sacdallago/bio_embeddings

Issues

• Not able to run and pip install bioembeddings

  #245 opened 5 months ago by rmagesh148
  5

• Cant install bio_embeddings in colab

  #236 opened a year ago by IliasGewr
  4

• OSError: Unable to open file (truncated file: eof = 63504384, sblock->base_addr = 0, stored_eof = 374434776)

  #224 opened 2 years ago by gerdos
  1

• Can't install well to run bio_embed

  #246 opened 5 months ago by Lsz-20
  1

• Installation error in installing bio embedding package via pip

  #247 opened 5 months ago by amalislam675
  0

• Package dependency error.

  #205 opened 2 years ago by DimitrisAlivas
  3

• Protocol prottrans_t5_bfd: HTTPError: HTTP Error 406: Not Acceptable

  #244 opened 7 months ago by jiaming28
  0

• 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

  #243 opened 9 months ago by faruk17035
  0

• 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.

  #242 opened 10 months ago by Meng-AnunaAI
  0

• Cannot Import Any Embedder "load()" has been removed, use yaml = YAML(typ='rt') yaml.load(...)

  #241 opened 10 months ago by wijuliano
  0

• Can not install bio-embedding in wsl

  #230 opened 2 years ago by faruk17035
  2

• Can not install bioembedings on ubuntu? Please help

  #231 opened 2 years ago by faruk17035
  1

• Protocol esm1b: AttributeError: 'dict' object has no attribute 'startswith'

  #240 opened a year ago by dvonkan
  0

• from where comes the models in "bio_embeddings/utilities /defaults.yml", where is docs, parameters, dataset ?

  #239 opened a year ago by laraque
  0

• Tensor size issue

  #237 opened a year ago by J-JEMINA
  0

• Protocol prottrans_t5_xl_u50: PermissionError: [Errno 13] Permission denied: 'C:\\Users\\user\\AppData\\Local\\Temp\\tmpk7e1m0jg'

  #238 opened a year ago by jbattjes
  1

• AttributeError: 'dict' object has no attribute '__NUMPY_SETUP__'

  #235 opened a year ago by VarianZhou
  0

• 3D Protein Embeddings

  #234 opened a year ago by ChatterjeeAyan
  0

• I want to know the configuration of the people who run successfully

  #216 opened 2 years ago by sudo349
  2

• Add support for ESM-2 and ESMFold

  #218 opened 2 years ago by fedorn
  3

• Error during first step - greenlet size changed, may indicate binary incompatibility.

  #233 opened 2 years ago by igwill
  1

• Hard times trying to run the bindEmbed21 example.

  #232 opened 2 years ago by Ravy-LFL
  0

• Docker containers shutting down within a few seconds of starting

  #228 opened 2 years ago by kthurimella
  0

• Custom embeddings

  #225 opened 2 years ago by rhysnewell
  0

• detokenize/reverse embedded array

  #199 opened 2 years ago by drorhunvural
  1

• Protocol prottrans_t5_xl_u50: URLError: <urlopen error [Errno 113] No route to host>

  #223 opened 2 years ago by Azai-yx
  1

• segmentation fault

  #211 opened 2 years ago by yangyangdotcom
  1

• ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

  #184 opened 3 years ago by FYY99117
  5

• Update jax-unirep dependency version

  #219 opened 2 years ago by fedorn
  0

• CUDA out of memory.

  #217 opened 2 years ago by wenyuhaokikika
  2

• AssertionError: Failed in nopython mode pipeline (step: native lowering) Storing i64 to ptr of i32 ('dim'). FE type int32

  #215 opened 2 years ago by sudo349
  0

• ImportError when importing ProtTransT5XLU50Embedder

  #200 opened 2 years ago by AugustEhl
  1

• Text on embed.predictprotein.org

  #202 opened 2 years ago by C-Marquet
  1

• It may be better to let the user define whether the same redundant is allowed or not

  #212 opened 2 years ago by wenyuhaokikika
  1

• Protocol deepblast: AttributeError: can't set attribute

  #203 opened 2 years ago by XiaofangJ
  0

• Feature Request: Add Worker version to status API

  #210 opened 2 years ago by t03i
  0

• Protocol esm: UnpicklingError: invalid load key, '<'.

  #204 opened 2 years ago by wenyuhaokikika
  1

• render_3D_scatter_plotly Error

  #201 opened 2 years ago by drorhunvural
  0

• webserver worker failing on no flask?

  #197 opened 3 years ago by sacdallago
  1

• Import error

  #190 opened 3 years ago by kvetab
  7

• Protocol prottrans_bert_bfd: BadZipFile: File is not a zip file

  #189 opened 3 years ago by pskvins
  2

• How to solve this error?

  #196 opened 3 years ago by faruk17035
  2

• pytorch compatibility with NVIDIA A100

  #195 opened 3 years ago by abdush
  2

• Feature importances with protein embedders

  #191 opened 3 years ago by evabalini
  2

• Solubility / Aggregability / Stability

  #193 opened 3 years ago by avilella
  5

• How to reset a corrupted model download?

  #182 opened 3 years ago by ms337
  2

• docker: Error response from daemon: could not select device driver "" with capabilities: [[gpu]].

  #194 opened 3 years ago by avilella
  4

• Change default cache dir?

  #183 opened 3 years ago by hoangthienan95
  5

• Add merck/sapiens

  #187 opened 3 years ago by sacdallago
  1

• Add nferruz/ProtGPT2

  #186 opened 3 years ago by sacdallago
  0