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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Protocol seqvec: I

#145 faruk17035 closed 3 years ago
1
Protocol word2vec: InvalidParameterError: Invalid protocol selection: word2vec

#144 faruk17035 closed 3 years ago
1
Please give me how i could solve this error

#143 faruk17035 closed 3 years ago
1
ESM-1v support as a ESM1vEmbedder

#142 ptynecki closed 3 years ago
6
Protocol plotly: RuntimeError: Expected embeddings in projected_reduced_embeddings_file to be of shape (3,), not (2,)

#141 nilsoberg2 closed 3 years ago
3
UniRep memory usage issue on CPU

#140 tijeco opened 3 years ago
2
Webserver backend worker didn't restart after automatic reboot

#139 sacdallago closed 3 years ago
1
AlphaFold 2 support?

#138 ptynecki closed 3 years ago
1
ProteinBert Support?

#137 ddofer opened 3 years ago
3
Per-sequence pedictions not written to file?

#136 sacdallago closed 3 years ago
2
Bump urllib3 from 1.26.4 to 1.26.5

#135 dependabot[bot] closed 3 years ago
1
reduce_per_protein for glove, word2vec and fasttext

#134 tijeco closed 3 years ago
1
Protocol plotly: RuntimeError: Expected embeddings in projected_reduced_embeddings_file to be of shape (3,), not (2,)

#133 ptizei closed 3 years ago
1
pip install not updating PATH in fresh conda env (Ubuntu 18.04.5)

#132 ptizei closed 3 years ago
2
Issue installing bioembeddings in google colab

#131 tijeco closed 3 years ago
3
I stop downloading the pre-train model at the first time to use SeqVecEmbedder

#130 1511878618 closed 3 years ago
5
Protocol prottrans_t5_xl_u50: RuntimeError: "baddbmm__mkl" not implemented for 'Half'

#129 sacdallago closed 3 years ago
3
Installation produces errors, imports don't work

#128 LiorZ closed 3 years ago
6
Check T5 on CPU

#127 konstin closed 3 years ago
3
Should not run half_precision_model on CPU!

#126 sacdallago closed 3 years ago
1
Documentation improvements

#125 sacdallago opened 3 years ago
3
Can't install version beyond 0.1.4

#124 willfinnigan closed 3 years ago
2
Getting tqdm error on Colab

#123 sacdallago closed 3 years ago
2
Weird logic in T5?

#122 sacdallago closed 3 years ago
12
Forward references break give a confusing error

#121 konstin opened 3 years ago
0
ESM1b with more than 1000 residues leaves GPU in cursed state

#120 konstin closed 3 years ago
3
Pinned dependencies in pyproject.toml

#119 jzazo closed 3 years ago
3
UniRep creates a jax.interpreters.xla.DeviceArray instead of a numpy array

#118 konstin closed 3 years ago
0
UniRep fails on empty sequences

#117 konstin closed 3 years ago
1
bepler fails on empty sequence

#116 konstin closed 3 years ago
0
Update conllu to 4.4

#115 EmilStenstrom closed 3 years ago
2
Using cached weights with bio-emebdddings

#114 deniseduma closed 3 years ago
2
Issue with installing the package

#113 deniseduma closed 3 years ago
7
Where is the docker image?

#112 deniseduma closed 3 years ago
6
BUG: AttributeError: module 'torch.jit' has no attribute '_script_if_tracing'

#111 KacperStasieluk closed 3 years ago
3
[Feature] EmbedderInterface class with device_index attribute and set_device_index method

#110 ptynecki closed 3 years ago
2
T5 embeddings and transformer 4.0

#109 sacdallago closed 3 years ago
0
Limit embedding requests to 1/10m

#108 sacdallago opened 3 years ago
0
Webserver umap: zero-size array to reduction operation maximum which has no identity

#107 konstin opened 3 years ago
3
Add description, inputs and outputs for bio_embeddings.visualize.html

#106 konstin closed 3 years ago
1
Pipeline fails if specialized install

#105 sacdallago closed 3 years ago
0
BasicAnnotationExtractor should donwload weights

#104 konstin closed 3 years ago
1
ESM updates and versioning

#103 konstin closed 3 years ago
1
Caching, ma' old friend

#102 sacdallago closed 3 years ago
2
Use k-nn output as DeepBLAST input

#98 konstin closed 3 years ago
0
EZ viz of distance/attention?

#97 sacdallago opened 3 years ago
1
Crash in PLUS with GPU

#96 konstin closed 3 years ago
0
Add goPredSim parser for PP frontend

#95 sacdallago closed 3 years ago
1
Include advanced machine learning example

#94 sacdallago opened 3 years ago
0
Expand the documentation

#93 konstin closed 3 years ago
3

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