ProGen2-base

HF mirror for ProGen2-base for Protein Engineering

Official GitHub of ProGen2 by Nijkamp et al..

• 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

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-base").to(torch.float16).to(device).eval()
tokenizer = AutoTokenizer.from_pretrained("jinyuan22/ProGen2-base")

# 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 - 1.9) < 0.1