Hannes Stärk

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icon company Massachusetts Institute of Technology icon location Cambridge, MA icon location MIT PhD student • ML for biomolecules

Results 2 issues of Hannes Stärk

Protocol unirep: ImportError: cannot import name 'cusolver' from 'jaxlib' (/mnt/lsf-nas-1/os-shared/anaconda3/envs/hannes_bio_embeddings/lib/python3.7/site-packages/jaxlib/__init__.py)

4 comment

## Metadata |key|value| |--|--| |**version**|0.2.1| |**cuda**|True| ## Parameter |key|value| |--|--| type|embed protocol|unirep reduce|True ## Traceback ``` Traceback (most recent call last): File "/mnt/lsf-nas-1/os-shared/anaconda3/envs/hannes_bio_embeddings/lib/python3.7/site-packages/bio_embeddings/utilities/pipeline.py", line 284, in execute_pipeline_from_config stage_output_parameters = stage_runnable(**stage_parameters)...

How to deal with Amino Acids that are not in the vocabulary

1 comment

Thanks for ESM! I am trying to generate language model embeddings with ESM2. However, some of the protein sequences that I have contain AAs that are not in the vocabulary...