Comments (4)
Proper python packages with python 3.6 support, but not published on pypi. Also all requirements are pinned to exact versions, which will clash with our other requirements (esp. their torch==1.4.0
)
from bio_embeddings.
That's nice and bad at the same time :D
from bio_embeddings.
provis is actually just an evaluation of tape's bert model (it even uses tape's download mechanism). So if we'd do this it would rather be integrating tape.
from bio_embeddings.
RE Tape, the thing that would be interesting is the evaluation pipeline. I have a hunch that this is going to be picked by less experienced peer reviewers as a "should be in there".
from bio_embeddings.
Related Issues (20)
- Update jax-unirep dependency version
- Protocol prottrans_t5_xl_u50: URLError: <urlopen error [Errno 113] No route to host> HOT 1
- OSError: Unable to open file (truncated file: eof = 63504384, sblock->base_addr = 0, stored_eof = 374434776)
- Custom embeddings
- Docker containers shutting down within a few seconds of starting
- Can not install bio-embedding in wsl HOT 2
- Can not install bioembedings on ubuntu? Please help HOT 1
- Hard times trying to run the bindEmbed21 example.
- Error during first step - greenlet size changed, may indicate binary incompatibility. HOT 1
- 3D Protein Embeddings
- AttributeError: 'dict' object has no attribute '__NUMPY_SETUP__'
- Cant install bio_embeddings in colab HOT 2
- Tensor size issue
- Protocol prottrans_t5_xl_u50: PermissionError: [Errno 13] Permission denied: 'C:\\Users\\user\\AppData\\Local\\Temp\\tmpk7e1m0jg' HOT 1
- from where comes the models in "bio_embeddings/utilities /defaults.yml", where is docs, parameters, dataset ?
- Protocol esm1b: AttributeError: 'dict' object has no attribute 'startswith'
- Cannot Import Any Embedder "load()" has been removed, use yaml = YAML(typ='rt') yaml.load(...)
- Protocol prottrans_bert_bfd: OSError: Unable to load weights from pytorch checkpoint file for .catch/bio_embeddings/prottrans_bert_bfd/model_directory/pytorch_model.bin' at '.catch/bio_embeddings/prottrans_bert_bfd/model_directory/pytorch_model.bin'. If you tried to load a PyTorch model from a TF 2.0 checkpoint, please set from_tf=True.
- Can Word2Vec be used for 4, 5 and 6 kmer? If possible, which file I need to changed and which parameter. I am seeking Guidance on Adapting Word2Vec Code for 4kmer Sequences
- Protocol prottrans_t5_bfd: HTTPError: HTTP Error 406: Not Acceptable
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from bio_embeddings.