bio-transformers

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This PR fixes the typo ```compute_``` in loglikelihood documentation

hunarbatra

pytorch_lightning.utilities.exceptions.MisconfigurationException: You have asked for `amp_level='O2'` but it's only supported with `amp_backend='apex'`.

1

I am trying to fine-tune on a set of sequences, using a A100 GPU and the exact example script from the github mainpage, and it throws this error. What to...

OlfwayAdbayIgbay

I'm not sure if I'm either not saving or loading the finetuned model correctly. After fine-tuning and running an evaluation script, the accuracy before loading model and after loading model...

maggieelkin

While doing the MR #31 I followed the CONTRIBUTING step-by-step and I have some feedbacks / remarks / problems: 1. Once the conda environment is installed, the `pre-commit` was not...

martinp7

a worker died or was killed while executing a task by an unexpected system error

6

I use 4 GPUs to calculate MSA embeddings, but each time the process terminated, the error was raise by ray, the error message is " a worker died or was...

wushixian

add jupyter example

1

delfosseaurelien

save the embeddings with the format : `f"{variable_name}_{model_name}_{embeddings_type}_embeddings.npy"`

delfosseaurelien

Is there a way to use any of the ESM models? There seems to be links here: https://github.com/facebookresearch/esm#available-models

DNA2RNA

ValueError: Connection error, and we cannot find the requested files in the cached path. Please try again or make sure your Internet connection is on.

1

When I called BioTransformers using transformer_bfd = BioTransformers(backend='protbert_bfd', num_gpus=num_gpus), I encountered an error. I want to download protbert_bfd locally, but I couldn't find a way to specify the path in...

wbw1111

**Description** We were facing issues with installing dependencies through pip due to the upper version limits specified in the requirements.txt file. These limits were causing conflicts with other packages that...

bolak92