AttributeError: 'MolformerModel' object has no attribute 'warn_if_padding_and_no_attention_mask'

[tkrwy]

Hello, Thank you for your useful tool! when I use the model, it appears the following error:

AttributeError: 'MolformerModel' object has no attribute 'warn_if_padding_and_no_attention_mask'

How I can skip the step, thank you!

[hoffmansc]

Can you provide a code snippet to reproduce your error? It sounds like you're using the HuggingFace model not this version

[tkrwy]

Thank you for your reply. Yes, I'm using HuggingFace, because I want to use your molecule embedding in our downstream anlaysis. Bellow is the code snippet. Is there another easy way to cite your model, if I don't use HuggingFace?

import torch
from transformers import AutoModel, AutoTokenizer

model = AutoModel.from_pretrained("ibm/MoLFormer-XL-both-10pct", deterministic_eval=True, trust_remote_code=True)
tokenizer = AutoTokenizer.from_pretrained("ibm/MoLFormer-XL-both-10pct", trust_remote_code=True)

smiles = ["Cn1c(=O)c2c(ncn2C)n(C)c1=O", "CC(=O)Oc1ccccc1C(=O)O"]
inputs = tokenizer(smiles, padding=True, return_tensors="pt")
with torch.no_grad():
    outputs = model(**inputs)
outputs.pooler_output

[hoffmansc]

I think you just need to update your version of transformers -- it looks like this feature was added in v4.31.0.

For future reference, this repo contains a standalone version of the code which can be used for training, etc. It does not contain the huggingface code.