|
|
--- |
|
|
base_model: westlake-repl/SaProt_35M_AF2 |
|
|
library_name: peft |
|
|
--- |
|
|
# Base model: [westlake-repl/SaProt_35M_AF2](https://huggingface.co/westlake-repl/SaProt_35M_AF2) |
|
|
|
|
|
# Model Card for Model ID |
|
|
|
|
|
<!-- Provide a quick summary of what the model is/does. --> |
|
|
This model is trained on a sigle site deep mutation scanning dataset and |
|
|
can be used to predict fitness score of mutant amino acid sequence of protein [RASH_HUMAN](https://www.uniprot.org/uniprotkb/P01112/entry) (GTPase HRas). |
|
|
|
|
|
## Protein Function |
|
|
This protein involved in the activation of Ras protein signal transduction. |
|
|
Ras proteins bind GDP/GTP and possess intrinsic GTPase activity. |
|
|
|
|
|
### Task type |
|
|
protein level regression |
|
|
|
|
|
### Dataset description |
|
|
The dataset is from [Deep generative models of genetic variation capture the effects of mutations](https://www.nature.com/articles/s41592-018-0138-4). |
|
|
And can also be found on [SaprotHub dataset](https://huggingface.co/datasets/SaProtHub/DMS_RASH_HUMAN). |
|
|
|
|
|
Label means fitness score of each mutant amino acid sequence, ranging from minus infinity to positive infinity where 0 is value of wildtype, |
|
|
larger means higher fitness. |
|
|
### Model input type |
|
|
Amino acid sequence |
|
|
|
|
|
### Performance |
|
|
0.64 Spearman's ρ |
|
|
|
|
|
### LoRA config |
|
|
lora_dropout: 0.0 |
|
|
|
|
|
lora_alpha: 16 |
|
|
|
|
|
target_modules: ["query", "key", "value", "intermediate.dense", "output.dense"] |
|
|
|
|
|
modules_to_save: ["classifier"] |
|
|
|
|
|
### Training config |
|
|
class: AdamW |
|
|
|
|
|
betas: (0.9, 0.98) |
|
|
|
|
|
weight_decay: 0.01 |
|
|
|
|
|
learning rate: 1e-4 |
|
|
|
|
|
epoch: 50 |
|
|
|
|
|
batch size: 256 |
|
|
|
|
|
precision: 16-mixed |
