ProtTrans

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Using [CLS] token for classification task?

9

Hello! Thanks for your great work! I'm trying to do some classification tasks on protein-protein interaction. I was wondering that as Next Sentence Prediction was not used when training these...

gitwangxf

Using subnets of ProtTrans for protein understanding/classification tasks

1

First of all, many thanks to the authors of ProtTrans for releasing these amazing protein language models and code. Second, for those who may be interested, there is our recent...

xinshao-wang

Fine tuning ProtBert model for language modelling task

7

I want to fine tune protbert model on some protein data for language modelling task say given a protein sequence "ACDRFG" if I replace D with mask token and try...

shu1273

Do we have pre-computed embeddings of known protein sequences available for download?

13

I am trying to prepare the ProtTrans embeddings for UniRef50. Do we have such pre-computed embeddings available for download? Thanks!

johnnytam100

Fine-tuning on multiple GPUs in parralle mode

2

Hello, thanks a lot for your great work! Question is about ProtTrans/Fine-Tuning/ProtBert-BFD-FineTuning-PyTorchLightning-Localization.ipynb It took ~8 hours of computer time to rerun this jupyter notebook on 24Gb P40 node on not...

denysm

Precomputed embedding for all huuman proteins

2

Hi everyone, I would like to know if you have the precomputed embedding for the human proteins (not for other sequences). I am just interested in the vectors for the...

SalvatoreRa

Hello, First off, thanks a lot for creating this project! I'm trying to use the cls tokens generated to perform a downstream classification task. I tried fine-tuning ProtT5_XL, but there...

wwwhhhccc

Generating embedding from finetuned model

3

Hello, I needed help on how to go about generating embedding after ProtT5 has been finetuned. I have carried out finetuning of the model using the sample code 'PT5_LoRA_Finetuning_per_residue_class.ipynb' on...

abelavit

(Question) Can I use this for protein homology to UniRef50?

2

I'm looking for a faster alternative to Diamond for aligning proteins to UniRef50 so I can map identifiers to de novo proteins. Can I use this tool to accomplish this...

jolespin

Error in Generation of Embeddings from list of sequences via ProtT5

5

I am generating the embedding on my protein sequences via ProtT5 by the following code. I have total 5000 protein sequences which I am providing as list. I am fixing...

amalislam675