, `Rise`, `Roll`, `Shift`, `Slide`, `Tilt` |
|
|
| Each feature also has a `-FL` variant trained with extended flanking regions. |
|
|
| ## Usage |
|
|
| ```python |
| import torch |
| from huggingface_hub import hf_hub_download |
| |
| path = hf_hub_download(repo_id="<this-repo>", filename="MGW.pt") |
| state_dict = torch.load(path, weights_only=True) |
| ``` |
|
|
| The `state_dict` targets a 7-layer message-passing architecture with 64 filters. |
| See the pyaptamer `deepdnashape` module for the matching model definition. |
|
|
| ## Credit |
|
|
| Original method, training and weights by Jinsen Li, Tsu-Pei Chiu and Remo Rohs. |
|
|
| - Source repository: <https://github.com/JinsenLi/deepDNAshape> |
| - Webserver: <https://deepdnashape.usc.edu/> |
|
|
| If you use these weights, please cite the original work: |
|
|
| > Li, J., Chiu, T.-P. & Rohs, R. Predicting DNA structure using a deep learning |
| > method. *Nature Communications* **15**, 1243 (2024). |
| > <https://doi.org/10.1038/s41467-024-45191-5> |
|
|
| ## License |
|
|
| BSD 3-Clause, inherited from the upstream project. |
| Copyright (c) 2023, JinsenLi. The full license text is in `LICENSE`. |
|
|
