prot_t5_xl_bfd EU AI Act Compliance Profile

ProtT5-XL-BFD model

Pretrained model on protein sequences using a masked language modeling (MLM) objective. It was introduced in this paper and first released in this repository. This model is trained on uppercase amino acids: it only works with capital letter amino acids.

Model description

ProtT5-XL-BFD is based on the t5-3b model and was pretrained on a large corpus of protein sequences in a self-supervised fashion. This means it was pretrained on the raw protein sequences only, with no humans labelling them in any way (which is why it can use lots of publicly available data) with an automatic process to generate inputs and labels from those protein sequences.

One important difference between this T5 model and the original T5 version is the denosing objective. The original T5-3B model was pretrained using a span denosing objective, while this model was pre-trained with a Bart-like MLM denosing objective. The masking probability is consistent with the original T5 training by randomly masking 15% of the amino acids in the input.

It has been shown that the features extracted from this self-supervised model (LM-embeddings) captured important biophysical properties governing protein shape. shape. This implied learning some of the grammar of the language of life realized in protein sequences.

Intended uses & limitations

The model could be used for protein feature extraction or to be fine-tuned on downstream tasks. We have noticed in some tasks on can gain more accuracy by fine-tuning the model rather than using it as a feature extractor. We have also noticed that for feature extraction, its better to use the feature extracted from the encoder not from the decoder.

How to use

Here is how to use this model to extract the features of a given protein sequence in PyTorch:

from transformers import T5Tokenizer, T5Model
import re
import torch

tokenizer =

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