sacdallago bio_embeddings issues

sacdallago / bio_embeddings

Get protein embeddings from protein sequences

http://docs.bioembeddings.com

MIT License

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issues

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pytorch compatibility with NVIDIA A100

#195 abdush closed 2 years ago
2
docker: Error response from daemon: could not select device driver "" with capabilities: [[gpu]].

#194 avilella closed 2 years ago
4
Solubility / Aggregability / Stability

#193 avilella closed 2 years ago
5
Bump notebook from 6.4.3 to 6.4.10

#192 dependabot[bot] closed 2 years ago
1
Feature importances with protein embedders

#191 evabalini closed 2 years ago
2
Import error

#190 kvetab closed 2 years ago
7
Protocol prottrans_bert_bfd: BadZipFile: File is not a zip file

#189 pskvins closed 2 years ago
2
Bump jupyter-server from 1.10.2 to 1.15.4

#188 dependabot[bot] closed 2 years ago
1
Add merck/sapiens

#187 sacdallago opened 2 years ago
1
Add nferruz/ProtGPT2

#186 sacdallago opened 2 years ago
0
Bump pillow from 8.3.2 to 9.0.1

#185 dependabot[bot] closed 2 years ago
1
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

#184 FYY99117 opened 2 years ago
5
Change default cache dir?

#183 hoangthienan95 closed 2 years ago
5
How to reset a corrupted model download?

#182 ms337 closed 2 years ago
2
Bump pyyaml from 5.3.1 to 5.4

#181 dependabot[bot] closed 2 years ago
1
Bump celery from 5.1.2 to 5.2.2

#180 dependabot[bot] closed 2 years ago
1
Bump nltk from 3.6.2 to 3.6.6

#179 dependabot[bot] closed 2 years ago
1
Bump nbdime from 3.1.0 to 3.1.1

#178 dependabot[bot] closed 2 years ago
1
Bump ipython from 7.27.0 to 7.31.1

#177 dependabot[bot] closed 2 years ago
1
Bump pillow from 8.3.2 to 9.0.0

#176 dependabot[bot] closed 2 years ago
1
TypeError: load() missing 1 required positional argument: 'Loader'

#175 nhowla closed 2 years ago
2
Handling X characters

#174 GiovannaNicora closed 2 years ago
2
Getting residue scores (original MLM head predictions)

#173 prihoda closed 2 years ago
2
How to emb some proteins which are not same length to same length？

#172 viko-3 closed 2 years ago
4
Including Sapiens antibody embeddings

#171 prihoda opened 2 years ago
2
After converting protein sequences into numbers, Can we apply LSTM model on the generated numerical datset?

#170 faruk17035 closed 2 years ago
1
Take too long to initialize an embedder function

#169 DeepColin closed 2 years ago
1
Get activations

#168 kvetab closed 2 years ago
3
Bump sqlparse from 0.4.1 to 0.4.2

#167 dependabot[bot] closed 2 years ago
1
Scheduled builds are failing

#166 konstin opened 3 years ago
0
Docker image not building

#165 sacdallago opened 3 years ago
0
The relevent source/paper to cite for each method

#164 Xinxinatg opened 3 years ago
4
Getting HTTP 406 error when sequence emedding.

#163 rjtevon closed 3 years ago
1
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)

#162 HannesStark opened 3 years ago
4
Old jaxlib releases are gone, breaking poetry's version resolution

#161 konstin opened 3 years ago
6
FileNotFoundError METADATA

#160 nprime496 opened 3 years ago
3
HTTP Error 406: Not Acceptable when downloading model

#159 victormaricato closed 3 years ago
1
ESM pipeline failing?

#158 sacdallago closed 3 years ago
7
Re-impmenet progress bar on weights download

#157 sacdallago opened 3 years ago
0
HTTPError: HTTP Error 406: Not Acceptable SeqVecEmbedder

#156 nprime496 closed 3 years ago
10
change final out embedding dimension

#155 BioLaoXu closed 3 years ago
2
files should terminate in _file

#154 sacdallago closed 3 years ago
0
Getting basic disorder prediction scores

#153 prihoda opened 3 years ago
2
the bio_embeddings Give me error of Invalid fasta sequence? But I think I could give the correct sequence as input in fasta file. How could I solve this error?(I use '>' before my fasta file.Please give me some guideline dear Dallago Sir)

#152 faruk17035 opened 3 years ago
1
How to solve this error, I put a DNA sequence here in fasta format...But it gives me error(When convet to numerical form using wor2vec). Please give me some guideline.

#151 faruk17035 closed 3 years ago
2
Can A DNA sequence be converted to numbers using word2vec,Glove and Fasttext protocol? Please give me some guideline

#150 faruk17035 closed 3 years ago
1
Which is my output embedding file from these files(converted to numerical form) and how I work with it ? Please help dear Dallago Sir

#149 faruk17035 closed 3 years ago
3
TypeError: argument of type 'NoneType' is not iterable

#148 faruk17035 opened 3 years ago
3
Reverse the embedding execution and get the original AA sequence?

#147 kandoigaurav closed 3 years ago
2
Protocol word2vec: error wor2vec invalid protocol

#146 faruk17035 closed 3 years ago
1

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