README.md

---
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 [PTEN_HUMAN](https://www.uniprot.org/uniprotkb/P60484/entry) (Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase). 


## Protein Function
Dual-specificity protein phosphatase, dephosphorylating tyrosine-, serine- and threonine-phosphorylated proteins.
Also functions as a lipid phosphatase, removing the phosphate in the D3 position of the inositol ring of PtdIns(3,4,5)P3/phosphatidylinositol 3,4,5-trisphosphate, PtdIns(3,4)P2/phosphatidylinositol 3,4-diphosphate and PtdIns3P/phosphatidylinositol 3-phosphate with a preference for PtdIns(3,4,5)P3.
Furthermore, this enzyme can also act as a cytosolic inositol 3-phosphatase acting on Ins(1,3,4,5,6)P5/inositol 1,3,4,5,6 pentakisphosphate and possibly Ins(1,3,4,5)P4/1D-myo-inositol 1,3,4,5-tetrakisphosphate.

### 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_PTEN_HUMAN).

Label means fitness score of each mutant amino acid sequence, ranging from minus infinity to positive infinity, smaller means more stable.
### Model input type
Amino acid sequence

### Performance
0.62 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: 64

precision: 16-mixed