---
license: mit
tags:
- biology
- protein
---
# PLTNUM-SaProt-NIH3T3
PLTNUM is a protein language model trained to predict protein half-lives based on their sequences.  
This model was created based on [westlake-repl/SaProt_650M_AF2](https://huggingface.co/westlake-repl/SaProt_650M_AF2) and trained on protein half-life dataset of NIH3T3 mouse embryo fibroblast cell line ([paper link](https://www.nature.com/articles/nature10098)).

### Model Sources
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- **Repository:** https://github.com/sagawatatsuya/PLTNUM
- **Paper:** [Prediction of Protein Half-lives from Amino Acid Sequences by Protein Language Models](https://www.biorxiv.org/content/10.1101/2024.09.10.612367v1)
- **Demo:** https://huggingface.co/spaces/sagawa/PLTNUM

## Uses

<!-- Address questions around how the model is intended to be used, including the foreseeable users of the model and those affected by the model. -->

## How to Get Started with the Model

Use the code below to get started with the model.

```python
from torch import sigmoid
import torch.nn as nn
from transformers import AutoModel, AutoConfig, PreTrainedModel, AutoTokenizer


class PLTNUM_PreTrainedModel(PreTrainedModel):
    config_class = AutoConfig

    def __init__(self, config):
        super(PLTNUM_PreTrainedModel, self).__init__(config)
        self.model = AutoModel.from_pretrained(self.config._name_or_path)

        self.fc_dropout1 = nn.Dropout(0.8)
        self.fc_dropout2 = nn.Dropout(0.4)
        self.fc = nn.Linear(self.config.hidden_size, 1)
        self._init_weights(self.fc)

    def _init_weights(self, module):
        if isinstance(module, nn.Linear):
            nn.init.normal_(module.weight, mean=0.0, std=self.config.initializer_range)
            if module.bias is not None:
                nn.init.constant_(module.bias, 0)
        elif isinstance(module, nn.Embedding):
            nn.init.normal_(module.weight, mean=0.0, std=self.config.initializer_range)
            if module.padding_idx is not None:
                nn.init.constant_(module.weight[module.padding_idx], 0.0)
        elif isinstance(module, nn.LayerNorm):
            nn.init.constant_(module.bias, 0)
            nn.init.constant_(module.weight, 1.0)

    def forward(self, inputs):
        outputs = self.model(**inputs)
        last_hidden_state = outputs.last_hidden_state[:, 0]
        output = (
            self.fc(self.fc_dropout1(last_hidden_state))
            + self.fc(self.fc_dropout2(last_hidden_state))
        ) / 2
        return output

    def create_embedding(self, inputs):
        outputs = self.model(**inputs)
        last_hidden_state = outputs.last_hidden_state[:, 0]
        return last_hidden_state


model = PLTNUM_PreTrainedModel.from_pretrained("sagawa/PLTNUM-SaProt-NIH3T3")
tokenizer = AutoTokenizer.from_pretrained("sagawa/PLTNUM-SaProt-NIH3T3")
seq = "MdSdGdRdGdKpQpGpGpKdApRpApKpAdKdTaRpScSvRvAlGvLaQpFfPrVlGvRvVqHvRvLvLvRvKvGvNpYpSdEpRdVdGdAsGcAnPsVsYvLvArAvVvLvErYvLvTvAvEqIlLcEvLqAlGcNvAqAcRvDvNvKvKhTrRdIrIdPlRlHsLsQqLvAsIqRcNvDdEpEvLsNcKvLvLcGvRpVpTdIrApQpGnGdVhLdPdNdIdQdApVvLpLdPdKdKdTdEpSpHpHpKpPpKpGdKd"
input = tokenizer(
    [seq],
    add_special_tokens=True,
    max_length=512,
    padding="max_length",
    truncation=True,
    return_offsets_mapping=False,
    return_attention_mask=True,
    return_tensors="pt",
)
print(sigmoid(model(input)))  # tensor([[0.9798]], grad_fn=<SigmoidBackward0>)
```

## Citation
Prediction of Protein Half-lives from Amino Acid Sequences by Protein Language Models  
Tatsuya Sagawa, Eisuke Kanao, Kosuke Ogata, Koshi Imami, Yasushi Ishihama  
bioRxiv 2024.09.10.612367; doi: https://doi.org/10.1101/2024.09.10.612367
<!-- If there is a paper or blog post introducing the model, the APA and Bibtex information for that should go in this section. -->