ProtT5 XL UniRef50 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 UniRef50 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…
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