PyTorch implementations of protein secondary structure prediction on CB513.
I implemented them based on https://github.com/alrojo/CB513 and https://github.com/jadore801120/attention-is-all-you-need-pytorch.
I used CB513 dataset of https://github.com/alrojo/CB513.
| sequence length (train) | sequence length (test) |
|---|---|
 |
 |
| amino acid (train) | amino acid (test) |
|---|---|
 |
 |
| secondary structure label(train) | secondary structure label (test) |
|---|---|
 |
 |
You can get more infomations by adding -h option.
python main.py
python preprocess.py
python main.py
- https://github.com/alrojo/CB513
- https://github.com/jadore801120/attention-is-all-you-need-pytorch
- Li, Zhen; Yu, Yizhou, Protein Secondary Structure Prediction Using Cascaded Convolutional and Recurrent Neural Networks, 2016.
- Ashish Vaswani, Noam Shazeer, Niki Parmar, Jakob Uszkoreit, Llion Jones, Aidan N. Gomez, Lukasz Kaiser, Illia Polosukhin, Attention Is All You Need