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---
license: bsd-3-clause
---
# ProGen2-small
HF mirror for ProGen2-small for **Protein Engineering**
[Official GitHub](https://github.com/salesforce/progen/tree/main/progen2) of [ProGen2 by Nijkamp et al.](https://www.cell.com/cell-systems/fulltext/S2405-4712(23)00272-7).
- The ProGen2 suite of protein language models are scaled to 6.4B parameters
- Models with increased scale better capture the distribution of protein sequences
- ProGen2 models generate novel protein sequences adopting natural folds
- ProGen2 model likelihoods are effective for zero-shot fitness prediction
```python
import torch
from faesm.progen2 import ProGenForCausalLM
from transformers import AutoTokenizer
device = 'cuda' if torch.cuda.is_available() else 'cpu'
model = ProGenForCausalLM.from_pretrained("jinyuan22/ProGen2-small").to(torch.float16).to(device).eval()
tokenizer = AutoTokenizer.from_pretrained("jinyuan22/ProGen2-small")
# sequence = "1" + "ACDEFGHIKLMNPQRSTVWY" * 50 + "2" # 1002 token
sequence = "2GFLPFRGADEGLAAREAATLAARGTAARAYREDSWAVPVPRGLLGDLTARVAALGAASPPPADPLAVTLDLHHVTAEVALTTVLDAATLVHGQTRVLSAEDAAEAATAAAAATEAYLERLQDFVLFMSASVRVWRRGNAAGATGPEWDQWYTVADRDALGSAPTHLAVLGRQADALCHFVLDRVAWGTCGTPLWSGDEDLGNVVATFAGYADRLATAPRDLIM1"
inputs = tokenizer(sequence, return_tensors="pt").to(device)
with torch.no_grad():
logits = model(inputs.input_ids, labels=inputs.input_ids).logits
logits = logits[0][:-1, ...]
target = inputs.input_ids[0, 1:]
# remove unused logits
first_token, last_token = 5, 29
logits = logits[:, first_token:(last_token+1)]
target = target - first_token
ce_eval = torch.nn.functional.cross_entropy(input=logits.view(-1, logits.size(-1)), target=target.view(-1), reduction="mean").item()
print(ce_eval)
assert abs(ce_eval - 2.4) < 0.1
``` |